Zinc in PDB 4hdg: Crystal Structure of Viral Rdrp in Complex with Gtp

All present enzymatic activity of Crystal Structure of Viral Rdrp in Complex with Gtp:
2.7.7.48;

The structure of Crystal Structure of Viral Rdrp in Complex with Gtp, PDB code: 4hdg was solved by P.Surana, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.38
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	144.574, 86.554, 112.650, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.6

The binding sites of Zinc atom in the Crystal Structure of Viral Rdrp in Complex with Gtp (pdb code 4hdg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Viral Rdrp in Complex with Gtp, PDB code: 4hdg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Viral Rdrp in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Viral Rdrp in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:33.0 occ:1.00 OE2 A:GLU440 2.0 40.3 1.0 NE2 A:HIS444 2.0 39.1 1.0 SG A:CYS449 2.1 30.6 1.0 SG A:CYS452 2.1 30.6 1.0 CE1 A:HIS444 2.9 38.2 1.0 CB A:CYS452 3.0 29.6 1.0 CD A:GLU440 3.1 36.6 1.0 CD2 A:HIS444 3.1 36.8 1.0 CB A:CYS449 3.1 36.6 1.0 CA A:CYS449 3.5 36.8 1.0 CG A:GLU440 3.5 34.7 1.0 N A:CYS452 3.6 32.0 1.0 CA A:CYS452 3.9 30.1 1.0 N A:HIS450 4.0 37.0 1.0 ND1 A:HIS444 4.1 35.5 1.0 C A:CYS449 4.2 36.9 1.0 OE1 A:GLU440 4.2 38.4 1.0 CG A:HIS444 4.2 37.9 1.0 N A:THR451 4.3 37.2 1.0 OG1 A:THR451 4.4 40.3 1.0 CG2 A:THR574 4.5 41.0 1.0 C A:THR451 4.6 34.6 1.0 N A:CYS449 4.7 38.1 1.0 O A:GLU448 4.8 39.7 1.0 O A:HOH1188 4.8 43.8 1.0 CA A:THR451 5.0 36.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Viral Rdrp in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Viral Rdrp in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:36.8 occ:0.75 SG A:CYS852 2.0 41.2 1.0 SG A:CYS733 2.1 47.4 1.0 CE1 A:HIS717 2.3 34.6 1.0 NE2 A:HIS717 2.4 34.9 1.0 O A:HOH1309 2.7 58.9 1.0 CB A:CYS733 2.9 27.4 1.0 CB A:CYS852 3.0 30.8 1.0 ND1 A:HIS717 3.6 32.1 1.0 CD2 A:HIS717 3.7 32.9 1.0 CA A:CYS733 4.1 28.8 1.0 C A:CYS733 4.2 28.0 1.0 CG A:HIS717 4.3 27.7 1.0 CA A:CYS852 4.3 29.9 1.0 O A:GLU848 4.5 33.5 1.0 O A:CYS733 4.5 28.1 1.0 N A:ARG734 4.5 26.9 1.0 N A:CYS852 4.7 29.4 1.0 NH1 A:ARG774 4.9 22.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Viral Rdrp in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Viral Rdrp in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:31.7 occ:1.00 OE2 B:GLU440 2.0 36.7 1.0 SG B:CYS452 2.1 35.9 1.0 SG B:CYS449 2.2 33.4 1.0 NE2 B:HIS444 2.2 33.8 1.0 CB B:CYS452 2.9 32.3 1.0 CE1 B:HIS444 3.1 32.3 1.0 CD B:GLU440 3.1 37.4 1.0 CD2 B:HIS444 3.2 33.2 1.0 CB B:CYS449 3.3 38.9 1.0 CG B:GLU440 3.6 35.1 1.0 CA B:CYS449 3.6 39.1 1.0 N B:CYS452 3.7 34.9 1.0 CA B:CYS452 4.0 32.4 1.0 N B:HIS450 4.0 38.0 1.0 OE1 B:GLU440 4.2 40.2 1.0 C B:CYS449 4.2 38.9 1.0 ND1 B:HIS444 4.2 35.0 1.0 CG B:HIS444 4.3 37.7 1.0 N B:THR451 4.3 38.7 1.0 CG2 B:THR574 4.4 42.9 1.0 O B:HOH1207 4.4 36.9 1.0 OG1 B:THR451 4.6 42.2 1.0 C B:THR451 4.8 36.4 1.0 N B:CYS449 4.9 41.0 1.0 O B:GLU448 4.9 41.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Viral Rdrp in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Viral Rdrp in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:37.7 occ:0.75 SG B:CYS733 1.9 39.2 1.0 CE1 B:HIS717 2.0 37.4 1.0 SG B:CYS852 2.2 40.2 1.0 NE2 B:HIS717 2.2 37.4 1.0 O B:HOH1344 2.7 68.6 1.0 CB B:CYS852 3.2 30.7 1.0 ND1 B:HIS717 3.3 36.2 1.0 CB B:CYS733 3.5 30.3 1.0 CD2 B:HIS717 3.6 37.3 1.0 CG B:HIS717 4.1 33.6 1.0 C B:CYS733 4.1 29.4 1.0 O B:CYS733 4.1 30.6 1.0 CA B:CYS733 4.4 30.1 1.0 N B:ARG734 4.5 28.4 1.0 CA B:CYS852 4.5 30.5 1.0 O B:GLU848 4.6 34.9 1.0 N B:CYS852 4.9 32.1 1.0 NH1 B:ARG774 5.0 22.0 1.0 CA B:ARG734 5.0 27.7 1.0

P.Surana, V.Satchidanandam, D.T.Nair. Rna-Dependent Rna Polymerase of Japanese Encephalitis Virus Binds the Initiator Nucleotide Gtp to Form A Mechanistically Important Pre-Initiation State. Nucleic Acids Res. V. 42 2758 2014.
ISSN: ISSN 0305-1048
PubMed: 24293643
DOI: 10.1093/NAR/GKT1106