SMTL ID : 4k7z.1

Crystal structure of the C136(42)A/C141(47)A double mutant of Tn501 MerA in complex with NADP and Hg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 35 residues within 4Å: Chain A: I.10, G.11, S.12, G.13, G.14, A.15, I.33, E.34, R.35, G.40, T.41, A.42, G.46, A.47, S.50, K.51, G.115, E.116, A.117, A.145, T.146, G.147, S.166, R.269, L.276, G.308, D.309, Q.315, F.316, V.317, Y.318, A.320, F.348 Chain B: Y.441 Ligands: NAP.2 29 PLIP interactions: 1 interactions with chain B, 28 interactions with chain A Water bridges: B:Y.441, A:A.16, A:E.34, A:R.35, A:R.35, A:R.35, A:R.35, A:G.40, A:G.147, A:A.148, A:A.148, A:D.309, A:C.310 Hydrophobic interactions: A:T.41 Hydrogen bonds: A:G.13, A:G.14, A:A.15, A:R.35, A:T.41, A:T.41, A:A.42, A:S.50, A:K.51, A:A.117, A:A.117, A:D.309, A:Q.315, A:V.317 pi-Cation interactions: A:R.35 FAD.26: 35 residues within 4Å: Chain A: Y.441 Chain B: I.10, G.11, S.12, G.13, G.14, A.15, I.33, E.34, R.35, G.40, T.41, A.42, G.46, A.47, S.50, K.51, G.115, E.116, A.117, A.145, T.146, G.147, S.166, R.269, L.276, G.308, D.309, Q.315, F.316, V.317, Y.318, A.320, F.348 Ligands: NAP.27 30 PLIP interactions: 29 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.41 Hydrogen bonds: B:G.13, B:G.14, B:A.15, B:R.35, B:T.41, B:T.41, B:T.41, B:A.42, B:S.50, B:K.51, B:A.117, B:A.117, B:D.309, B:Q.315, B:V.317 Water bridges: B:A.16, B:E.34, B:R.35, B:R.35, B:R.35, B:R.35, B:G.40, B:G.147, B:A.148, B:A.148, B:A.148, B:C.310, A:Y.441 pi-Cation interactions: B:R.35

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 19 residues within 4Å: Chain A: P.153, S.184, S.185, V.186, V.187, E.190, R.207, N.208, F.212, R.213, A.266, T.267, G.268, R.269, Q.315, F.316, V.346, F.348 Ligands: FAD.1 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:V.186, A:V.186, A:V.187 Hydrogen bonds: A:K.51, A:S.184, A:S.184, A:S.184, A:S.184, A:S.185, A:V.187, A:E.190, A:N.208, A:N.208, A:G.268, A:Q.315 Water bridges: A:G.183, A:G.183, A:A.188, A:A.188, A:R.207, A:F.212, A:R.213, A:R.213, A:R.213, A:Q.238, A:T.267, A:R.269, A:Q.315, A:V.346, A:V.346, A:V.346 Salt bridges: A:R.207, A:R.213 pi-Cation interactions: A:R.207 NAP.27: 19 residues within 4Å: Chain B: P.153, S.184, S.185, V.186, V.187, E.190, R.207, N.208, F.212, R.213, A.266, T.267, G.268, R.269, Q.315, F.316, V.346, F.348 Ligands: FAD.26 35 PLIP interactions: 35 interactions with chain B Hydrophobic interactions: B:V.186, B:V.186, B:V.187 Hydrogen bonds: B:K.51, B:S.184, B:S.184, B:S.184, B:S.184, B:S.185, B:V.187, B:E.190, B:N.208, B:N.208, B:G.268, B:Q.315 Water bridges: B:G.183, B:G.183, B:A.188, B:A.188, B:R.207, B:F.212, B:R.213, B:R.213, B:R.213, B:Q.238, B:T.267, B:T.267, B:R.269, B:Q.315, B:V.346, B:V.346, B:V.346 Salt bridges: B:R.207, B:R.213 pi-Cation interactions: B:R.207

2 x HG: MERCURY (II) ION(Non-covalent)

HG.3: 4 residues within 4Å: Chain A: Y.441, C.464, C.465 Chain B: V.317 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.464, A:C.465 HG.28: 4 residues within 4Å: Chain A: V.317 Chain B: Y.441, C.464, C.465 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.464, B:C.465

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: R.35, N.272, T.273, R.274, S.275 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.272, A:R.274, A:S.275, A:S.275 Water bridges: A:R.35, A:R.35, A:R.35, A:R.35, A:T.273, A:T.273 Salt bridges: A:R.35 SO4.5: 3 residues within 4Å: Chain A: W.164, S.172, K.262 7 PLIP interactions: 7 interactions with chain A Water bridges: A:W.164, A:S.172, A:D.173, A:K.262, A:K.262, A:K.262 Salt bridges: A:K.262 SO4.6: 2 residues within 4Å: Chain A: R.141, N.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.303 Salt bridges: A:R.141 SO4.29: 5 residues within 4Å: Chain B: R.35, N.272, T.273, R.274, S.275 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.272, B:R.274, B:S.275, B:S.275 Water bridges: B:R.35, B:R.35, B:R.35, B:R.35, B:T.273, B:T.273 Salt bridges: B:R.35 SO4.30: 3 residues within 4Å: Chain B: W.164, S.172, K.262 7 PLIP interactions: 7 interactions with chain B Water bridges: B:W.164, B:S.172, B:D.173, B:K.262, B:K.262, B:K.262 Salt bridges: B:K.262 SO4.31: 2 residues within 4Å: Chain B: R.141, N.303 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.303 Salt bridges: B:R.141

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: H.61, L.62, E.65, S.66, P.67, D.388, R.390 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.66 Water bridges: A:E.229, A:R.390, A:R.390, A:R.390 GOL.8: 5 residues within 4Å: Chain A: Q.6, Q.29, T.31, T.111, R.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.6, A:T.111, A:R.135, A:R.135 Water bridges: A:T.31 GOL.9: 4 residues within 4Å: Chain A: S.161, P.162, Y.163, E.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.168 Water bridges: A:S.161 GOL.32: 7 residues within 4Å: Chain B: H.61, L.62, E.65, S.66, P.67, D.388, R.390 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.66 Water bridges: B:E.65, B:E.229, B:E.229, B:R.390, B:R.390 GOL.33: 5 residues within 4Å: Chain B: Q.6, Q.29, T.31, T.111, R.135 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.6, B:T.31, B:T.111, B:T.111, B:R.135, B:R.135 GOL.34: 4 residues within 4Å: Chain B: S.161, P.162, Y.163, E.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.168 Water bridges: B:S.161, B:Y.163

32 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.10: 3 residues within 4Å: Chain A: Q.453, A.466, G.467 Ligand excluded by PLIP UNX.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.13: 1 residues within 4Å: Chain A: T.167 Ligand excluded by PLIP UNX.14: 1 residues within 4Å: Chain A: R.178 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: Q.123, M.138, F.139 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: G.133, E.134 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: N.286, A.287 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: G.256, E.257 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: D.378, L.384 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain A: R.373, T.374 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: Q.437 Chain B: R.426 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain A: N.286, A.287 Ligand excluded by PLIP UNX.23: 1 residues within 4Å: Chain A: E.177 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain A: R.326, A.337 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain A: F.348, Q.352, E.416 Chain B: R.382, L.442 Ligand excluded by PLIP UNX.35: 3 residues within 4Å: Chain B: Q.453, A.466, G.467 Ligand excluded by PLIP UNX.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.38: 1 residues within 4Å: Chain B: T.167 Ligand excluded by PLIP UNX.39: 1 residues within 4Å: Chain B: R.178 Ligand excluded by PLIP UNX.40: 3 residues within 4Å: Chain B: Q.123, M.138, F.139 Ligand excluded by PLIP UNX.41: 2 residues within 4Å: Chain B: G.133, E.134 Ligand excluded by PLIP UNX.42: 2 residues within 4Å: Chain B: N.286, A.287 Ligand excluded by PLIP UNX.43: 2 residues within 4Å: Chain B: G.256, E.257 Ligand excluded by PLIP UNX.44: 2 residues within 4Å: Chain B: D.378, L.384 Ligand excluded by PLIP UNX.45: 2 residues within 4Å: Chain B: R.373, T.374 Ligand excluded by PLIP UNX.46: 2 residues within 4Å: Chain A: R.426 Chain B: Q.437 Ligand excluded by PLIP UNX.47: 2 residues within 4Å: Chain B: N.286, A.287 Ligand excluded by PLIP UNX.48: 1 residues within 4Å: Chain B: E.177 Ligand excluded by PLIP UNX.49: 2 residues within 4Å: Chain B: R.326, A.337 Ligand excluded by PLIP UNX.50: 5 residues within 4Å: Chain A: R.382, L.442 Chain B: F.348, Q.352, E.416 Ligand excluded by PLIP

Links

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Citation

Dong, A. et al., Crystal structure of the C136(42)A/C141(47)A double mutant of Tn501 MerA in complex with NADP and Hg2+. To be Published

Release Date

2013-05-15

Peptides

Mercuric reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Mercuric reductase