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Zinc in PDB 6h9r: Dengue-RDRP3-Inhibitor Complex Soaking

Enzymatic activity of Dengue-RDRP3-Inhibitor Complex Soaking

All present enzymatic activity of Dengue-RDRP3-Inhibitor Complex Soaking:
2.1.1.56; 2.1.1.57; 2.7.7.48; 3.4.21.91; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Dengue-RDRP3-Inhibitor Complex Soaking, PDB code: 6h9r was solved by S.K.Talapatra, F.Kozielski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.79 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 164.691, 181.210, 57.900, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Dengue-RDRP3-Inhibitor Complex Soaking (pdb code 6h9r). 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-RDRP3-Inhibitor Complex Soaking, PDB code: 6h9r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6h9r

Go back to Zinc Binding Sites List in 6h9r
Zinc binding site 1 out of 2 in the Dengue-RDRP3-Inhibitor Complex Soaking


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue-RDRP3-Inhibitor Complex Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:51.1
occ:1.00
NE2 A:HIS441 2.1 54.5 1.0
SG A:CYS449 2.2 51.1 1.0
SG A:CYS446 2.4 49.0 1.0
OE1 A:GLU437 2.4 65.0 1.0
CE1 A:HIS441 3.0 53.2 1.0
CD2 A:HIS441 3.0 51.9 1.0
CB A:CYS449 3.1 53.5 1.0
CD A:GLU437 3.2 61.1 1.0
CG A:GLU437 3.4 56.9 1.0
CB A:CYS446 3.5 54.8 1.0
CA A:CYS446 3.8 53.0 1.0
N A:CYS449 3.8 58.3 1.0
N A:GLY447 4.0 55.1 1.0
CA A:CYS449 4.1 61.7 1.0
ND1 A:HIS441 4.1 53.0 1.0
CG A:HIS441 4.2 47.9 1.0
C A:CYS446 4.3 56.7 1.0
N A:SER448 4.3 58.9 1.0
OE2 A:GLU437 4.4 67.3 1.0
C A:SER448 4.7 59.8 1.0
CB A:GLU437 4.9 55.8 1.0
CD1 A:LEU483 5.0 51.5 1.0

Zinc binding site 2 out of 2 in 6h9r

Go back to Zinc Binding Sites List in 6h9r
Zinc binding site 2 out of 2 in the Dengue-RDRP3-Inhibitor Complex Soaking


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue-RDRP3-Inhibitor Complex Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:48.2
occ:1.00
NE2 A:HIS712 2.1 46.7 1.0
NE2 A:HIS714 2.1 48.6 1.0
SG A:CYS728 2.3 41.9 1.0
SG A:CYS847 2.5 49.0 1.0
CE1 A:HIS712 3.0 46.8 1.0
CB A:CYS728 3.0 34.2 1.0
CE1 A:HIS714 3.1 42.7 1.0
CD2 A:HIS712 3.1 46.1 1.0
CD2 A:HIS714 3.1 39.8 1.0
CB A:CYS847 3.4 47.2 1.0
CD1 A:LEU839 4.0 42.5 1.0
ND1 A:HIS712 4.1 45.8 1.0
CG A:HIS712 4.2 40.3 1.0
ND1 A:HIS714 4.2 47.0 1.0
CG A:HIS714 4.3 41.9 1.0
CA A:CYS728 4.4 38.0 1.0
C A:CYS728 4.6 39.0 1.0
N A:ARG729 4.8 32.0 1.0
CA A:CYS847 4.8 36.2 1.0
NH2 A:ARG769 4.9 37.1 1.0

Reference:

F.Riccio, S.K.Talapatra, S.Oxenford, R.Angell, M.Mazzon, F.Kozielski. Development and Validation of Rdrp Screen, A Crystallization Screen For Viral Rna-Dependent Rna Polymerases. Biol Open V. 8 2019.
ISSN: ESSN 2046-6390
PubMed: 30602529
DOI: 10.1242/BIO.037663
Page generated: Wed Dec 16 11:56:15 2020

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