Mercury in PDB 1urj: Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Protein crystallography data
The structure of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1, PDB code: 1urj
was solved by
S.Panjikar,
M.Mapelli,
P.A.Tucker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
3.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.910,
145.370,
162.030,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.5 /
28.6
|
Other elements in 1urj:
The structure of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 also contains other interesting chemical elements:
Mercury Binding Sites:
The binding sites of Mercury atom in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
(pdb code 1urj). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 8 binding sites of Mercury where determined in the
Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1, PDB code: 1urj:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Mercury binding site 1 out
of 8 in 1urj
Go back to
Mercury Binding Sites List in 1urj
Mercury binding site 1 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg2132
b:49.3
occ:0.50
|
SG
|
A:CYS1013
|
2.6
|
36.6
|
1.0
|
CZ
|
A:PHE963
|
2.9
|
49.4
|
1.0
|
CE2
|
A:PHE963
|
2.9
|
46.8
|
1.0
|
CE1
|
A:PHE963
|
2.9
|
48.5
|
1.0
|
CD2
|
A:PHE963
|
3.0
|
46.8
|
1.0
|
CD1
|
A:PHE963
|
3.0
|
46.6
|
1.0
|
CG
|
A:PHE963
|
3.0
|
45.6
|
1.0
|
CB
|
A:CYS1013
|
3.4
|
34.0
|
1.0
|
CG2
|
A:ILE917
|
3.6
|
21.7
|
1.0
|
CD2
|
A:LEU1026
|
3.6
|
21.5
|
1.0
|
CB
|
A:PHE963
|
4.1
|
41.4
|
1.0
|
CD1
|
A:LEU1026
|
4.2
|
22.1
|
1.0
|
CA
|
A:CYS1013
|
4.3
|
33.0
|
1.0
|
CG
|
A:LEU1026
|
4.5
|
21.1
|
1.0
|
CD
|
A:PRO1014
|
4.6
|
31.8
|
1.0
|
CB
|
A:ILE917
|
4.6
|
20.9
|
1.0
|
O
|
A:GLY370
|
4.7
|
20.4
|
1.0
|
CB
|
A:LEU1026
|
5.0
|
20.7
|
1.0
|
|
Mercury binding site 2 out
of 8 in 1urj
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Mercury Binding Sites List in 1urj
Mercury binding site 2 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg2133
b:59.4
occ:0.40
|
SG
|
A:CYS966
|
2.4
|
28.2
|
1.0
|
CG
|
A:PRO597
|
3.4
|
28.5
|
1.0
|
CB
|
A:CYS966
|
3.5
|
28.7
|
1.0
|
CD
|
A:PRO597
|
3.8
|
28.2
|
1.0
|
CG2
|
A:VAL972
|
3.9
|
21.8
|
1.0
|
O
|
A:LEU968
|
4.0
|
28.5
|
1.0
|
CB
|
A:PRO971
|
4.5
|
24.3
|
1.0
|
CD1
|
A:ILE918
|
4.6
|
21.1
|
1.0
|
CB
|
A:PRO597
|
4.8
|
28.2
|
1.0
|
CG
|
A:PRO971
|
4.8
|
26.2
|
1.0
|
CG1
|
A:ILE918
|
4.8
|
18.6
|
1.0
|
CA
|
A:CYS966
|
4.9
|
27.8
|
1.0
|
N
|
A:VAL972
|
4.9
|
23.8
|
1.0
|
|
Mercury binding site 3 out
of 8 in 1urj
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Mercury Binding Sites List in 1urj
Mercury binding site 3 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg2134
b:85.6
occ:0.20
|
SG
|
A:CYS26
|
2.8
|
60.2
|
1.0
|
CD
|
A:ARG154
|
3.3
|
53.8
|
1.0
|
CB
|
A:CYS26
|
3.4
|
57.0
|
1.0
|
O
|
A:CYS26
|
3.6
|
58.7
|
1.0
|
NE
|
A:ARG154
|
3.7
|
59.0
|
1.0
|
O
|
A:PRO27
|
4.0
|
58.2
|
1.0
|
C
|
A:CYS26
|
4.2
|
57.1
|
1.0
|
CA
|
A:CYS26
|
4.4
|
56.0
|
1.0
|
CZ
|
A:ARG154
|
4.6
|
62.1
|
1.0
|
CG
|
A:ARG154
|
4.8
|
49.3
|
1.0
|
C
|
A:PRO27
|
4.9
|
58.9
|
1.0
|
CB
|
A:SER28
|
5.0
|
61.1
|
1.0
|
|
Mercury binding site 4 out
of 8 in 1urj
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Mercury Binding Sites List in 1urj
Mercury binding site 4 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg2135
b:24.4
occ:0.10
|
OG
|
A:SER754
|
2.6
|
64.9
|
1.0
|
SG
|
A:CYS740
|
3.3
|
61.1
|
1.0
|
CB
|
A:CYS740
|
3.9
|
56.8
|
1.0
|
CB
|
A:ALA752
|
3.9
|
59.9
|
1.0
|
CB
|
A:SER754
|
4.0
|
62.7
|
1.0
|
O
|
A:ALA752
|
4.2
|
60.6
|
1.0
|
C
|
A:ALA752
|
4.6
|
60.6
|
1.0
|
N
|
A:SER754
|
4.7
|
61.5
|
1.0
|
CA
|
A:CYS740
|
4.8
|
55.1
|
1.0
|
CA
|
A:SER754
|
4.8
|
61.4
|
1.0
|
CA
|
A:ALA752
|
4.8
|
60.2
|
1.0
|
|
Mercury binding site 5 out
of 8 in 1urj
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Mercury Binding Sites List in 1urj
Mercury binding site 5 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg2132
b:57.8
occ:0.50
|
CE2
|
B:PHE963
|
2.8
|
47.8
|
1.0
|
CZ
|
B:PHE963
|
2.8
|
50.0
|
1.0
|
SG
|
B:CYS1013
|
2.8
|
38.3
|
1.0
|
CD2
|
B:PHE963
|
2.9
|
47.2
|
1.0
|
CE1
|
B:PHE963
|
3.0
|
49.5
|
1.0
|
CG
|
B:PHE963
|
3.1
|
45.5
|
1.0
|
CD1
|
B:PHE963
|
3.1
|
47.3
|
1.0
|
CD2
|
B:LEU1026
|
3.5
|
23.8
|
1.0
|
CB
|
B:CYS1013
|
3.6
|
34.4
|
1.0
|
CG2
|
B:ILE917
|
3.6
|
22.6
|
1.0
|
CD1
|
B:LEU1026
|
4.0
|
21.2
|
1.0
|
CB
|
B:PHE963
|
4.2
|
41.5
|
1.0
|
CG
|
B:LEU1026
|
4.3
|
22.7
|
1.0
|
CB
|
B:ILE917
|
4.5
|
23.1
|
1.0
|
O
|
B:GLY370
|
4.5
|
21.6
|
1.0
|
CA
|
B:CYS1013
|
4.5
|
34.7
|
1.0
|
CB
|
B:LEU1026
|
4.8
|
22.0
|
1.0
|
CD
|
B:PRO1014
|
4.8
|
34.4
|
1.0
|
C
|
B:GLY370
|
5.0
|
21.6
|
1.0
|
|
Mercury binding site 6 out
of 8 in 1urj
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Mercury Binding Sites List in 1urj
Mercury binding site 6 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 6 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg2133
b:66.7
occ:0.40
|
SG
|
B:CYS966
|
2.5
|
32.4
|
1.0
|
CB
|
B:CYS966
|
3.3
|
30.0
|
1.0
|
CG2
|
B:VAL972
|
3.5
|
25.1
|
1.0
|
CG
|
B:PRO597
|
3.7
|
31.7
|
1.0
|
O
|
B:LEU968
|
3.8
|
27.9
|
1.0
|
CD
|
B:PRO597
|
4.2
|
31.6
|
1.0
|
CD1
|
B:ILE918
|
4.3
|
23.1
|
1.0
|
CB
|
B:PRO971
|
4.5
|
24.5
|
1.0
|
CG1
|
B:ILE918
|
4.6
|
21.3
|
1.0
|
N
|
B:VAL972
|
4.6
|
25.0
|
1.0
|
CA
|
B:CYS966
|
4.8
|
29.9
|
1.0
|
CB
|
B:VAL972
|
4.8
|
23.2
|
1.0
|
CG
|
B:PRO971
|
4.9
|
25.6
|
1.0
|
C
|
B:LEU968
|
5.0
|
26.9
|
1.0
|
CA
|
B:VAL972
|
5.0
|
23.1
|
1.0
|
|
Mercury binding site 7 out
of 8 in 1urj
Go back to
Mercury Binding Sites List in 1urj
Mercury binding site 7 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 7 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg2134
b:58.6
occ:0.20
|
O
|
B:PRO27
|
2.5
|
59.5
|
1.0
|
SG
|
B:CYS26
|
2.6
|
59.2
|
1.0
|
C
|
B:PRO27
|
3.7
|
59.6
|
1.0
|
CA
|
B:SER28
|
3.9
|
62.5
|
1.0
|
O
|
B:CYS26
|
4.1
|
57.8
|
1.0
|
CB
|
B:CYS26
|
4.2
|
55.6
|
1.0
|
N
|
B:SER28
|
4.3
|
60.7
|
1.0
|
CB
|
B:SER28
|
4.3
|
61.7
|
1.0
|
C
|
B:CYS26
|
4.3
|
57.3
|
1.0
|
N
|
B:PRO27
|
4.7
|
58.7
|
1.0
|
CA
|
B:PRO27
|
4.8
|
59.0
|
1.0
|
CA
|
B:CYS26
|
4.9
|
55.3
|
1.0
|
CG2
|
B:ILE31
|
4.9
|
45.1
|
1.0
|
C
|
B:SER28
|
5.0
|
63.1
|
1.0
|
|
Mercury binding site 8 out
of 8 in 1urj
Go back to
Mercury Binding Sites List in 1urj
Mercury binding site 8 out
of 8 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 8 of Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg2135
b:25.9
occ:0.10
|
SG
|
B:CYS740
|
2.9
|
38.6
|
1.0
|
CB
|
B:SER754
|
3.2
|
51.2
|
1.0
|
O
|
B:ALA752
|
3.4
|
42.6
|
1.0
|
CB
|
B:CYS740
|
3.7
|
38.6
|
1.0
|
C
|
B:ALA752
|
3.8
|
43.9
|
1.0
|
N
|
B:SER754
|
3.8
|
49.8
|
1.0
|
CB
|
B:ALA752
|
3.8
|
43.0
|
1.0
|
CA
|
B:SER754
|
4.1
|
50.1
|
1.0
|
C
|
B:GLU753
|
4.1
|
48.9
|
1.0
|
OG
|
B:SER754
|
4.2
|
53.0
|
1.0
|
N
|
B:GLU753
|
4.4
|
45.5
|
1.0
|
CA
|
B:ALA752
|
4.4
|
42.5
|
1.0
|
O
|
B:GLU753
|
4.5
|
49.0
|
1.0
|
CA
|
B:GLU753
|
4.6
|
47.9
|
1.0
|
CA
|
B:CYS740
|
4.7
|
37.9
|
1.0
|
N
|
B:ALA752
|
4.9
|
42.1
|
1.0
|
|
Reference:
M.Mapelli,
S.Panjikar,
P.A.Tucker.
The Crystal Structure of the Herpes Simplex Virus 1 Ssdna-Binding Protein Suggests the Structural Basis For Flexible, Cooperative Single-Stranded Dna Binding. J. Biol. Chem. V. 280 2990 2005.
ISSN: ISSN 0021-9258
PubMed: 15507432
DOI: 10.1074/JBC.M406780200
Page generated: Sun Aug 11 01:41:17 2024
|