SMTL ID : 5onx.1

Resting state copper nitrite reductase determined by serial femtosecond rotation crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 6 residues within 4Å: Chain A: P.87, 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.2: 6 residues within 4Å: Chain A: D.91, H.93, H.128 Chain C: H.248, H.299 Ligands: OXY.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.93, A:H.128, C:H.299 CU.8: 6 residues within 4Å: Chain B: P.87, 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.9: 6 residues within 4Å: Chain A: H.248, H.299 Chain B: D.91, H.93, H.128 Ligands: OXY.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.93, B:H.128, A:H.299 CU.15: 6 residues within 4Å: Chain C: P.87, 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.16: 6 residues within 4Å: Chain B: H.248, H.299 Chain C: D.91, H.93, H.128 Ligands: OXY.18 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.93, C:H.128, B:H.299

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.10: 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 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

3 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 7 residues within 4Å: Chain A: D.91, H.93, H.128 Chain C: H.248, I.250, H.299 Ligands: CU.2 No protein-ligand interaction detected (PLIP) OXY.11: 7 residues within 4Å: Chain A: H.248, I.250, H.299 Chain B: D.91, H.93, H.128 Ligands: CU.9 No protein-ligand interaction detected (PLIP) OXY.18: 7 residues within 4Å: Chain B: H.248, I.250, H.299 Chain C: D.91, H.93, H.128 Ligands: CU.16 No protein-ligand interaction detected (PLIP)

6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 5 residues within 4Å: Chain A: P.162, L.163, H.164, T.233, T.287 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.164, A:T.233, A:T.287, A:T.287 MES.6: 6 residues within 4Å: Chain A: D.46, D.47, K.48, V.217, F.305, E.306 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.47, A:D.47, A:K.48 Salt bridges: A:K.48, A:E.306 MES.12: 5 residues within 4Å: Chain B: P.162, L.163, H.164, T.233, T.287 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.164, B:T.233, B:T.287, B:T.287 MES.13: 6 residues within 4Å: Chain B: D.46, D.47, K.48, V.217, F.305, E.306 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.47, B:D.47, B:K.48 Salt bridges: B:K.48, B:E.306 MES.19: 5 residues within 4Å: Chain C: P.162, L.163, H.164, T.233, T.287 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.164, C:T.233, C:T.287, C:T.287 MES.20: 6 residues within 4Å: Chain C: D.46, D.47, K.48, V.217, F.305, E.306 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.47, C:D.47, C:K.48 Salt bridges: C:K.48, C:E.306

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 6 residues within 4Å: Chain A: V.293, A.295, F.305, A.310, H.312 Chain B: L.99 No protein-ligand interaction detected (PLIP) PG4.14: 6 residues within 4Å: Chain B: V.293, A.295, F.305, A.310, H.312 Chain C: L.99 No protein-ligand interaction detected (PLIP) PG4.21: 6 residues within 4Å: Chain A: L.99 Chain C: V.293, A.295, F.305, A.310, H.312 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halsted, T.P. et al., An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase. IUCrJ (2018)

Release Date

2017-11-29

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase

Related Entries With Identical Sequence