Atomistry » Zinc » PDB 4k4f-4k98 » 4k6m
Atomistry »
  Zinc »
    PDB 4k4f-4k98 »
      4k6m »

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

Protein crystallography data

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

Zinc Binding Sites:

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 4k6m

Go back to Zinc Binding Sites List in 4k6m
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 4k6m

Go back to Zinc Binding Sites List in 4k6m
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 4k6m

Go back to Zinc Binding Sites List in 4k6m
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 4k6m

Go back to Zinc Binding Sites List in 4k6m
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

Reference:

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
Page generated: Sun Oct 27 01:45:03 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy