SMTL ID : 8jfy.1

Cryo-EM structure of RDGC/Ca2+-CaM complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.94, D.96, N.98, F.100, I.101, S.102, E.105 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.94, A:D.96, A:D.96, A:F.100, A:E.105 CA.2: 5 residues within 4Å: Chain A: D.130, D.132, D.134, Q.136, E.141 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.130, A:D.132, A:Q.136, A:E.141, A:E.141 CA.3: 6 residues within 4Å: Chain A: D.21, D.23, D.25, T.27, T.29, E.32 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.21, A:D.23, A:D.25, A:T.27, A:E.32 CA.4: 5 residues within 4Å: Chain A: D.57, D.59, N.61, T.63, E.68 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.57, A:D.57, A:T.63, A:E.68, A:E.68 CA.8: 6 residues within 4Å: Chain B: D.533, D.535, S.537, I.540, T.541, E.544 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.533, B:D.535, B:T.541, B:E.544 CA.9: 5 residues within 4Å: Chain B: D.573, N.575, D.577, K.579, E.584 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.573, B:D.577, B:D.577, B:K.579, B:E.584 CA.10: 7 residues within 4Å: Chain C: D.94, D.96, N.98, F.100, I.101, S.102, E.105 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.94, C:D.96, C:D.96, C:F.100, C:E.105 CA.11: 5 residues within 4Å: Chain C: D.130, D.132, D.134, Q.136, E.141 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.130, C:D.132, C:Q.136, C:E.141, C:E.141 CA.12: 6 residues within 4Å: Chain C: D.21, D.23, D.25, T.27, T.29, E.32 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.21, C:D.23, C:D.25, C:T.27, C:E.32 CA.13: 5 residues within 4Å: Chain C: D.57, D.59, N.61, T.63, E.68 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.57, C:D.57, C:T.63, C:E.68, C:E.68 CA.17: 6 residues within 4Å: Chain D: D.533, D.535, S.537, I.540, T.541, E.544 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.533, D:D.535, D:T.541, D:E.544 CA.18: 5 residues within 4Å: Chain D: D.573, N.575, D.577, K.579, E.584 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.573, D:D.577, D:D.577, D:K.579, D:E.584

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain B: D.152, D.181, N.213, H.265, H.354 Ligands: FE.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.181, B:H.265, B:H.354 ZN.14: 6 residues within 4Å: Chain D: D.152, D.181, N.213, H.265, H.354 Ligands: FE.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.181, D:H.265, D:H.354

2 x FE: FE (III) ION(Non-covalent)

FE.6: 5 residues within 4Å: Chain B: D.152, H.154, D.181, H.214 Ligands: ZN.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.152, B:H.154, B:D.181 FE.15: 5 residues within 4Å: Chain D: D.152, H.154, D.181, H.214 Ligands: ZN.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.152, D:H.154, D:D.181

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

PO4.7: 5 residues within 4Å: Chain B: R.185, H.214, Y.223, R.327, Y.378 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.327 Salt bridges: B:R.185, B:H.214 PO4.16: 5 residues within 4Å: Chain D: R.185, H.214, Y.223, R.327, Y.378 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.327 Salt bridges: D:R.185, D:H.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z.M. et al., Cryo-EM structure of RDGC/Ca2+-CaM complex. To Be Published

Release Date

2024-11-27

Peptides

AT15141p: AC
Serine/threonine-protein phosphatase rdgC: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
D

D
C

AT15141p

Serine/threonine-protein phosphatase rdgC

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