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
|