SMTL ID : 3pot.1

Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

hetero-2-2-2-mer

Ligands

12 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain A: K.531 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: D.271 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.271, H2O.26, H2O.28, H2O.28, H2O.34, H2O.36 MG.13: 2 residues within 4Å: Chain C: E.30, K.135 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.30, H2O.42, H2O.49, H2O.49, H2O.49, H2O.50 MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain E: D.147 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.147, H2O.50, H2O.80, H2O.82, H2O.89 MG.24: 1 residues within 4Å: Chain F: E.30 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.30, H2O.92, H2O.92, H2O.100, H2O.100, H2O.100

2 x F43: FACTOR 430(Non-covalent)

F43.5: 36 residues within 4Å: Chain A: A.144, V.145, V.146, Q.147, M.150, M.229, Q.230, M.233, I.236, A.243 Chain D: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443 Chain E: S.365, I.366, Y.367 Chain F: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158 Ligands: COM.19, 06C.20 38 PLIP interactions: 14 interactions with chain D, 14 interactions with chain F, 7 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: D:V.328, D:F.330, D:Y.333, D:Y.333, D:Y.333, D:F.396, D:F.443, F:L.117, A:Q.147, A:I.236 Hydrogen bonds: D:G.329, D:Q.332, D:Q.332, D:Y.333, D:Y.333, F:S.118, F:G.119, F:R.120, F:S.154, F:V.155, F:G.157, A:V.145, A:V.146, A:Q.147, A:Q.230, E:I.366, E:Y.367, E:Y.367 Water bridges: D:T.331, D:S.399, F:S.118, F:H.156, F:H.158, F:H.158, F:H.158, A:Q.147 Salt bridges: F:H.156, F:H.158 F43.16: 36 residues within 4Å: Chain A: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443 Chain B: S.365, I.366, Y.367 Chain C: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158 Chain D: A.144, V.145, V.146, Q.147, M.150, M.229, Q.230, M.233, I.236, A.243 Ligands: COM.6, 06C.9 34 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B, 11 interactions with chain A, 14 interactions with chain C, Hydrophobic interactions: D:Q.147, D:I.236, A:V.328, A:F.330, A:Y.333, A:Y.333, A:F.443, C:L.117 Hydrogen bonds: D:V.145, D:V.146, D:Q.147, D:Q.230, B:I.366, B:Y.367, A:G.329, A:Q.332, A:Q.332, A:Y.333, C:S.118, C:G.119, C:R.120, C:S.154, C:V.155 Water bridges: D:Q.147, A:T.331, A:S.399, C:S.118, C:H.156, C:H.156, C:G.157, C:G.157, C:H.158 Salt bridges: C:H.156, C:H.158

2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)

COM.6: 10 residues within 4Å: Chain A: Y.333, F.443, Y.444 Chain B: F.361, S.365, Y.367 Chain C: L.117, R.120 Ligands: 06C.9, F43.16 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:R.120, C:R.120 Salt bridges: C:R.120 Hydrogen bonds: A:Y.444 COM.19: 10 residues within 4Å: Chain D: Y.333, F.443, Y.444 Chain E: F.361, S.365, Y.367 Chain F: L.117, R.120 Ligands: F43.5, 06C.20 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Water bridges: F:R.120, F:R.120 Salt bridges: F:R.120 Hydrogen bonds: D:Y.444

2 x TXZ: O-phosphono-N-(6-sulfanylhexanoyl)-L-threonine(Non-covalent)

TXZ.7: 20 residues within 4Å: Chain A: R.270, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain B: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 Chain D: R.225, K.256, H.257 Ligands: TP7.8 18 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: B:F.362, B:F.362, B:Y.367, B:I.380, B:V.381, A:F.330 Hydrogen bonds: B:Y.367, B:G.369, D:K.256 Water bridges: B:G.369, A:R.270, D:R.225, D:R.225 Salt bridges: B:H.379, A:R.270, D:R.225, D:K.256, D:K.256 TXZ.18: 20 residues within 4Å: Chain A: R.225, K.256, H.257 Chain D: R.270, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain E: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 Ligands: TP7.17 18 PLIP interactions: 3 interactions with chain D, 9 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: D:F.330, E:F.362, E:F.362, E:Y.367, E:I.380, E:V.381 Water bridges: D:R.270, E:G.369, A:R.225, A:R.225 Salt bridges: D:R.270, E:H.379, A:R.225, A:K.256, A:K.256 Hydrogen bonds: E:Y.367, E:G.369, A:K.256

2 x TP7: Coenzyme B(Non-covalent)

TP7.8: 21 residues within 4Å: Chain A: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain B: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 Chain D: R.225, K.256, H.257 Ligands: TXZ.7 19 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: B:F.362, B:F.362, B:Y.367, B:I.380, B:V.381, A:M.324, A:F.330 Hydrogen bonds: B:G.369, D:K.256, D:K.256 Salt bridges: B:H.379, A:R.270, D:R.225, D:K.256, D:K.256 Water bridges: A:R.270, A:R.270, D:R.225, D:R.225 TP7.17: 21 residues within 4Å: Chain A: R.225, K.256, H.257 Chain D: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain E: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 Ligands: TXZ.18 21 PLIP interactions: 4 interactions with chain D, 11 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: D:M.324, D:F.330, E:F.361, E:F.362, E:F.362, E:Y.367, E:Y.367, E:I.380, E:V.381 Water bridges: D:R.270, E:G.369, A:R.225, A:R.225 Salt bridges: D:R.270, E:H.379, A:R.225, A:K.256, A:K.256 Hydrogen bonds: E:Y.367, E:G.369, A:K.256

2 x 06C: Iodomethane(Non-covalent)

06C.9: 6 residues within 4Å: Chain A: Y.333 Chain B: F.361, Y.367 Chain C: L.117 Ligands: COM.6, F43.16 No protein-ligand interaction detected (PLIP) 06C.20: 5 residues within 4Å: Chain D: Y.333 Chain E: Y.367 Chain F: L.117 Ligands: F43.5, COM.19 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.10: 8 residues within 4Å: Chain A: R.102, S.215, R.216, C.218 Chain D: R.102, S.215, R.216, C.218 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:R.216, A:C.218, D:R.216, D:C.218

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.21: 1 residues within 4Å: Chain D: Y.348 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cedervall, P.E. et al., Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis. J.Am.Chem.Soc. (2011)

Release Date

2011-04-13

Peptides

Methyl-coenzyme M reductase I subunit alpha: AD
Methyl-coenzyme M reductase I subunit beta: BE
Methyl-coenzyme M reductase I subunit gamma: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Methyl-coenzyme M reductase I subunit alpha

Methyl-coenzyme M reductase I subunit beta

Methyl-coenzyme M reductase I subunit gamma

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