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Zinc in PDB 5k5m: Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27

Protein crystallography data

The structure of Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27, PDB code: 5k5m was solved by R.Arora, T.E.Benson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.32 / 2.01
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 82.140, 115.770, 148.590, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27 (pdb code 5k5m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27, PDB code: 5k5m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5k5m

Go back to Zinc Binding Sites List in 5k5m
Zinc binding site 1 out of 2 in the Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:20.8
occ:1.00
NE2 A:HIS712 2.1 19.1 1.0
NE2 A:HIS714 2.1 20.4 1.0
SG A:CYS847 2.3 21.1 1.0
SG A:CYS728 2.3 21.7 1.0
CE1 A:HIS714 3.0 21.0 1.0
CE1 A:HIS712 3.1 19.0 1.0
CD2 A:HIS712 3.1 19.6 1.0
CD2 A:HIS714 3.1 21.1 1.0
CB A:CYS728 3.1 18.9 1.0
CB A:CYS847 3.3 18.3 1.0
ND1 A:HIS714 4.2 22.1 1.0
CG A:HIS712 4.2 19.4 1.0
ND1 A:HIS712 4.2 20.1 1.0
CG A:HIS714 4.2 21.5 1.0
CD1 A:LEU839 4.4 20.3 1.0
CA A:CYS728 4.5 18.2 1.0
O A:HOH1380 4.6 19.1 1.0
C A:CYS728 4.6 20.3 1.0
CA A:CYS847 4.6 18.5 1.0
N A:ARG729 4.8 17.1 1.0
NH2 A:ARG769 5.0 14.1 1.0

Zinc binding site 2 out of 2 in 5k5m

Go back to Zinc Binding Sites List in 5k5m
Zinc binding site 2 out of 2 in the Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of Dengue Virus Serotype 2 Rna Dependent Rna Polymerase with Compound 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:50.8
occ:1.00
NE2 A:HIS442 2.0 62.7 1.0
SG A:CYS450 2.2 50.1 1.0
SG A:CYS447 2.3 54.0 1.0
OE1 A:GLU438 2.6 72.7 1.0
CE1 A:HIS442 3.0 62.6 1.0
CB A:CYS450 3.1 47.0 1.0
CD2 A:HIS442 3.1 63.2 1.0
CB A:CYS447 3.3 51.2 1.0
CD A:GLU438 3.4 83.2 1.0
CG A:GLU438 3.6 63.7 1.0
N A:CYS450 3.7 50.0 1.0
CA A:CYS447 3.7 52.3 1.0
CA A:CYS450 4.0 47.9 1.0
N A:GLU448 4.1 56.3 1.0
ND1 A:HIS442 4.1 63.9 1.0
CG A:HIS442 4.2 62.5 1.0
C A:CYS447 4.4 57.8 1.0
CG2 A:THR572 4.4 56.2 1.0
OE2 A:GLU438 4.4 85.1 1.0
N A:THR449 4.5 55.7 1.0
C A:THR449 4.8 57.2 1.0
O A:HOH1227 4.8 47.4 1.0
O A:LYS446 4.9 59.1 1.0
OG1 A:THR449 5.0 61.5 1.0

Reference:

S.P.Lim, C.G.Noble, C.C.Seh, T.S.Soh, A.El Sahili, G.K.Chan, J.Lescar, R.Arora, T.Benson, S.Nilar, U.Manjunatha, K.F.Wan, H.Dong, X.Xie, P.Y.Shi, F.Yokokawa. Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling. Plos Pathog. V. 12 05737 2016.
ISSN: ESSN 1553-7374
PubMed: 27500641
DOI: 10.1371/JOURNAL.PPAT.1005737
Page generated: Wed Dec 16 06:26:21 2020

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