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Zinc 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 (Hg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1, PDB code: 1urj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1urj

Go back to Zinc Binding Sites List in 1urj
Zinc binding site 1 out of 2 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn2131

b:35.7
occ:1.00
ND1 A:HIS512 2.1 29.8 1.0
SG A:CYS499 2.3 41.5 1.0
SG A:CYS502 2.3 36.1 1.0
SG A:CYS510 2.4 31.7 1.0
CE1 A:HIS512 2.7 29.9 1.0
CG A:HIS512 3.0 29.6 1.0
CB A:CYS499 3.0 45.4 1.0
CB A:CYS510 3.5 33.4 1.0
CB A:CYS502 3.5 37.2 1.0
CB A:HIS512 3.6 30.4 1.0
NE2 A:HIS512 3.6 29.5 1.0
CD2 A:HIS512 3.8 29.7 1.0
N A:CYS502 4.0 37.6 1.0
CA A:CYS502 4.4 38.1 1.0
CA A:CYS499 4.4 46.6 1.0
N A:HIS512 4.6 31.0 1.0
CA A:HIS512 4.6 30.3 1.0
CB A:LEU501 4.7 37.1 1.0
C A:CYS499 4.8 46.5 1.0
O A:CYS499 4.8 47.6 1.0
CD A:ARG507 4.8 38.5 1.0
CA A:CYS510 4.9 33.3 1.0
C A:LEU501 4.9 37.5 1.0
N A:LEU501 4.9 40.1 1.0
N A:THR513 4.9 27.0 1.0
NE A:ARG507 5.0 38.8 1.0
CG1 A:VAL497 5.0 60.5 1.0
OG1 A:THR513 5.0 24.3 1.0

Zinc binding site 2 out of 2 in 1urj

Go back to Zinc Binding Sites List in 1urj
Zinc binding site 2 out of 2 in the Single Stranded Dna-Binding Protein(ICP8) From Herpes Simplex Virus-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn2131

b:29.3
occ:1.00
ND1 B:HIS512 2.1 29.8 1.0
SG B:CYS502 2.2 32.1 1.0
SG B:CYS499 2.3 38.9 1.0
SG B:CYS510 2.3 29.5 1.0
CE1 B:HIS512 2.7 29.2 1.0
CG B:HIS512 3.0 28.6 1.0
CB B:CYS499 3.0 44.3 1.0
CB B:CYS510 3.4 31.2 1.0
CB B:CYS502 3.6 34.6 1.0
CB B:HIS512 3.6 28.3 1.0
NE2 B:HIS512 3.7 30.4 1.0
CD2 B:HIS512 3.8 29.6 1.0
N B:CYS502 4.1 36.0 1.0
CA B:CYS502 4.4 36.1 1.0
CA B:CYS499 4.4 45.4 1.0
N B:HIS512 4.5 30.0 1.0
CA B:HIS512 4.6 28.6 1.0
CB B:LEU501 4.7 35.1 1.0
C B:CYS499 4.8 44.9 1.0
O B:CYS499 4.8 46.4 1.0
CA B:CYS510 4.8 31.0 1.0
CD B:ARG507 4.9 34.8 1.0
C B:LEU501 4.9 36.2 1.0
N B:THR513 4.9 27.5 1.0
N B:LEU501 4.9 38.7 1.0
OG1 B:THR513 5.0 23.9 1.0
NE B:ARG507 5.0 35.6 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: Mon Jan 25 16:14:45 2021

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