SMTL ID : 3ie9.2 (2 other biounits)

Structure of oxidized M98L mutant of amicyanin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: K.2 Chain E: K.2, E.84 Ligands: PO4.21 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Salt bridges: E:K.2, A:K.2 PO4.6: 4 residues within 4Å: Chain B: K.2 Chain D: K.2, E.84 Ligands: PO4.16 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Salt bridges: D:K.2, B:K.2 PO4.11: 4 residues within 4Å: Chain C: K.2 Chain F: K.2, E.84 Ligands: PO4.26 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Salt bridges: C:K.2, F:K.2 PO4.16: 4 residues within 4Å: Chain B: K.2, E.84 Chain D: K.2 Ligands: PO4.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:K.2, D:K.2 PO4.21: 4 residues within 4Å: Chain A: K.2, E.84 Chain E: K.2 Ligands: PO4.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Salt bridges: A:K.2, E:K.2 PO4.26: 4 residues within 4Å: Chain C: K.2, E.84 Chain F: K.2 Ligands: PO4.11 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Salt bridges: C:K.2, F:K.2

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

CU.2: 5 residues within 4Å: Chain A: P.52, H.53, C.92, H.95, L.98 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.53, A:C.92, A:H.95 CU.7: 5 residues within 4Å: Chain B: P.52, H.53, C.92, H.95, L.98 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.53, B:C.92, B:H.95 CU.12: 5 residues within 4Å: Chain C: P.52, H.53, C.92, H.95, L.98 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.53, C:C.92, C:H.95 CU.17: 5 residues within 4Å: Chain D: P.52, H.53, C.92, H.95, L.98 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.53, D:C.92, D:H.95 CU.22: 5 residues within 4Å: Chain E: P.52, H.53, C.92, H.95, L.98 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.53, E:C.92, E:H.95 CU.27: 5 residues within 4Å: Chain F: P.52, H.53, C.92, H.95, L.98 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.53, F:C.92, F:H.95

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 8 residues within 4Å: Chain A: M.51, H.95 Chain B: M.51, H.95 Chain C: M.51, H.95 Ligands: ZN.8, ZN.13 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:H.95, C:H.95, A:H.95 ZN.8: 8 residues within 4Å: Chain A: M.51, H.95 Chain B: M.51, H.95 Chain C: M.51, H.95 Ligands: ZN.3, ZN.13 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:H.95, C:H.95, A:H.95 ZN.13: 8 residues within 4Å: Chain A: M.51, H.95 Chain B: M.51, H.95 Chain C: M.51, H.95 Ligands: ZN.3, ZN.8 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:H.95, C:H.95, A:H.95 ZN.18: 8 residues within 4Å: Chain D: M.51, H.95 Chain E: M.51, H.95 Chain F: M.51, H.95 Ligands: ZN.23, ZN.28 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F Metal complexes: E:H.95, D:H.95, F:H.95 ZN.23: 8 residues within 4Å: Chain D: M.51, H.95 Chain E: M.51, H.95 Chain F: M.51, H.95 Ligands: ZN.18, ZN.28 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F Metal complexes: E:H.95, D:H.95, F:H.95 ZN.28: 8 residues within 4Å: Chain D: M.51, H.95 Chain E: M.51, H.95 Chain F: M.51, H.95 Ligands: ZN.18, ZN.23 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F Metal complexes: E:H.95, D:H.95, F:H.95

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

CL.4: 3 residues within 4Å: Chain A: K.68 Chain C: K.29 Chain E: R.99 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: K.29 Chain B: K.68 Chain D: R.99 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: K.29 Chain C: K.68 Chain F: R.99 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: R.99 Chain D: K.68 Chain F: K.29 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: R.99 Chain D: K.29 Chain E: K.68 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain C: R.99 Chain E: K.29 Chain F: K.68 Ligand excluded by PLIP

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

ACT.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, M. et al., Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine. Biochemistry (2009)

Release Date

2009-10-06

Peptides

Amicyanin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Amicyanin

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