SMTL ID : 6k9c.1

The apo structure of NrS-1 C terminal region (305-718)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-hexamer

Ligands

6 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 5 residues within 4Å: Chain A: L.183, L.218, N.232, F.233, C.234 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.183, A:C.234 HG.4: 5 residues within 4Å: Chain B: L.183, L.218, N.232, F.233, C.234 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:L.183, B:C.234 HG.8: 5 residues within 4Å: Chain C: L.183, L.218, N.232, F.233, C.234 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:L.183, C:C.234 HG.11: 5 residues within 4Å: Chain D: L.183, L.218, N.232, F.233, C.234 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:L.183, D:C.234 HG.15: 5 residues within 4Å: Chain E: L.183, L.218, N.232, F.233, C.234 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:L.183, E:C.234 HG.18: 5 residues within 4Å: Chain F: L.183, L.218, N.232, F.233, C.234 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:L.183, F:C.234

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: A.67, Y.68, E.69, I.230, K.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.68, A:Y.68, A:E.69, A:K.231 Salt bridges: A:K.24 SO4.3: 7 residues within 4Å: Chain A: Q.147, G.148, T.149, G.150, K.151, G.152 Chain F: R.253 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.148, A:T.149, A:G.150, A:K.151, A:G.152 Salt bridges: A:K.151, F:R.253 SO4.5: 7 residues within 4Å: Chain B: Q.147, G.148, T.149, G.150, K.151, G.152 Ligands: SO4.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.148, B:T.149, B:G.150, B:K.151, B:G.152 Salt bridges: B:K.151 SO4.6: 6 residues within 4Å: Chain A: R.253 Chain B: Q.147, K.151, N.192, N.239 Ligands: SO4.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.253, B:Q.147 Salt bridges: B:K.151 SO4.7: 4 residues within 4Å: Chain B: D.250, S.251, K.320 Chain C: K.146 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Salt bridges: C:K.146, B:K.320 Hydrogen bonds: B:D.250, B:D.250, B:D.250, B:S.251 SO4.9: 5 residues within 4Å: Chain C: A.67, Y.68, E.69, I.230, K.231 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.68, C:Y.68, C:K.231 Salt bridges: C:K.24 SO4.10: 7 residues within 4Å: Chain B: R.253 Chain C: Q.147, G.148, T.149, G.150, K.151, G.152 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.148, C:T.149, C:G.150, C:K.151, C:G.152 Salt bridges: C:K.151, B:R.253 SO4.12: 7 residues within 4Å: Chain D: Q.147, G.148, T.149, G.150, K.151, G.152 Ligands: SO4.13 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.148, D:T.149, D:G.150, D:K.151, D:G.152 Salt bridges: D:K.151 SO4.13: 6 residues within 4Å: Chain C: R.253 Chain D: Q.147, K.151, N.192, N.239 Ligands: SO4.12 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.147, C:R.253 Salt bridges: D:K.151 SO4.14: 4 residues within 4Å: Chain D: D.250, S.251, K.320 Chain E: K.146 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:D.250, D:D.250, D:S.251 Salt bridges: D:K.320, E:K.146 SO4.16: 5 residues within 4Å: Chain E: A.67, Y.68, E.69, I.230, K.231 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.68, E:Y.68, E:K.231 Salt bridges: E:K.24 SO4.17: 7 residues within 4Å: Chain D: R.253 Chain E: Q.147, G.148, T.149, G.150, K.151, G.152 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.148, E:T.149, E:G.150, E:K.151, E:G.152 Salt bridges: E:K.151, D:R.253 SO4.19: 7 residues within 4Å: Chain F: Q.147, G.148, T.149, G.150, K.151, G.152 Ligands: SO4.20 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.148, F:T.149, F:G.150, F:K.151, F:G.152 Salt bridges: F:K.151 SO4.20: 6 residues within 4Å: Chain E: R.253 Chain F: Q.147, K.151, N.192, N.239 Ligands: SO4.19 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.147, E:R.253 Salt bridges: F:K.151 SO4.21: 4 residues within 4Å: Chain A: K.146 Chain F: D.250, S.251, K.320 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:D.250, F:D.250, F:S.251 Salt bridges: F:K.320, A:K.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structural studies reveal a ring-shaped architecture of deep-sea vent phage NrS-1 polymerase. Nucleic Acids Res. (2020)

Release Date

2020-04-08

Peptides

Primase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Primase

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