SMTL ID : 6ak6.1

Binary Complex of Human DNA Polymerase Mu with MnCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.204, D.206 Ligands: MN.2, CTP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.8 MN.2: 6 residues within 4Å: Chain A: D.204, D.206, R.278, D.280 Ligands: MN.1, CTP.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, A:D.280, H2O.6, H2O.7

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.3: 13 residues within 4Å: Chain A: G.193, G.194, R.197, K.199, G.202, H.203, D.204, D.206, G.295, W.296, G.298 Ligands: MN.1, MN.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.194, A:H.203, A:D.204 Water bridges: A:F.195, A:R.197, A:R.197, A:K.199, A:K.199, A:H.203, A:D.204, A:D.204, A:D.206 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203 pi-Stacking: A:W.296

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

SO4.4: 4 residues within 4Å: Chain A: G.121, V.122, K.123, T.124 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.121, A:G.121, A:K.123, A:T.124 Water bridges: A:T.124, A:T.124 SO4.5: 4 residues within 4Å: Chain A: R.307, N.319, S.320, H.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.320 Water bridges: A:N.319 Salt bridges: A:R.307 SO4.6: 3 residues within 4Å: Chain A: R.308, R.311, K.312 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.308, A:R.311, A:K.312 SO4.7: 4 residues within 4Å: Chain A: S.46, E.47, G.48, R.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.48, A:R.49 SO4.8: 2 residues within 4Å: Chain A: T.147, Q.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.148 Water bridges: A:Q.149 SO4.9: 1 residues within 4Å: Chain A: H.203 5 PLIP interactions: 5 interactions with chain A Water bridges: A:T.115, A:G.119, A:G.119, A:R.278 Salt bridges: A:H.203 SO4.10: 2 residues within 4Å: Chain A: R.127, R.130 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.131, A:E.131 Salt bridges: A:R.127, A:R.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, Y.K. et al., Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. J.Am.Chem.Soc. (2019)

Release Date

2019-05-29

Peptides

DNA-directed DNA/RNA polymerase mu: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed DNA/RNA polymerase mu

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