Zinc in PDB 4k6m: Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5

The structure of Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5, PDB code: 4k6m was solved by G.Lu, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.22 / 2.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	272.293, 272.293, 177.248, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.8

The binding sites of Zinc atom in the Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5 (pdb code 4k6m). 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 the Full-Length Japanese Encephalitis Virus NS5, PDB code: 4k6m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5


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 the Full-Length Japanese Encephalitis Virus NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1012 b:45.4 occ:1.00 NE2 A:HIS444 1.9 44.8 1.0 OE2 A:GLU440 2.0 45.3 1.0 SG A:CYS452 2.2 43.8 1.0 SG A:CYS449 2.2 46.4 1.0 CE1 A:HIS444 2.8 43.0 1.0 CD A:GLU440 3.0 48.5 1.0 CD2 A:HIS444 3.1 46.1 1.0 CB A:CYS452 3.1 44.2 1.0 CB A:CYS449 3.3 43.9 1.0 CG A:GLU440 3.5 38.8 1.0 N A:CYS452 3.7 47.7 1.0 CA A:CYS449 3.7 49.6 1.0 ND1 A:HIS444 4.0 43.6 1.0 CA A:CYS452 4.0 48.1 1.0 N A:HIS450 4.0 46.6 1.0 CG A:HIS444 4.1 46.1 1.0 OE1 A:GLU440 4.1 51.3 1.0 C A:CYS449 4.3 49.4 1.0 N A:THR451 4.3 44.8 1.0 O A:HOH1154 4.4 43.0 1.0 OG1 A:THR574 4.6 55.1 1.0 C A:THR451 4.7 47.1 1.0 OG1 A:THR451 4.9 43.0 1.0 O A:GLU448 5.0 51.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5


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 the Full-Length Japanese Encephalitis Virus NS5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1013 b:89.9 occ:1.00 NE2 A:HIS717 2.2 62.9 1.0 SG A:CYS852 2.4 61.5 1.0 SG A:CYS733 2.5 68.8 1.0 CE1 A:HIS717 2.7 56.2 1.0 OE1 A:GLU848 2.8 69.5 1.0 CB A:CYS733 3.1 57.3 1.0 CB A:CYS852 3.3 51.4 1.0 CD2 A:HIS717 3.4 58.5 1.0 CD A:GLU848 3.7 70.8 1.0 ND1 A:HIS717 3.9 56.3 1.0 CG A:GLU848 4.0 63.4 1.0 C A:CYS733 4.0 56.7 1.0 N A:ARG734 4.1 54.3 1.0 CA A:CYS733 4.2 57.1 1.0 CG A:HIS717 4.3 57.3 1.0 O A:CYS733 4.3 55.4 1.0 O A:GLU848 4.6 56.8 1.0 CA A:ARG734 4.7 51.1 1.0 NH1 A:ARG774 4.7 52.2 1.0 CA A:CYS852 4.7 51.8 1.0 OE2 A:GLU848 4.7 74.8 1.0 CG A:GLN719 4.9 61.2 1.0 O A:ARG734 5.0 48.7 1.0 C A:ARG734 5.0 51.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5


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 the Full-Length Japanese Encephalitis Virus NS5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1010 b:74.6 occ:1.00 NE2 B:HIS717 2.3 49.2 1.0 OE1 B:GLU848 2.4 48.8 1.0 SG B:CYS852 2.4 56.1 1.0 SG B:CYS733 2.4 59.7 1.0 CE1 B:HIS717 2.6 47.1 1.0 CB B:CYS733 3.3 42.1 1.0 CB B:CYS852 3.4 44.7 1.0 CD B:GLU848 3.5 55.0 1.0 CD2 B:HIS717 3.5 45.0 1.0 ND1 B:HIS717 3.8 46.3 1.0 CG B:GLU848 4.0 55.8 1.0 C B:CYS733 4.1 44.8 1.0 CG B:HIS717 4.3 46.9 1.0 CA B:CYS733 4.3 42.1 1.0 O B:CYS733 4.4 45.8 1.0 N B:ARG734 4.4 44.6 1.0 OE2 B:GLU848 4.6 55.0 1.0 O B:GLU848 4.6 47.9 1.0 CA B:CYS852 4.8 43.6 1.0 NH1 B:ARG774 4.9 42.2 1.0 CG B:GLN719 4.9 48.4 1.0 CA B:ARG734 4.9 43.1 1.0 NE2 B:GLN719 4.9 51.9 1.0 O B:ARG734 5.0 44.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5


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 the Full-Length Japanese Encephalitis Virus NS5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1011 b:70.8 occ:1.00 NE2 B:HIS444 2.0 70.8 1.0 OE2 B:GLU440 2.1 76.7 1.0 SG B:CYS449 2.2 76.5 1.0 SG B:CYS452 2.4 77.7 1.0 CE1 B:HIS444 2.9 67.6 1.0 CD2 B:HIS444 3.0 73.0 1.0 CD B:GLU440 3.0 77.1 1.0 CB B:CYS452 3.1 70.6 1.0 CG B:GLU440 3.3 71.8 1.0 CB B:CYS449 3.4 73.6 1.0 N B:CYS452 3.6 72.6 1.0 CA B:CYS449 3.8 78.7 1.0 CA B:CYS452 4.0 70.8 1.0 ND1 B:HIS444 4.0 68.0 1.0 N B:HIS450 4.1 75.8 1.0 CG B:HIS444 4.1 73.3 1.0 OE1 B:GLU440 4.2 77.7 1.0 N B:THR451 4.3 74.3 1.0 C B:CYS449 4.3 77.5 1.0 C B:THR451 4.6 75.8 1.0 OG1 B:THR451 4.7 66.0 1.0 OG1 B:THR574 4.7 71.3 1.0 CB B:GLU440 4.9 74.0 1.0 O B:GLU448 4.9 84.5 1.0 CD1 B:LEU486 5.0 62.8 1.0 CA B:THR451 5.0 74.4 1.0

G.Lu, P.Gong. Crystal Structure of the Full-Length Japanese Encephalitis Virus NS5 Reveals A Conserved Methyltransferase-Polymerase Interface Plos Pathog. V. 9 03549 2013.
ISSN: ISSN 1553-7366
PubMed: 23950717
DOI: 10.1371/JOURNAL.PPAT.1003549