SMTL ID : 2pp9.1

Nitrate bound wild type oxidized AfNiR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x CU1: COPPER (I) ION(Non-covalent)

CU1.1: 4 residues within 4Å: Chain A: H.92, C.133, H.142, M.147 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:C.133, A:H.142 CU1.6: 4 residues within 4Å: Chain B: H.92, C.133, H.142, M.147 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.92, B:C.133, B:H.142 CU1.12: 4 residues within 4Å: Chain C: H.92, C.133, H.142, M.147 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.92, C:C.133, C:H.142

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

CU.2: 4 residues within 4Å: Chain A: H.97, H.132 Chain B: H.303 Ligands: NO3.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.97, A:H.132, B:H.303 CU.7: 4 residues within 4Å: Chain B: H.97, H.132 Chain C: H.303 Ligands: NO3.8 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.303, B:H.97, B:H.132 CU.13: 4 residues within 4Å: Chain A: H.303 Chain C: H.97, H.132 Ligands: NO3.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.97, C:H.132, A:H.303

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 8 residues within 4Å: Chain A: D.95, H.97, H.132, A.134 Chain B: I.254, H.303, L.305 Ligands: CU.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.95 NO3.8: 8 residues within 4Å: Chain B: D.95, H.97, H.132, A.134 Chain C: I.254, H.303, L.305 Ligands: CU.7 No protein-ligand interaction detected (PLIP) NO3.14: 8 residues within 4Å: Chain A: I.254, H.303, L.305 Chain C: D.95, H.97, H.132, A.134 Ligands: CU.13 No protein-ligand interaction detected (PLIP)

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 9 residues within 4Å: Chain A: G.137, M.138, V.139, P.140, W.141, Y.200, V.204, M.207 Chain B: E.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.138, A:W.141, A:Y.200 ACT.9: 6 residues within 4Å: Chain B: T.225, G.226, A.229, I.297, H.316, K.318 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.297 Hydrogen bonds: B:G.226 Water bridges: B:K.318 Salt bridges: B:H.316, B:K.318 ACT.10: 4 residues within 4Å: Chain B: D.170, G.235, E.236, K.237 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.237 ACT.11: 9 residues within 4Å: Chain B: G.137, M.138, V.139, P.140, W.141, Y.200, V.204, M.207 Chain C: E.310 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.310, B:M.138, B:W.141 ACT.15: 2 residues within 4Å: Chain B: F.279 Chain C: F.279 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.279 Water bridges: C:F.279 ACT.16: 6 residues within 4Å: Chain C: V.56, H.57, Y.181, V.182, P.183, T.203 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.203 Hydrogen bonds: C:H.57 Water bridges: C:V.144, C:Y.181, C:T.203, C:T.203 ACT.17: 9 residues within 4Å: Chain A: E.310 Chain C: G.137, M.138, V.139, P.140, W.141, Y.200, V.204, M.207 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.138, C:W.141, C:Y.200 ACT.18: 6 residues within 4Å: Chain C: T.225, G.226, A.229, I.297, H.316, K.318 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.297 Hydrogen bonds: C:G.226 Salt bridges: C:H.316, C:K.318

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 9 residues within 4Å: Chain A: T.209, L.210, T.211 Chain B: T.209, L.210, T.211 Chain C: T.209, L.210, T.211 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.209, A:T.209 Water bridges: A:R.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tocheva, E.I. et al., Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules. Biochemistry (2008)

Release Date

2008-04-01

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Copper-containing nitrite reductase

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