SMTL ID : 4rkm.4 (3 other biounits)

Wolinella succinogenes octaheme sulfite reductase MccA, form I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 x CU1: COPPER (I) ION(Non-covalent)

CU1.1: 4 residues within 4Å: Chain A: C.411, C.507 Ligands: SX.2, HEM.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.411, A:C.507 CU1.15: 5 residues within 4Å: Chain B: K.405, C.411, C.507 Ligands: SX.16, HEM.21 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.411, B:C.507 CU1.28: 6 residues within 4Å: Chain C: K.405, C.411, C.507 Ligands: SX.29, HEM.34, SO2.41 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.411, C:C.507

3 x SX: SULFUR OXIDE(Non-covalent)

SX.2: 5 residues within 4Å: Chain A: R.378, K.405, C.411 Ligands: CU1.1, HEM.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.378, A:R.378, A:K.405 Water bridges: A:K.220, A:Y.313 SX.16: 7 residues within 4Å: Chain B: Y.297, Y.313, R.378, K.405, C.411 Ligands: CU1.15, HEM.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.297, B:Y.313, B:R.378, B:R.378, B:K.405 SX.29: 7 residues within 4Å: Chain C: Y.297, R.378, K.405, C.411 Ligands: CU1.28, HEM.34, SO2.41 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.297, C:R.378, C:R.378, C:K.405

7 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.3: 4 residues within 4Å: Chain A: I.369, S.370 Chain C: I.369 Ligands: HEM.35 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.369, A:I.369 Water bridges: A:S.370 BU3.4: 5 residues within 4Å: Chain A: K.300, S.406, Y.511, D.552, G.553 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.300, A:K.300 BU3.5: 8 residues within 4Å: Chain A: I.632, Y.636, Y.653, I.656, E.657, Q.660 Chain C: K.487, Y.679 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.660, A:Q.660 BU3.17: 4 residues within 4Å: Chain A: I.369 Chain B: I.369, N.371 Ligands: HEM.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.371, A:I.369 Water bridges: B:S.370 BU3.18: 4 residues within 4Å: Chain B: K.300, S.406, Y.511, D.552 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.300, B:K.300, B:S.406 BU3.30: 4 residues within 4Å: Chain B: I.369 Chain C: I.369, N.371 Ligands: HEM.20 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.369, C:N.371 BU3.31: 5 residues within 4Å: Chain C: S.406, Y.511, R.551, D.552, G.553 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.406

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 5 residues within 4Å: Chain A: N.371, Q.377, G.415, T.418, Y.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.377 Water bridges: A:Y.424 ACT.19: 7 residues within 4Å: Chain B: E.373, Q.377, G.415, T.418, Y.419, Y.424 Ligands: HEM.24 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.419, B:Y.424 Hydrogen bonds: B:T.418, B:T.418 Water bridges: B:Y.424 ACT.32: 5 residues within 4Å: Chain C: N.371, Q.377, G.415, T.418, Y.424 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.377, C:T.418

24 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)(Covalent)

HEM.7: 25 residues within 4Å: Chain A: K.154, C.155, C.158, H.159, C.351, E.352, H.355, G.358, G.359, H.360, L.361, L.367 Chain B: L.68, Y.71, R.136, V.137, A.138, I.369, S.370, N.371, C.372, E.373, R.374 Ligands: HEM.9, BU3.17 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:Y.71, B:A.138, B:E.373, B:R.374, A:E.352, A:H.355, A:L.361, A:L.367, A:L.367 Hydrogen bonds: B:N.371, B:C.372, B:E.373, B:R.374 Water bridges: B:I.369, B:I.369 Metal complexes: A:H.159, A:H.360 HEM.8: 28 residues within 4Å: Chain A: Y.135, R.170, V.214, G.215, H.216, R.218, T.219, K.220, F.221, G.222, F.224, R.230, Y.313, C.314, C.317, H.318, C.375, H.376, R.378, C.411, G.412, E.414, C.507, R.525 Ligands: CU1.1, SX.2, HEM.10, HEM.11 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.214, A:K.220, A:F.224, A:R.230, A:Y.313, A:Y.313, A:Y.313 Hydrogen bonds: A:H.216, A:T.219, A:T.219, A:K.220, A:K.220, A:G.412, A:R.525 Salt bridges: A:H.216, A:H.376, A:R.525 pi-Cation interactions: A:K.220, A:R.378 Metal complexes: A:H.318 HEM.9: 22 residues within 4Å: Chain A: C.155, H.159, Q.162, Y.163, W.166, H.171, V.349, S.350, C.351, C.354, H.355, I.369, S.370, A.431, P.436, H.437, K.471 Chain B: N.371, E.373, R.429 Ligands: HEM.7, HEM.10 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:H.159, A:Y.163, A:W.166, A:W.166, A:V.349, A:P.436 Water bridges: A:Q.162, A:Q.162, B:R.429 Salt bridges: A:K.471, B:R.429 Metal complexes: A:H.355, A:H.437 Hydrogen bonds: B:N.371 HEM.10: 25 residues within 4Å: Chain A: R.170, H.171, T.174, G.215, H.216, V.316, C.317, H.318, V.349, C.354, S.370, C.372, R.374, C.375, H.376, C.430, P.436, V.439, T.440, S.466, P.468, R.525 Ligands: HEM.8, HEM.9, HEM.11 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.349, A:P.436, A:V.439, A:V.439, A:P.468 Hydrogen bonds: A:T.174, A:T.440, A:S.466, A:R.525 Salt bridges: A:R.170, A:H.216, A:R.525 Metal complexes: A:H.171, A:H.376 HEM.11: 23 residues within 4Å: Chain A: R.218, H.376, E.414, G.415, H.423, M.428, R.429, C.430, C.433, H.434, S.466, K.467, P.468, L.470, M.501, F.503, R.525, R.526, H.528, W.530 Ligands: HEM.8, HEM.10, HEM.12 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:H.376, A:E.414, A:E.414, A:P.468, A:L.470, A:R.526, A:W.530, A:W.530 Hydrogen bonds: A:S.466 Water bridges: A:S.466, A:S.466, A:R.526, A:R.526 Salt bridges: A:R.218, A:K.467, A:R.525, A:R.526 Metal complexes: A:H.434, A:H.528 HEM.12: 16 residues within 4Å: Chain A: A.422, H.423, K.426, M.428, K.472, E.473, C.474, C.477, H.478, H.500, M.501, W.530, K.531, R.565 Ligands: HEM.11, HEM.13 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:A.422, A:K.426, A:K.472, A:H.500 Water bridges: A:A.422, A:E.563, A:R.565 Salt bridges: A:K.426, A:K.531, A:R.565 Metal complexes: A:H.423, A:H.478 HEM.13: 20 residues within 4Å: Chain A: C.474, T.475, H.478, Q.481, A.482, Q.485, H.491, C.496, C.499, H.500, I.532, V.534, Q.618, D.669, G.670, S.671, W.672, H.675 Ligands: HEM.12, HEM.14 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:T.475, A:H.478, A:Q.481, A:H.491, A:I.532 Hydrogen bonds: A:Q.618 Water bridges: A:K.531, A:I.532, A:K.622, A:E.667 Salt bridges: A:K.531, A:K.531 Metal complexes: A:H.500, A:H.675 HEM.14: 21 residues within 4Å: Chain A: T.490, H.491, N.494, S.498, C.499, L.570, A.573, C.574, R.576, A.587, C.590, H.591, L.598, L.602, F.604, V.610, E.613, V.614, W.617, M.674 Ligands: HEM.13 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:L.570, A:A.587, A:L.598, A:L.602, A:F.604, A:V.610, A:V.614, A:W.617, A:W.617 Metal complexes: A:H.491, A:H.591 HEM.20: 26 residues within 4Å: Chain B: I.150, K.154, C.155, C.158, H.159, C.351, E.352, H.355, G.358, G.359, H.360, L.361, L.367 Chain C: L.68, Y.71, R.136, V.137, A.138, I.369, S.370, N.371, C.372, E.373, R.374 Ligands: HEM.22, BU3.30 19 PLIP interactions: 11 interactions with chain C, 8 interactions with chain B, Hydrophobic interactions: C:Y.71, C:R.136, C:A.138, C:E.373, C:R.374, B:I.150, B:E.352, B:H.355, B:L.361, B:L.361, B:L.367 Hydrogen bonds: C:N.371, C:N.371, C:C.372, C:R.374 Water bridges: C:I.369, C:I.369 Metal complexes: B:H.159, B:H.360 HEM.21: 29 residues within 4Å: Chain B: Y.135, R.170, V.214, G.215, H.216, R.218, T.219, K.220, F.221, F.224, R.230, Q.308, Y.313, C.314, C.317, H.318, R.374, C.375, H.376, R.378, C.411, G.412, E.414, C.507, R.525 Ligands: CU1.15, SX.16, HEM.23, HEM.24 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:V.214, B:K.220, B:F.224, B:R.230, B:Y.313, B:Y.313, B:Y.313 Hydrogen bonds: B:H.216, B:T.219, B:T.219, B:K.220, B:K.220, B:G.412 Water bridges: B:R.525 Salt bridges: B:H.216, B:H.376, B:R.525, B:R.525 pi-Cation interactions: B:K.220, B:R.378 Metal complexes: B:H.318 HEM.22: 22 residues within 4Å: Chain B: C.155, H.159, Q.162, Y.163, W.166, H.171, V.349, S.350, C.351, C.354, H.355, I.369, S.370, A.431, P.436, H.437, K.471 Chain C: N.371, E.373, R.429 Ligands: HEM.20, HEM.23 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain B, Hydrogen bonds: C:N.371 Water bridges: C:R.429, C:R.429, B:Q.162 Salt bridges: C:R.429, B:K.471 Hydrophobic interactions: B:H.159, B:Q.162, B:Y.163, B:W.166, B:W.166, B:V.349, B:P.436 Metal complexes: B:H.355, B:H.437 HEM.23: 25 residues within 4Å: Chain B: R.170, H.171, T.174, H.216, V.316, C.317, H.318, V.349, C.354, S.370, C.372, R.374, C.375, H.376, C.430, H.434, P.436, V.439, T.440, S.466, P.468, R.525 Ligands: HEM.21, HEM.22, HEM.24 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:V.349, B:H.434, B:P.436, B:V.439, B:V.439, B:V.439, B:P.468 Hydrogen bonds: B:T.174, B:T.174, B:T.440, B:S.466, B:R.525 Salt bridges: B:R.170, B:H.216, B:R.525 Metal complexes: B:H.171, B:H.376 HEM.24: 24 residues within 4Å: Chain B: R.218, H.376, E.414, G.415, H.423, M.428, R.429, C.430, C.433, H.434, S.466, K.467, P.468, L.470, M.501, F.503, R.525, R.526, H.528, W.530 Ligands: ACT.19, HEM.21, HEM.23, HEM.25 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:H.376, B:E.414, B:E.414, B:P.468, B:L.470, B:R.526, B:W.530, B:W.530 Hydrogen bonds: B:S.466 Water bridges: B:S.466, B:S.466, B:R.526, B:R.526 Salt bridges: B:R.218, B:K.467, B:R.525, B:R.526 Metal complexes: B:H.434, B:H.528 HEM.25: 16 residues within 4Å: Chain B: A.422, H.423, K.426, M.428, K.472, E.473, C.474, C.477, H.478, H.500, M.501, W.530, K.531, R.565 Ligands: HEM.24, HEM.26 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:K.426, B:K.472, B:H.500 Water bridges: B:A.422, B:R.565, B:R.565 Salt bridges: B:K.426, B:K.531, B:R.565 Metal complexes: B:H.423, B:H.478 HEM.26: 20 residues within 4Å: Chain B: C.474, T.475, H.478, Q.481, A.482, Q.485, H.491, C.496, C.499, H.500, I.532, V.534, Q.618, D.669, G.670, S.671, W.672, H.675 Ligands: HEM.25, HEM.27 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:T.475, B:H.478, B:Q.481, B:I.532 Hydrogen bonds: B:Q.618, B:D.669 Water bridges: B:K.531, B:K.531, B:I.532 Salt bridges: B:K.531, B:K.531 Metal complexes: B:H.500, B:H.675 HEM.27: 20 residues within 4Å: Chain B: T.490, H.491, N.494, S.498, C.499, L.570, A.573, C.574, R.576, A.587, C.590, H.591, L.598, L.602, V.610, E.613, V.614, W.617, M.674 Ligands: HEM.26 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:L.570, B:A.587, B:L.598, B:L.598, B:L.602, B:V.610, B:V.614, B:W.617 Metal complexes: B:H.491, B:H.591 HEM.33: 24 residues within 4Å: Chain A: L.68, Y.71, R.136, V.137, A.138, I.369, S.370, N.371, C.372, E.373, R.374 Chain C: K.154, C.155, C.158, H.159, C.351, E.352, H.355, G.358, G.359, H.360, L.361, L.367 Ligands: HEM.35 18 PLIP interactions: 8 interactions with chain C, 10 interactions with chain A, Hydrophobic interactions: C:E.352, C:H.355, C:L.361, C:L.361, C:L.367, C:L.367, A:L.68, A:Y.71, A:R.136, A:R.136, A:A.138, A:E.373, A:R.374 Metal complexes: C:H.159, C:H.360 Hydrogen bonds: A:N.371, A:C.372, A:R.374 HEM.34: 29 residues within 4Å: Chain C: Y.135, R.170, V.214, G.215, H.216, R.218, T.219, K.220, F.221, F.224, R.230, Q.308, Y.313, C.314, C.317, H.318, C.375, H.376, R.378, C.411, G.412, E.414, C.507, R.525 Ligands: CU1.28, SX.29, HEM.36, HEM.37, SO2.41 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:V.214, C:K.220, C:F.224, C:R.230, C:Y.313, C:Y.313, C:Y.313 Hydrogen bonds: C:H.216, C:T.219, C:K.220, C:K.220, C:G.412 Water bridges: C:T.219 Salt bridges: C:H.216, C:H.376, C:R.525, C:R.525 pi-Cation interactions: C:K.220, C:R.378 Metal complexes: C:H.318 HEM.35: 23 residues within 4Å: Chain A: N.371, E.373, R.429 Chain C: C.155, H.159, Q.162, Y.163, W.166, H.171, V.349, S.350, C.351, C.354, H.355, I.369, S.370, A.431, P.436, H.437, K.471 Ligands: BU3.3, HEM.33, HEM.36 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain A, Hydrophobic interactions: C:H.159, C:Q.162, C:Q.162, C:Y.163, C:W.166, C:W.166, C:V.349, C:P.436 Water bridges: C:K.471, A:Y.424, A:R.429 Salt bridges: C:K.471, A:R.429 Metal complexes: C:H.355, C:H.437 Hydrogen bonds: A:N.371 HEM.36: 26 residues within 4Å: Chain C: R.170, H.171, T.174, G.215, H.216, V.316, C.317, H.318, V.349, C.354, S.370, C.372, R.374, C.375, H.376, C.430, H.434, P.436, V.439, T.440, S.466, P.468, R.525 Ligands: HEM.34, HEM.35, HEM.37 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:V.349, C:P.436, C:V.439, C:V.439, C:V.439, C:P.468 Hydrogen bonds: C:T.174, C:T.440, C:S.466, C:R.525 Salt bridges: C:R.170, C:H.216, C:R.525 Metal complexes: C:H.171, C:H.376 HEM.37: 23 residues within 4Å: Chain C: R.218, H.376, E.414, G.415, H.423, M.428, R.429, C.430, C.433, H.434, S.466, K.467, P.468, L.470, M.501, F.503, R.525, R.526, H.528, W.530 Ligands: HEM.34, HEM.36, HEM.38 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:H.376, C:E.414, C:E.414, C:P.468, C:L.470, C:R.526, C:W.530, C:W.530 Hydrogen bonds: C:S.466 Water bridges: C:S.466, C:S.466, C:S.466, C:R.526 Salt bridges: C:R.218, C:K.467, C:R.525, C:R.526 Metal complexes: C:H.434, C:H.528 HEM.38: 16 residues within 4Å: Chain C: A.422, H.423, K.426, M.428, K.472, E.473, C.474, C.477, H.478, H.500, M.501, W.530, K.531, R.565 Ligands: HEM.37, HEM.39 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:A.422, C:K.472, C:H.500 Water bridges: C:R.565, C:R.565 Salt bridges: C:K.426, C:K.531, C:R.565 Metal complexes: C:H.423, C:H.478 HEM.39: 22 residues within 4Å: Chain C: C.474, T.475, H.478, Q.481, A.482, Q.485, H.491, N.494, C.496, C.499, H.500, I.532, V.534, Q.618, D.669, G.670, S.671, W.672, M.674, H.675 Ligands: HEM.38, HEM.40 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:T.475, C:H.478, C:Q.481, C:Q.481, C:N.494, C:I.532 Hydrogen bonds: C:Q.618 Water bridges: C:D.669 Salt bridges: C:K.531, C:K.531 Metal complexes: C:H.500, C:H.675 HEM.40: 19 residues within 4Å: Chain C: T.490, H.491, N.494, S.498, C.499, L.570, A.573, C.574, A.587, C.590, H.591, L.598, L.602, F.604, E.613, V.614, W.617, M.674 Ligands: HEM.39 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:L.570, C:A.587, C:L.598, C:L.598, C:L.602, C:F.604, C:V.614, C:W.617, C:W.617 Hydrogen bonds: C:T.490 Metal complexes: C:H.491, C:H.591

1 x SO2: SULFUR DIOXIDE(Non-covalent)

SO2.41: 8 residues within 4Å: Chain C: K.220, Y.297, K.405, C.411, C.507 Ligands: CU1.28, SX.29, HEM.34 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hermann, B. et al., The octahaem MccA is a haem c-copper sulfite reductase. Nature (2015)

Release Date

2015-02-04

Peptides

MccA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
G

MccA

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