SMTL ID : 6njt.1

Mouse endonuclease G mutant - H97A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: N.128, E.136 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: A.97, N.128, E.136 No protein-ligand interaction detected (PLIP)

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: R.72, E.73, N.85 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: D.94, R.95 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.160, K.170 Chain B: R.160, K.170 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: A.101, A.102 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: S.225 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: E.19, L.20 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: R.72, E.73, N.85 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: A.101, A.102 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: D.94, R.95 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: Y.171, Q.172, V.181 Ligand excluded by PLIP

8 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.9: 5 residues within 4Å: Chain A: G.90, S.91, Q.172, I.174, G.175 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.174 Hydrogen bonds: A:G.175 Water bridges: A:Q.172, A:V.173, A:V.173, B:S.167 IPA.10: 3 residues within 4Å: Chain A: P.182, T.183, N.207 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.207 IPA.11: 2 residues within 4Å: Chain A: N.134, E.212 No protein-ligand interaction detected (PLIP) IPA.17: 3 residues within 4Å: Chain B: S.91, I.174, G.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.175 Water bridges: B:D.87, B:Q.172 IPA.18: 5 residues within 4Å: Chain B: R.66, R.72, D.112, F.115, Y.116 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.72, B:Y.116, B:Y.116 Hydrogen bonds: B:R.66, B:R.66 Water bridges: B:R.72 IPA.19: 3 residues within 4Å: Chain B: V.204, V.221, S.225 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.204, B:V.221 Hydrogen bonds: B:S.225 IPA.20: 4 residues within 4Å: Chain B: D.75, V.77, H.78, R.82 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.82 IPA.21: 8 residues within 4Å: Chain A: I.190, F.234, N.237, I.238 Chain B: Y.23, G.24, L.25, P.26 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.190, A:N.237, A:I.238 Hydrogen bonds: A:N.237, B:G.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vander Zanden, C.M. et al., Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function. Nucleic Acids Res. (2020)

Release Date

2020-01-08

Peptides

Endonuclease G, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endonuclease G, mitochondrial

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