SMTL ID : 6ipn.1

Binary Complex of Human DNA Polymerase Mu with MgdGTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.204, D.206 Ligands: DGT.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:D.206, H2O.4

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.2: 17 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, S.299, K.300, R.307, S.320 Ligands: MG.1, SO4.7 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.194, A:R.197, A:H.203, A:D.204, A:G.295, A:R.307, A:S.320, A:S.320 Water bridges: A:R.197, A:R.197, A:K.199, A:K.199, A:K.199, A:K.199, A:R.261, A:R.307, A:R.307 Salt bridges: A:R.197, A:K.199, A:K.199, A:H.203, A:H.203 pi-Stacking: A:W.296, A:W.296, A:W.296 pi-Cation interactions: A:W.296

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

SO4.3: 4 residues within 4Å: Chain A: G.121, V.122, K.123, T.124 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.121, A:G.121, A:K.123, A:T.124 Water bridges: A:K.123, A:T.124, A:T.124, A:R.127 Salt bridges: A:K.123 SO4.4: 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 SO4.5: 1 residues within 4Å: Chain A: R.103 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.109 Salt bridges: A:R.103 SO4.6: 2 residues within 4Å: Chain A: R.127, R.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.127 Water bridges: A:E.131 Salt bridges: A:R.130 SO4.7: 5 residues within 4Å: Chain A: R.307, N.319, S.320, H.321 Ligands: DGT.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.320, A:S.320 Water bridges: A:R.307, A:S.320, A:S.320 Salt bridges: A:R.307 SO4.8: 2 residues within 4Å: Chain A: H.203, R.278 7 PLIP interactions: 7 interactions with chain A Water bridges: A:G.119, A:G.119, A:R.278, A:R.278, A:R.278 Salt bridges: A:H.203, A:R.278

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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