SMTL ID : 6tgt.1

The Calcium soaked crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 2.16A resolution (Soaked in CaCl2 [5mM] for 20 min).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-12-mer

Ligands

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

FE.1: 2 residues within 4Å: Chain A: H.70, W.71 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.70, H2O.1, H2O.3, H2O.4, H2O.12 FE.5: 2 residues within 4Å: Chain B: H.70, W.71 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.70, H2O.5, H2O.8, H2O.8, H2O.16 FE.9: 2 residues within 4Å: Chain C: H.70, W.71 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.70, H2O.3, H2O.9, H2O.12, H2O.13 FE.13: 2 residues within 4Å: Chain D: H.70, W.71 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:H.70, H2O.7, H2O.14, H2O.16, H2O.17 FE.17: 2 residues within 4Å: Chain E: H.70, W.71 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:H.70, H2O.18, H2O.21, H2O.22, H2O.30 FE.21: 2 residues within 4Å: Chain F: H.70, W.71 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:H.70, H2O.23, H2O.25, H2O.26, H2O.34 FE.25: 2 residues within 4Å: Chain G: H.70, W.71 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:H.70, H2O.21, H2O.27, H2O.30, H2O.31 FE.29: 2 residues within 4Å: Chain H: H.70, W.71 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:H.70, H2O.25, H2O.32, H2O.34, H2O.35 FE.33: 2 residues within 4Å: Chain I: H.70, W.71 5 PLIP interactions: 1 interactions with chain I, 4 Ligand-Water interactions Metal complexes: I:H.70, H2O.36, H2O.38, H2O.39, H2O.47 FE.37: 2 residues within 4Å: Chain J: H.70, W.71 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:H.70, H2O.40, H2O.43, H2O.44, H2O.52 FE.41: 2 residues within 4Å: Chain K: H.70, W.71 5 PLIP interactions: 1 interactions with chain K, 4 Ligand-Water interactions Metal complexes: K:H.70, H2O.38, H2O.45, H2O.47, H2O.48 FE.45: 2 residues within 4Å: Chain L: H.70, W.71 5 PLIP interactions: 1 interactions with chain L, 4 Ligand-Water interactions Metal complexes: L:H.70, H2O.43, H2O.49, H2O.52, H2O.53

36 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.132, D.133, I.200 Chain H: D.193, N.195 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: A:D.132, A:D.132, A:D.133, H:D.193, H2O.2 CA.3: 8 residues within 4Å: Chain A: N.167, Q.170 Chain E: N.167, Q.170 Chain I: N.167, Q.170 Ligands: CA.19, CA.35 No protein-ligand interaction detected (PLIP) CA.4: 8 residues within 4Å: Chain A: N.167, E.171 Chain E: N.167, E.171 Chain I: N.167, E.171 Ligands: CA.20, CA.36 No protein-ligand interaction detected (PLIP) CA.6: 5 residues within 4Å: Chain B: D.132, D.133, I.200 Chain F: D.193, N.195 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:D.132, B:D.132, B:D.133, F:D.193, H2O.6 CA.7: 8 residues within 4Å: Chain B: N.167, Q.170 Chain G: N.167, Q.170 Chain L: N.167, Q.170 Ligands: CA.27, CA.47 No protein-ligand interaction detected (PLIP) CA.8: 8 residues within 4Å: Chain B: N.167, E.171 Chain G: N.167, E.171 Chain L: N.167, E.171 Ligands: CA.28, CA.48 No protein-ligand interaction detected (PLIP) CA.10: 5 residues within 4Å: Chain C: D.132, D.133, I.200 Chain E: D.193, N.195 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:D.193, C:D.132, C:D.132, C:D.133, H2O.10 CA.11: 8 residues within 4Å: Chain C: N.167, Q.170 Chain H: N.167, Q.170 Chain J: N.167, Q.170 Ligands: CA.31, CA.39 No protein-ligand interaction detected (PLIP) CA.12: 8 residues within 4Å: Chain C: N.167, E.171 Chain H: N.167, E.171 Chain J: N.167, E.171 Ligands: CA.32, CA.40 No protein-ligand interaction detected (PLIP) CA.14: 5 residues within 4Å: Chain D: D.132, D.133, I.200 Chain G: D.193, N.195 5 PLIP interactions: 1 interactions with chain G, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: G:D.193, D:D.132, D:D.132, D:D.133, H2O.15 CA.15: 8 residues within 4Å: Chain D: N.167, Q.170 Chain F: N.167, Q.170 Chain K: N.167, Q.170 Ligands: CA.23, CA.43 No protein-ligand interaction detected (PLIP) CA.16: 8 residues within 4Å: Chain D: N.167, E.171 Chain F: N.167, E.171 Chain K: N.167, E.171 Ligands: CA.24, CA.44 No protein-ligand interaction detected (PLIP) CA.18: 5 residues within 4Å: Chain E: D.132, D.133, I.200 Chain L: D.193, N.195 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: E:D.132, E:D.132, E:D.133, L:D.193, H2O.19 CA.19: 8 residues within 4Å: Chain A: N.167, Q.170 Chain E: N.167, Q.170 Chain I: N.167, Q.170 Ligands: CA.3, CA.35 No protein-ligand interaction detected (PLIP) CA.20: 8 residues within 4Å: Chain A: N.167, E.171 Chain E: N.167, E.171 Chain I: N.167, E.171 Ligands: CA.4, CA.36 No protein-ligand interaction detected (PLIP) CA.22: 5 residues within 4Å: Chain F: D.132, D.133, I.200 Chain J: D.193, N.195 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: F:D.132, F:D.132, F:D.133, J:D.193, H2O.24 CA.23: 8 residues within 4Å: Chain D: N.167, Q.170 Chain F: N.167, Q.170 Chain K: N.167, Q.170 Ligands: CA.15, CA.43 No protein-ligand interaction detected (PLIP) CA.24: 8 residues within 4Å: Chain D: N.167, E.171 Chain F: N.167, E.171 Chain K: N.167, E.171 Ligands: CA.16, CA.44 No protein-ligand interaction detected (PLIP) CA.26: 5 residues within 4Å: Chain G: D.132, D.133, I.200 Chain I: D.193, N.195 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: G:D.132, G:D.132, G:D.133, I:D.193, H2O.28 CA.27: 8 residues within 4Å: Chain B: N.167, Q.170 Chain G: N.167, Q.170 Chain L: N.167, Q.170 Ligands: CA.7, CA.47 No protein-ligand interaction detected (PLIP) CA.28: 8 residues within 4Å: Chain B: N.167, E.171 Chain G: N.167, E.171 Chain L: N.167, E.171 Ligands: CA.8, CA.48 No protein-ligand interaction detected (PLIP) CA.30: 5 residues within 4Å: Chain H: D.132, D.133, I.200 Chain K: D.193, N.195 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: H:D.132, H:D.132, H:D.133, K:D.193, H2O.32 CA.31: 8 residues within 4Å: Chain C: N.167, Q.170 Chain H: N.167, Q.170 Chain J: N.167, Q.170 Ligands: CA.11, CA.39 No protein-ligand interaction detected (PLIP) CA.32: 8 residues within 4Å: Chain C: N.167, E.171 Chain H: N.167, E.171 Chain J: N.167, E.171 Ligands: CA.12, CA.40 No protein-ligand interaction detected (PLIP) CA.34: 5 residues within 4Å: Chain D: D.193, N.195 Chain I: D.132, D.133, I.200 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: I:D.132, I:D.132, I:D.133, D:D.193, H2O.37 CA.35: 8 residues within 4Å: Chain A: N.167, Q.170 Chain E: N.167, Q.170 Chain I: N.167, Q.170 Ligands: CA.3, CA.19 No protein-ligand interaction detected (PLIP) CA.36: 8 residues within 4Å: Chain A: N.167, E.171 Chain E: N.167, E.171 Chain I: N.167, E.171 Ligands: CA.4, CA.20 No protein-ligand interaction detected (PLIP) CA.38: 5 residues within 4Å: Chain B: D.193, N.195 Chain J: D.132, D.133, I.200 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: B:D.193, J:D.132, J:D.132, J:D.133, H2O.41 CA.39: 8 residues within 4Å: Chain C: N.167, Q.170 Chain H: N.167, Q.170 Chain J: N.167, Q.170 Ligands: CA.11, CA.31 No protein-ligand interaction detected (PLIP) CA.40: 8 residues within 4Å: Chain C: N.167, E.171 Chain H: N.167, E.171 Chain J: N.167, E.171 Ligands: CA.12, CA.32 No protein-ligand interaction detected (PLIP) CA.42: 5 residues within 4Å: Chain A: D.193, N.195 Chain K: D.132, D.133, I.200 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: K:D.132, K:D.132, K:D.133, A:D.193, H2O.46 CA.43: 8 residues within 4Å: Chain D: N.167, Q.170 Chain F: N.167, Q.170 Chain K: N.167, Q.170 Ligands: CA.15, CA.23 No protein-ligand interaction detected (PLIP) CA.44: 8 residues within 4Å: Chain D: N.167, E.171 Chain F: N.167, E.171 Chain K: N.167, E.171 Ligands: CA.16, CA.24 No protein-ligand interaction detected (PLIP) CA.46: 5 residues within 4Å: Chain C: D.193, N.195 Chain L: D.132, D.133, I.200 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: L:D.132, L:D.132, L:D.133, C:D.193, H2O.50 CA.47: 8 residues within 4Å: Chain B: N.167, Q.170 Chain G: N.167, Q.170 Chain L: N.167, Q.170 Ligands: CA.7, CA.27 No protein-ligand interaction detected (PLIP) CA.48: 8 residues within 4Å: Chain B: N.167, E.171 Chain G: N.167, E.171 Chain L: N.167, E.171 Ligands: CA.8, CA.28 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuypers, M.G. et al., The Calcium soaked crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 2.16A resolution (Soaked in CaCl2 [5mM] for 20 min). To Be Published

Release Date

2020-12-02

Peptides

DNA protection during starvation protein 2: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

DNA protection during starvation protein 2