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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:

Zinc (Zn) 2 atoms

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

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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 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 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 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 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 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

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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: Wed Oct 28 18:40:47 2020

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