SMTL ID : 4csz.1

STRUCTURE OF F306C MUTANT OF NITRITE REDUCTASE FROM Achromobacter XYLOSOXIDANS WITH NITRITE BOUND

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

21 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.4: 3 residues within 4Å: Chain A: H.164, D.166, T.233 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.164, A:D.166, A:D.166 ZN.6: 3 residues within 4Å: Chain A: G.133, Y.196 Chain B: E.306 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.306, H2O.6, H2O.23, H2O.23, H2O.23 ZN.7: 2 residues within 4Å: Chain A: H.69, D.72 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.69, A:D.72, H2O.2, H2O.2, H2O.4 ZN.8: 1 residues within 4Å: Chain A: H.312 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.312, H2O.12, H2O.12, H2O.12 ZN.9: 1 residues within 4Å: Chain A: C.305 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.305, H2O.11 ZN.10: 2 residues within 4Å: Chain A: D.3, H.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.7, H2O.1, H2O.1 ZN.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.15: 3 residues within 4Å: Chain B: H.164, D.166, T.233 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.164, B:D.166, B:D.166 ZN.17: 3 residues within 4Å: Chain B: G.133, Y.196 Chain C: E.306 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.306, H2O.18, H2O.35, H2O.35, H2O.35 ZN.18: 2 residues within 4Å: Chain B: H.69, D.72 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.69, B:D.72, H2O.14, H2O.14, H2O.16 ZN.19: 1 residues within 4Å: Chain B: H.312 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.312, H2O.23, H2O.23, H2O.24 ZN.20: 1 residues within 4Å: Chain B: C.305 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.305, H2O.23 ZN.21: 2 residues within 4Å: Chain B: D.3, H.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.7, H2O.12, H2O.13 ZN.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.26: 3 residues within 4Å: Chain C: H.164, D.166, T.233 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.164, C:D.166, C:D.166 ZN.28: 3 residues within 4Å: Chain A: E.306 Chain C: G.133, Y.196 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.306, H2O.11, H2O.11, H2O.11, H2O.30 ZN.29: 2 residues within 4Å: Chain C: H.69, D.72 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.69, C:D.72, H2O.26, H2O.26, H2O.28 ZN.30: 1 residues within 4Å: Chain C: H.312 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.312, H2O.35, H2O.35, H2O.36 ZN.31: 1 residues within 4Å: Chain C: C.305 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.305, H2O.35 ZN.32: 2 residues within 4Å: Chain C: D.3, H.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.7, H2O.24, H2O.25

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

CU.2: 5 residues within 4Å: Chain A: H.88, C.129, P.131, H.138, M.143 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.88, A:C.129, A:H.138 CU.3: 6 residues within 4Å: Chain A: D.91, H.93, H.128 Chain B: H.248, H.299 Ligands: NO2.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.299, A:H.93, A:H.128 CU.13: 5 residues within 4Å: Chain B: H.88, C.129, P.131, H.138, M.143 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.88, B:C.129, B:H.138 CU.14: 6 residues within 4Å: Chain B: D.91, H.93, H.128 Chain C: H.248, H.299 Ligands: NO2.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.93, B:H.128, C:H.299 CU.24: 5 residues within 4Å: Chain C: H.88, C.129, P.131, H.138, M.143 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.88, C:C.129, C:H.138 CU.25: 6 residues within 4Å: Chain A: H.248, H.299 Chain C: D.91, H.93, H.128 Ligands: NO2.27 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Metal complexes: A:H.299, C:H.93, C:H.128

3 x NO2: NITRITE ION(Non-covalent)

NO2.5: 8 residues within 4Å: Chain A: D.91, H.93, H.128 Chain B: H.248, I.250, H.299, L.301 Ligands: CU.3 No protein-ligand interaction detected (PLIP) NO2.16: 8 residues within 4Å: Chain B: D.91, H.93, H.128 Chain C: H.248, I.250, H.299, L.301 Ligands: CU.14 No protein-ligand interaction detected (PLIP) NO2.27: 8 residues within 4Å: Chain A: H.248, I.250, H.299, L.301 Chain C: D.91, H.93, H.128 Ligands: CU.25 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 5 residues within 4Å: Chain A: D.120, R.121 Chain B: D.255, R.269, K.289 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.269, A:R.121 Hydrogen bonds: A:D.120 PEG.22: 5 residues within 4Å: Chain B: D.120, R.121 Chain C: D.255, R.269, K.289 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.120 Water bridges: B:R.121, C:R.269 PEG.33: 5 residues within 4Å: Chain A: D.255, R.269, K.289 Chain C: D.120, R.121 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:R.269, C:R.121 Hydrogen bonds: C:D.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leferink, N.G.H. et al., Impact of Residues Remote from the Catalytic Centre on Enzyme Catalysis of Copper Nitrite Reductase. Nat.Commun. (2014)

Release Date

2014-07-30

Peptides

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE

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