Zinc in PDB 5f3z: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52, PDB code: 5f3z was solved by C.G.Noble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.28 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.300, 176.220, 57.840, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.9

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52 (pdb code 5f3z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52, PDB code: 5f3z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:26.8 occ:1.00 NE2 A:HIS712 2.1 25.2 1.0 NE2 A:HIS714 2.1 27.1 1.0 SG A:CYS847 2.3 26.8 1.0 SG A:CYS728 2.3 26.3 1.0 CE1 A:HIS712 3.0 25.1 1.0 CE1 A:HIS714 3.1 27.3 1.0 CD2 A:HIS712 3.1 25.3 1.0 CB A:CYS728 3.1 22.6 1.0 CD2 A:HIS714 3.1 26.4 1.0 CB A:CYS847 3.3 23.2 1.0 ND1 A:HIS712 4.2 26.5 1.0 CG A:HIS712 4.2 24.8 1.0 ND1 A:HIS714 4.2 27.6 1.0 CG A:HIS714 4.3 25.6 1.0 CD1 A:LEU839 4.3 27.3 1.0 CA A:CYS728 4.4 22.3 1.0 O A:HOH1472 4.4 36.7 1.0 O A:HOH1443 4.5 33.3 1.0 C A:CYS728 4.5 26.7 1.0 N A:ARG729 4.6 23.5 1.0 CA A:CYS847 4.7 24.0 1.0 O A:HOH1229 4.8 42.5 1.0 NH2 A:ARG769 4.9 22.4 1.0 O A:HOH1501 4.9 42.8 1.0 O A:GLU843 4.9 32.0 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Pc-79-SH52 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:37.4 occ:1.00 NE2 A:HIS441 2.1 36.0 1.0 OE1 A:GLU437 2.2 53.7 1.0 SG A:CYS446 2.2 37.8 1.0 SG A:CYS449 2.3 38.7 1.0 CD A:GLU437 3.0 46.4 1.0 CE1 A:HIS441 3.1 35.8 1.0 CD2 A:HIS441 3.1 36.0 1.0 CB A:CYS449 3.2 35.9 1.0 CG A:GLU437 3.4 36.7 1.0 CB A:CYS446 3.5 33.7 1.0 N A:CYS449 3.7 38.1 1.0 CA A:CYS446 3.8 34.2 1.0 CA A:CYS449 4.0 36.6 1.0 OE2 A:GLU437 4.0 43.3 1.0 N A:GLY447 4.2 36.6 1.0 CG A:HIS441 4.3 34.9 1.0 ND1 A:HIS441 4.3 36.2 1.0 N A:SER448 4.4 37.5 1.0 C A:CYS446 4.5 39.7 1.0 O A:HOH1220 4.6 38.1 1.0 C A:SER448 4.7 41.4 1.0 O A:HOH1128 4.8 42.1 1.0 CG2 A:THR571 4.8 41.7 1.0 O A:LYS445 4.9 37.7 1.0 CB A:GLU437 4.9 33.5 1.0

C.G.Noble, S.P.Lim, R.Arora, F.Yokokawa, S.Nilar, C.C.Seh, S.K.Wright, T.E.Benson, P.W.Smith, P.Y.Shi. A Conserved Pocket in the Dengue Virus Polymerase Identified Through Fragment-Based Screening J.Biol.Chem. V. 291 8541 2016.
ISSN: ESSN 1083-351X
PubMed: 26872970
DOI: 10.1074/JBC.M115.710731