Chlorine in PDB 6jim: Viral Helicase Protein
Protein crystallography data
The structure of Viral Helicase Protein, PDB code: 6jim
was solved by
Y.S.Law,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.32 /
2.00
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.888,
53.905,
100.718,
96.93,
94.07,
97.04
|
R / Rfree (%)
|
17.7 /
21.5
|
Other elements in 6jim:
The structure of Viral Helicase Protein also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Viral Helicase Protein
(pdb code 6jim). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the
Viral Helicase Protein, PDB code: 6jim:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 6jim
Go back to
Chlorine Binding Sites List in 6jim
Chlorine binding site 1 out
of 5 in the Viral Helicase Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Viral Helicase Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl2008
b:75.4
occ:1.00
|
N
|
A:ASN337
|
3.6
|
42.2
|
1.0
|
O
|
A:GLU335
|
4.0
|
38.9
|
1.0
|
CG
|
A:LYS338
|
4.2
|
56.4
|
1.0
|
O
|
A:HOH2272
|
4.2
|
68.6
|
1.0
|
CA
|
A:ASN337
|
4.2
|
40.8
|
1.0
|
C
|
A:ASN337
|
4.2
|
47.8
|
1.0
|
N
|
A:LYS338
|
4.2
|
48.1
|
1.0
|
CB
|
A:ASN337
|
4.3
|
46.1
|
1.0
|
CA
|
A:TYR336
|
4.4
|
42.0
|
1.0
|
C
|
A:TYR336
|
4.5
|
40.0
|
1.0
|
O
|
A:HOH2136
|
4.6
|
51.2
|
1.0
|
O
|
A:ASN337
|
4.8
|
45.6
|
1.0
|
C
|
A:GLU335
|
4.9
|
45.0
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 6jim
Go back to
Chlorine Binding Sites List in 6jim
Chlorine binding site 2 out
of 5 in the Viral Helicase Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Viral Helicase Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl2009
b:76.6
occ:1.00
|
O
|
A:HOH2225
|
2.5
|
76.7
|
1.0
|
ND1
|
A:HIS325
|
3.0
|
39.8
|
1.0
|
NZ
|
A:LYS282
|
3.2
|
61.2
|
1.0
|
CE1
|
A:HIS325
|
3.8
|
38.7
|
1.0
|
O
|
A:LEU324
|
3.8
|
46.2
|
1.0
|
CD
|
A:LYS282
|
4.0
|
42.2
|
1.0
|
CE
|
A:LYS282
|
4.0
|
52.8
|
1.0
|
CA
|
A:HIS325
|
4.0
|
37.8
|
1.0
|
CG
|
A:HIS325
|
4.0
|
36.8
|
1.0
|
CB
|
A:HIS325
|
4.3
|
35.0
|
1.0
|
C
|
A:LEU324
|
4.6
|
37.0
|
1.0
|
O
|
A:HIS325
|
4.6
|
39.6
|
1.0
|
O
|
A:THR406
|
4.8
|
37.1
|
1.0
|
N
|
A:HIS325
|
4.8
|
34.9
|
1.0
|
C
|
A:HIS325
|
4.9
|
41.8
|
1.0
|
CB
|
A:THR406
|
4.9
|
49.0
|
1.0
|
NE2
|
A:HIS325
|
5.0
|
40.3
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 6jim
Go back to
Chlorine Binding Sites List in 6jim
Chlorine binding site 3 out
of 5 in the Viral Helicase Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Viral Helicase Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl2010
b:84.2
occ:1.00
|
NH2
|
A:ARG311
|
3.2
|
70.5
|
1.0
|
OG1
|
A:THR333
|
3.3
|
39.6
|
1.0
|
O
|
A:ARG311
|
3.9
|
39.7
|
1.0
|
O
|
A:THR333
|
3.9
|
42.4
|
1.0
|
NE
|
A:ARG311
|
4.0
|
59.8
|
1.0
|
CZ
|
A:ARG311
|
4.0
|
62.8
|
1.0
|
O
|
A:HOH2242
|
4.0
|
63.4
|
1.0
|
C
|
A:THR333
|
4.1
|
43.6
|
1.0
|
CB
|
A:THR333
|
4.2
|
40.2
|
1.0
|
O
|
A:HOH2184
|
4.3
|
51.7
|
1.0
|
N
|
A:ASN334
|
4.4
|
39.8
|
1.0
|
CA
|
A:ASN334
|
4.5
|
37.7
|
1.0
|
CD1
|
A:ILE447
|
4.6
|
58.2
|
1.0
|
C
|
A:ARG311
|
4.8
|
38.8
|
1.0
|
CA
|
A:THR333
|
4.8
|
43.5
|
1.0
|
CB
|
A:ARG311
|
4.8
|
37.4
|
1.0
|
CA
|
A:ARG311
|
4.9
|
39.1
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 6jim
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Chlorine Binding Sites List in 6jim
Chlorine binding site 4 out
of 5 in the Viral Helicase Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Viral Helicase Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl2008
b:72.5
occ:1.00
|
CD
|
B:PRO111
|
4.8
|
61.9
|
1.0
|
CA
|
B:GLY110
|
5.0
|
62.9
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 6jim
Go back to
Chlorine Binding Sites List in 6jim
Chlorine binding site 5 out
of 5 in the Viral Helicase Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Viral Helicase Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl2009
b:78.5
occ:1.00
|
NH1
|
B:ARG311
|
3.0
|
56.8
|
1.0
|
OE1
|
B:GLU451
|
3.1
|
73.1
|
1.0
|
N6
|
B:ADP2001
|
3.9
|
53.0
|
1.0
|
CD
|
B:GLU451
|
4.0
|
68.0
|
1.0
|
CZ
|
B:ARG311
|
4.0
|
63.3
|
1.0
|
CG
|
B:GLU451
|
4.1
|
60.9
|
1.0
|
NH2
|
B:ARG311
|
4.2
|
57.9
|
1.0
|
CG2
|
B:ILE447
|
4.2
|
55.7
|
1.0
|
CZ3
|
B:TRP450
|
4.5
|
47.5
|
1.0
|
CE3
|
B:TRP450
|
4.7
|
39.3
|
1.0
|
C6
|
B:ADP2001
|
4.9
|
54.5
|
1.0
|
|
Reference:
Y.S.Law,
A.Utt,
Y.B.Tan,
J.Zheng,
S.Wang,
M.W.Chen,
P.R.Griffin,
A.Merits,
D.Luo.
Structural Insights Into Rna Recognition By the Chikungunya Virus NSP2 Helicase. Proc.Natl.Acad.Sci.Usa V. 116 9558 2019.
ISSN: ESSN 1091-6490
PubMed: 31000599
DOI: 10.1073/PNAS.1900656116
Page generated: Sat Dec 12 13:11:32 2020
|