SMTL ID : 1ir1.1

Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: T.173, K.177, K.201, D.203, E.204, H.294 Chain M: N.123 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 MG.3: 6 residues within 4Å: Chain C: K.177, K.201, D.203, E.204 Chain K: N.123 Ligands: CAP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 MG.5: 6 residues within 4Å: Chain E: K.177, K.201, D.203, E.204 Chain I: N.123 Ligands: CAP.6 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 MG.7: 7 residues within 4Å: Chain G: K.175, K.177, K.201, D.203, E.204 Chain O: N.123 Ligands: CAP.8 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 MG.9: 8 residues within 4Å: Chain E: N.123 Chain I: T.173, K.177, K.201, D.203, E.204, H.294 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.203, I:E.204 MG.11: 6 residues within 4Å: Chain C: N.123 Chain K: K.177, K.201, D.203, E.204 Ligands: CAP.12 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.203, K:E.204 MG.13: 6 residues within 4Å: Chain A: N.123 Chain M: K.177, K.201, D.203, E.204 Ligands: CAP.14 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.203, M:E.204 MG.15: 7 residues within 4Å: Chain G: N.123 Chain O: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.16 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.203, O:E.204

8 x CAP: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE(Non-covalent)

CAP.2: 22 residues within 4Å: Chain A: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain M: E.60, T.65, W.66, N.123 Ligands: MG.1 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain M Hydrogen bonds: A:T.173, A:K.175, A:G.381, A:G.403, A:G.404, M:T.65, M:N.123 Water bridges: A:T.173, A:T.173, A:K.177, A:K.177, A:K.177, A:K.177, A:R.295, A:R.295, A:H.327, A:H.327, A:G.329, A:S.379, A:S.379, A:G.380, A:I.382, A:I.382 Salt bridges: A:K.175, A:K.175, A:K.177, A:R.295, A:H.327, A:K.334, A:K.334 CAP.4: 22 residues within 4Å: Chain C: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain K: E.60, T.65, W.66, N.123 Ligands: MG.3 29 PLIP interactions: 26 interactions with chain C, 3 interactions with chain K Hydrogen bonds: C:T.173, C:K.175, C:G.381, C:G.403, C:G.404, K:T.65, K:N.123 Water bridges: C:T.173, C:T.173, C:K.177, C:K.177, C:K.177, C:H.294, C:R.295, C:R.295, C:H.327, C:S.379, C:S.379, C:G.380, C:I.382, C:I.382, K:E.60 Salt bridges: C:K.175, C:K.175, C:K.177, C:R.295, C:H.327, C:K.334, C:K.334 CAP.6: 22 residues within 4Å: Chain E: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain I: E.60, T.65, W.66, N.123 Ligands: MG.5 31 PLIP interactions: 29 interactions with chain E, 2 interactions with chain I Hydrogen bonds: E:T.173, E:K.175, E:S.379, E:G.381, E:G.403, E:G.404, I:T.65, I:N.123 Water bridges: E:T.173, E:T.173, E:K.177, E:K.177, E:K.177, E:K.177, E:R.295, E:R.295, E:R.295, E:H.327, E:H.327, E:G.329, E:S.379, E:G.380, E:I.382, E:I.382 Salt bridges: E:K.175, E:K.175, E:K.177, E:R.295, E:H.327, E:K.334, E:K.334 CAP.8: 22 residues within 4Å: Chain G: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain O: E.60, T.65, W.66, N.123 Ligands: MG.7 30 PLIP interactions: 28 interactions with chain G, 2 interactions with chain O Hydrogen bonds: G:T.173, G:K.175, G:G.381, G:G.403, G:G.404, O:T.65, O:N.123 Water bridges: G:T.173, G:T.173, G:K.177, G:K.177, G:K.177, G:K.177, G:R.295, G:R.295, G:H.327, G:H.327, G:G.329, G:S.379, G:S.379, G:G.380, G:I.382, G:I.382 Salt bridges: G:K.175, G:K.175, G:K.177, G:R.295, G:H.327, G:K.334, G:K.334 CAP.10: 22 residues within 4Å: Chain E: E.60, T.65, W.66, N.123 Chain I: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.9 31 PLIP interactions: 29 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:T.173, I:T.173, I:K.175, I:G.381, I:G.403, I:G.404, E:T.65, E:N.123 Water bridges: I:T.173, I:T.173, I:K.177, I:K.177, I:K.177, I:K.177, I:H.294, I:R.295, I:R.295, I:H.327, I:G.329, I:S.379, I:S.379, I:G.380, I:I.382, I:I.382 Salt bridges: I:K.175, I:K.175, I:K.177, I:R.295, I:H.327, I:K.334, I:K.334 CAP.12: 22 residues within 4Å: Chain C: E.60, T.65, W.66, N.123 Chain K: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.11 30 PLIP interactions: 28 interactions with chain K, 2 interactions with chain C Hydrogen bonds: K:T.173, K:T.173, K:K.175, K:G.381, K:G.403, K:G.404, C:T.65, C:N.123 Water bridges: K:T.173, K:T.173, K:K.177, K:K.177, K:K.177, K:K.177, K:H.294, K:R.295, K:R.295, K:H.327, K:S.379, K:S.379, K:G.380, K:I.382, K:I.382 Salt bridges: K:K.175, K:K.175, K:K.177, K:R.295, K:H.327, K:K.334, K:K.334 CAP.14: 22 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 Chain M: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.13 32 PLIP interactions: 2 interactions with chain A, 30 interactions with chain M Hydrogen bonds: A:T.65, A:N.123, M:T.173, M:T.173, M:K.175, M:S.379, M:G.381, M:G.403, M:G.404 Water bridges: M:T.173, M:T.173, M:K.177, M:K.177, M:K.177, M:K.177, M:H.294, M:R.295, M:R.295, M:R.295, M:H.327, M:G.329, M:S.379, M:G.380, M:I.382, M:I.382 Salt bridges: M:K.175, M:K.175, M:K.177, M:R.295, M:H.327, M:K.334, M:K.334 CAP.16: 22 residues within 4Å: Chain G: E.60, T.65, W.66, N.123 Chain O: T.173, K.175, K.177, K.201, D.203, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: MG.15 31 PLIP interactions: 29 interactions with chain O, 2 interactions with chain G Hydrogen bonds: O:T.173, O:T.173, O:K.175, O:G.381, O:G.403, O:G.404, G:T.65, G:N.123 Water bridges: O:T.173, O:T.173, O:K.177, O:K.177, O:K.177, O:K.177, O:H.294, O:R.295, O:R.295, O:H.327, O:G.329, O:S.379, O:S.379, O:G.380, O:I.382, O:I.382 Salt bridges: O:K.175, O:K.175, O:K.177, O:R.295, O:H.327, O:K.334, O:K.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizohata, E. et al., Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate. J.Mol.Biol. (2002)

Release Date

2002-03-13

Peptides

Large subunit of Rubisco: ACEGIKMO
Small subunit of Rubisco: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

I
A

K
B

M
C

O
D

B
S

D
T

F
U

H
V

J
S

L
T

N
U

P
V

Large subunit of Rubisco

Small subunit of Rubisco

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