SMTL ID : 4k8d.1

Crystal structure of the C558(464)A/C559(465)A double mutant of Tn501 MerA in complex with NADPH and Hg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.35, N.272, T.273, R.274, S.275 9 PLIP interactions: 9 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:T.273, A:T.273 Salt bridges: A:R.35 SO4.2: 3 residues within 4Å: Chain A: W.164, S.172, K.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.164 Water bridges: A:S.172, A:D.173 Salt bridges: A:K.262 SO4.24: 5 residues within 4Å: Chain B: R.35, N.272, T.273, R.274, S.275 9 PLIP interactions: 9 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:T.273, B:T.273 Salt bridges: B:R.35 SO4.25: 3 residues within 4Å: Chain B: W.164, S.172, K.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.164 Water bridges: B:S.172, B:D.173 Salt bridges: B:K.262

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Q.6, Q.29, T.31, T.111, R.135 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.6, A:Q.6, A:T.31, A:T.111, A:R.135 Water bridges: A:R.135 GOL.26: 5 residues within 4Å: Chain B: Q.6, Q.29, T.31, T.111, R.135 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.6, B:Q.6, B:T.31, B:T.111, B:T.111, B:R.135 Water bridges: B:R.135

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

FAD.4: 34 residues within 4Å: Chain A: I.10, G.11, G.13, G.14, A.15, I.33, E.34, R.35, G.40, T.41, C.42, V.45, G.46, C.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: NDP.5 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.13, A:G.14, A:A.15, A:R.35, A:T.41, A:T.41, A:C.42, A:S.50, A:K.51, A:A.117, A:A.117, A:D.309, A:Q.315, A:V.317 Water bridges: A:A.16, A:R.35, A:R.35, A:T.37, A:G.40, A:G.147, A:A.148, A:A.148, A:D.309, A:C.310, A:A.320, B:Y.441 pi-Cation interactions: A:R.35 FAD.27: 34 residues within 4Å: Chain B: I.10, G.11, G.13, G.14, A.15, I.33, E.34, R.35, G.40, T.41, C.42, V.45, G.46, C.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: NDP.28 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.13, B:G.14, B:A.15, B:R.35, B:T.41, B:T.41, B:T.41, B:C.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:R.35, B:R.35, B:T.37, B:G.40, B:G.147, B:A.148, B:A.148, B:A.148, B:C.310, B:A.320, A:Y.441 pi-Cation interactions: B:R.35

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.5: 23 residues within 4Å: Chain A: K.51, P.153, I.182, G.183, 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.4, UNX.23 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:V.186, A:V.187 Hydrogen bonds: A:S.184, A:S.184, A:S.184, A:S.184, A:S.185, A:V.187, A:E.190, A:R.207, A:N.208, A:N.208, A:G.268, A:Q.315 Water bridges: A:G.183, A:G.183, A:A.188, A:R.207, A:F.212, A:R.213, A:R.213, A:Q.238, A:A.266, A:T.267, A:R.269, A:V.346, A:V.346, A:V.346 Salt bridges: A:R.207, A:R.213, A:R.213 pi-Cation interactions: A:R.207 NDP.28: 23 residues within 4Å: Chain B: K.51, P.153, I.182, G.183, 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.27, UNX.46 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:V.186, B:V.187 Hydrogen bonds: B:S.184, B:S.184, B:S.184, B:S.184, B:S.185, B:V.187, B:E.190, B:R.207, B:N.208, B:N.208, B:G.268, B:Q.315 Water bridges: B:G.183, B:G.183, B:A.188, B:R.207, B:F.212, B:R.213, B:R.213, B:Q.238, B:A.266, B:T.267, B:T.267, B:R.269, B:V.346, B:V.346, B:V.346 Salt bridges: B:R.207, B:R.213, B:R.213 pi-Cation interactions: B:R.207

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

UNX.6: 3 residues within 4Å: Chain A: H.58 Chain B: H.58 Ligands: UNX.29 Ligand excluded by PLIP UNX.7: 1 residues within 4Å: Chain A: Y.163 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: N.286, A.287 Ligand excluded by PLIP UNX.9: 1 residues within 4Å: Chain A: E.101 Ligand excluded by PLIP UNX.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.11: 1 residues within 4Å: Chain A: R.227 Ligand excluded by PLIP UNX.12: 1 residues within 4Å: Chain A: G.357 Ligand excluded by PLIP UNX.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: D.436 Chain B: D.339 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: R.373, T.454, F.455 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: E.257, L.258 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: I.155, P.156 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: H.236, T.237, Q.238 Ligand excluded by PLIP UNX.20: 5 residues within 4Å: Chain A: T.376, L.377, D.378, T.389, G.391 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Chain A: R.227, A.228, G.230 Ligand excluded by PLIP UNX.22: 3 residues within 4Å: Chain A: T.376, D.378, N.379 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain A: R.207, F.212, R.213 Ligands: NDP.5 Ligand excluded by PLIP UNX.29: 3 residues within 4Å: Chain A: H.58 Chain B: H.58 Ligands: UNX.6 Ligand excluded by PLIP UNX.30: 1 residues within 4Å: Chain B: Y.163 Ligand excluded by PLIP UNX.31: 2 residues within 4Å: Chain B: N.286, A.287 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain B: E.101 Ligand excluded by PLIP UNX.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.34: 1 residues within 4Å: Chain B: R.227 Ligand excluded by PLIP UNX.35: 1 residues within 4Å: Chain B: G.357 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: 2 residues within 4Å: Chain A: D.339 Chain B: D.436 Ligand excluded by PLIP UNX.39: 3 residues within 4Å: Chain B: R.373, T.454, F.455 Ligand excluded by PLIP UNX.40: 2 residues within 4Å: Chain B: E.257, L.258 Ligand excluded by PLIP UNX.41: 2 residues within 4Å: Chain B: I.155, P.156 Ligand excluded by PLIP UNX.42: 3 residues within 4Å: Chain B: H.236, T.237, Q.238 Ligand excluded by PLIP UNX.43: 5 residues within 4Å: Chain B: T.376, L.377, D.378, T.389, G.391 Ligand excluded by PLIP UNX.44: 3 residues within 4Å: Chain B: R.227, A.228, G.230 Ligand excluded by PLIP UNX.45: 3 residues within 4Å: Chain B: T.376, D.378, N.379 Ligand excluded by PLIP UNX.46: 4 residues within 4Å: Chain B: R.207, F.212, R.213 Ligands: NDP.28 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 NADPH and Hg2+. to be published

Release Date

2013-05-22

Peptides

Mercuric reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Mercuric reductase