SMTL ID : 1upm.1

ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-8-8-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: K.177, K.201, D.203, E.204 Chain H: N.123 Ligands: CAP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.203, A:E.204 CA.3: 7 residues within 4Å: Chain C: K.175, K.177, K.201, D.203, E.204 Chain E: N.123 Ligands: CAP.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.203, C:E.204 CA.5: 7 residues within 4Å: Chain C: N.123 Chain E: K.175, K.177, K.201, D.203, E.204 Ligands: CAP.6 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.203, E:E.204 CA.7: 6 residues within 4Å: Chain G: K.177, K.201, D.203, E.204 Chain J: N.123 Ligands: CAP.8 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.203, G:E.204 CA.9: 6 residues within 4Å: Chain A: N.123 Chain H: K.177, K.201, D.203, E.204 Ligands: CAP.10 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.203, H:E.204 CA.11: 6 residues within 4Å: Chain G: N.123 Chain J: K.177, K.201, D.203, E.204 Ligands: CAP.12 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.203, J:E.204 CA.13: 7 residues within 4Å: Chain L: K.177, K.201, D.203, E.204, H.294 Chain O: N.123 Ligands: CAP.14 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.203, L:E.204 CA.15: 7 residues within 4Å: Chain L: 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, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Chain H: E.60, T.65, W.66, N.123 Ligands: CA.1 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain H Hydrogen bonds: A:T.173, A:T.173, A:K.175, A:H.298, A:S.379, A:G.381, A:G.403, A:G.404, H:T.65, H:N.123 Water bridges: A:T.173, A:K.177, A:R.295, A:R.295, A:G.329, A:S.379, A:G.380, A:I.382, A:G.405, H:T.65 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: 20 residues within 4Å: Chain C: T.173, K.175, K.177, K.201, E.204, H.294, R.295, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain E: E.60, T.65, W.66, N.123 Ligands: CA.3 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:T.173, C:K.175, C:H.298, C:S.379, C:G.381, C:G.403, C:G.404, E:T.65, E:T.65, E:N.123 Water bridges: C:K.177, C:K.177, C:R.295, C:S.328, C:S.379, C:S.379, C:S.379, C:G.380, C:Q.401, C:G.405 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: 21 residues within 4Å: Chain C: E.60, T.65, W.66, N.123 Chain E: T.173, K.175, K.177, K.201, 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: CA.5 25 PLIP interactions: 22 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:T.173, E:T.173, E:K.175, E:H.298, E:S.379, E:G.381, E:G.403, E:G.404, C:T.65, C:N.123 Water bridges: E:K.177, E:R.295, E:S.328, E:G.380, E:I.382, E:Q.401, E:G.405, C:T.65 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: 21 residues within 4Å: Chain G: T.173, K.175, K.177, K.201, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Chain J: E.60, T.65, W.66, N.123 Ligands: CA.7 29 PLIP interactions: 3 interactions with chain J, 26 interactions with chain G Hydrogen bonds: J:T.65, J:T.65, J:N.123, G:T.173, G:K.175, G:H.298, G:S.379, G:S.379, G:G.381, G:G.403, G:G.404 Water bridges: G:T.173, G:K.177, G:K.177, G:R.295, G:S.328, G:S.379, G:S.379, G:S.379, G:G.380, G:I.382, G:G.405 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: 21 residues within 4Å: Chain A: E.60, T.65, W.66, N.123 Chain H: T.173, K.175, K.177, K.201, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, G.403, G.404 Ligands: CA.9 29 PLIP interactions: 26 interactions with chain H, 3 interactions with chain A Hydrogen bonds: H:T.173, H:K.175, H:H.298, H:S.379, H:G.381, H:G.403, H:G.404, A:T.65, A:T.65, A:N.123 Water bridges: H:T.173, H:K.177, H:K.177, H:R.295, H:R.295, H:G.329, H:S.379, H:S.379, H:S.379, H:G.380, H:I.382, H:G.405 Salt bridges: H:K.175, H:K.175, H:K.177, H:R.295, H:H.327, H:K.334, H:K.334 CAP.12: 22 residues within 4Å: Chain G: E.60, T.65, W.66, N.123 Chain J: T.173, K.175, K.177, K.201, E.204, H.294, R.295, H.298, H.327, K.334, L.335, S.379, G.380, G.381, F.402, G.403, G.404 Ligands: CA.11 29 PLIP interactions: 3 interactions with chain G, 26 interactions with chain J Hydrogen bonds: G:T.65, G:N.123, J:T.173, J:T.173, J:K.175, J:H.298, J:S.379, J:G.381, J:G.403, J:G.404 Water bridges: G:T.65, J:T.173, J:K.177, J:R.295, J:R.295, J:S.328, J:G.329, J:G.380, J:I.382, J:I.382, J:I.382, J:Q.401 Salt bridges: J:K.175, J:K.175, J:K.177, J:R.295, J:H.327, J:K.334, J:K.334 CAP.14: 22 residues within 4Å: Chain L: T.173, K.175, K.177, K.201, E.204, H.294, R.295, H.298, 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: CA.13 25 PLIP interactions: 22 interactions with chain L, 3 interactions with chain O Hydrogen bonds: L:T.173, L:K.175, L:H.298, L:S.379, L:G.381, L:G.403, L:G.404, O:T.65, O:T.65, O:N.123 Water bridges: L:T.173, L:K.177, L:K.177, L:R.295, L:R.295, L:S.379, L:G.380, L:G.405 Salt bridges: L:K.175, L:K.175, L:K.177, L:R.295, L:H.327, L:K.334, L:K.334 CAP.16: 21 residues within 4Å: Chain L: E.60, T.65, W.66, N.123 Chain O: T.173, K.175, K.177, K.201, 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: CA.15 26 PLIP interactions: 23 interactions with chain O, 3 interactions with chain L Hydrogen bonds: O:T.173, O:T.173, O:K.175, O:H.298, O:S.379, O:G.381, O:G.403, O:G.404, L:T.65, L:N.123 Water bridges: O:T.173, O:K.177, O:R.295, O:R.295, O:S.379, O:S.379, O:G.380, O:I.382, L:T.65 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

Karkehabadi, S. et al., Calcium Supports Loop Closure But not Catalysis in Rubisco. J.Mol.Biol. (2003)

Release Date

2003-10-14

Peptides

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN: ACEGHJLO
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN: BDFIKMNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
E

E
H

G
K

H
L

J
O

L
R

O
V

B
C

D
F

F
I

I
M

K
P

M
S

N
T

P
W

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

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