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SMTL ID : 4rt2.1

Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA (5'-D(P*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.1:

18 residues within 4Å:

Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.5

5 PLIP interactions:

5 interactions with chain A

Hydrogen bonds: A:K.280, A:R.283
Water bridges: A:R.40
Salt bridges: A:K.280
pi-Stacking: A:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

4 residues within 4Å:

Chain A: D.190, D.192
Ligands: NA.3, N6T.7

3 PLIP interactions:

2 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.190, A:D.192, H₂O.1

3 x NA: SODIUM ION(Non-functional Binders)

NA.3:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: C.10 Ligands: MG.2, N6T.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.190
NA.4:	5 residues within 4Å: Chain A: T.101, V.103, G.105, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.5:	5 residues within 4Å: Chain A: K.60, K.61, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.60, A:G.64, A:V.65 Water bridges: A:K.60

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

CL.6:

4 residues within 4Å:

Chain A: A.32, I.33, H.34, K.35

Ligand excluded by PLIP

1 x N6T: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine(Non-covalent)

N6T.7:

18 residues within 4Å:

Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279
Chain B: A.6
Chain C: C.10
Ligands: MG.2, NA.3

15 PLIP interactions:

15 interactions with chain A

Hydrophobic interactions: A:D.276
Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.192, A:N.279
Water bridges: A:R.149, A:R.149, A:S.180, A:S.180, A:D.276, A:D.276

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kadina, A.P. et al., Two Scaffolds from Two Flips: (alpha, beta)/(beta, gamma) CH2/NH "Met-Im" Analogues of dTTP. Org.Lett. (2015)

Release Date

2015-07-01

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA polymerase beta

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