SMTL ID : 2iwf.1

RESTING FORM OF PINK NITROUS OXIDE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

4 x CU: COPPER (II) ION(Non-covalent)

CU.1: 6 residues within 4Å: Chain A: H.585, C.620, W.622, C.624, M.631 Ligands: CU.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.585, A:C.620, A:C.624 CU.2: 5 residues within 4Å: Chain A: C.620, W.622, C.624, H.628 Ligands: CU.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.620, A:W.622, A:C.624, A:H.628 CU.14: 6 residues within 4Å: Chain B: H.585, C.620, W.622, C.624, M.631 Ligands: CU.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.585, B:C.620, B:C.624 CU.15: 6 residues within 4Å: Chain B: C.620, W.622, F.623, C.624, H.628 Ligands: CU.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.620, B:W.622, B:C.624, B:H.628

2 x CUZ: (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION(Non-covalent)

CUZ.3: 8 residues within 4Å: Chain A: H.135, H.136, H.184, N.246, H.327, H.382, H.433, H.494 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.135, A:H.136, A:H.184, A:H.327, A:H.382, A:H.433, A:H.494, H2O.227, H2O.281 CUZ.16: 8 residues within 4Å: Chain B: H.135, H.136, H.184, N.246, H.327, H.382, H.433, H.494 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.135, B:H.136, B:H.184, B:H.327, B:H.382, B:H.433, B:H.494, H2O.603, H2O.642

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: K.454, E.469 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:K.454, A:E.469, H2O.309, H2O.734, H2O.736 CA.5: 5 residues within 4Å: Chain A: N.92, R.93, D.130 Chain B: R.93, S.95 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:R.93, A:D.130 CA.6: 5 residues within 4Å: Chain A: Y.261, E.264, M.272, D.278, N.325 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.261, A:E.264, A:E.264, A:M.272, A:D.278 CA.17: 2 residues within 4Å: Chain B: K.454, E.469 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:K.454, B:E.469, H2O.366, H2O.653, H2O.662 CA.18: 6 residues within 4Å: Chain B: Y.261, E.264, M.272, T.273, D.278, N.325 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.261, B:E.264, B:M.272, B:D.278, H2O.549

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 6 residues within 4Å: Chain A: R.187, N.246, G.328, C.329, N.330, H.382 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain B: R.187, N.246, G.328, C.329, N.330, H.382 Ligand excluded by PLIP

13 x NA: SODIUM ION(Non-functional Binders)

NA.8: 8 residues within 4Å: Chain A: P.206, N.209, D.210, G.211, S.212, M.214 Chain B: G.614 Ligands: NA.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.209, A:D.210, A:G.211 NA.9: 4 residues within 4Å: Chain A: F.460, L.461 Chain B: L.59, D.60 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.60, B:D.60, B:D.60, B:R.83, A:L.461 NA.10: 2 residues within 4Å: Chain A: V.482, L.483 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.483 NA.11: 6 residues within 4Å: Chain A: P.206, V.208, D.210, S.212, T.213 Ligands: NA.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.210, A:D.210, A:S.212, A:T.213, A:T.213 Water bridges: A:T.213 NA.12: 2 residues within 4Å: Chain A: W.236, I.292 No protein-ligand interaction detected (PLIP) NA.13: 5 residues within 4Å: Chain A: H.136, V.137, H.138, D.495, A.496 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.137, A:D.495, A:D.495 NA.20: 5 residues within 4Å: Chain B: R.165, K.170, T.171, D.172, L.517 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.165, B:T.171 NA.21: 3 residues within 4Å: Chain B: K.290, K.293, A.294 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.290 NA.22: 4 residues within 4Å: Chain B: I.108, R.111, D.172, A.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.172 Water bridges: B:R.111 NA.23: 6 residues within 4Å: Chain B: N.92, R.93, G.100, I.128, H.129, D.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.129 NA.24: 7 residues within 4Å: Chain A: N.131 Chain B: R.93, C.94, S.95, G.98, Q.101, A.595 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.93, B:R.93, B:G.98, B:Q.101, B:A.595 NA.25: 6 residues within 4Å: Chain B: F.91, H.109, H.129, D.130, N.131, R.160 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.109, B:R.160, B:R.160 NA.26: 1 residues within 4Å: Chain B: Y.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paraskevopoulos, K. et al., Insight Into Catalysis of Nitrous Oxide Reductase from High-Resolution Structures of Resting and Inhibitor-Bound Enzyme from Achromobacter Cycloclastes. J.Mol.Biol. (2006)

Release Date

2006-08-16

Peptides

NITROUS-OXIDE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NITROUS-OXIDE REDUCTASE

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