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Zinc in PDB 1njf: Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit

Enzymatic activity of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit

All present enzymatic activity of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit:
2.7.7.7;

Protein crystallography data

The structure of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit, PDB code: 1njf was solved by M.Podobnik, T.F.Weitze, M.O'donnell, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.84 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.708, 113.347, 121.355, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit (pdb code 1njf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit, PDB code: 1njf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1njf

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Zinc binding site 1 out of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:38.7
occ:1.00
SG A:CYS64 2.4 15.0 1.0
SG A:CYS73 2.4 21.3 1.0
SG A:CYS76 2.4 19.3 1.0
SG A:CYS79 2.5 26.5 1.0
CB A:CYS76 3.4 19.0 1.0
CB A:CYS79 3.4 18.8 1.0
CB A:CYS64 3.5 18.4 1.0
N A:CYS73 3.6 20.4 1.0
CB A:CYS73 3.6 18.2 1.0
N A:GLY74 3.6 22.8 1.0
CA A:CYS64 3.8 18.6 1.0
N A:CYS76 3.9 21.6 1.0
CA A:CYS73 4.0 19.5 1.0
N A:GLU65 4.1 23.9 1.0
CA A:CYS76 4.2 21.0 1.0
C A:CYS73 4.3 20.9 1.0
C A:CYS64 4.4 21.7 1.0
N A:CYS79 4.4 20.0 1.0
CA A:CYS79 4.5 22.5 1.0
O A:HOH514 4.5 17.2 1.0
C A:PRO72 4.5 20.8 1.0
N A:VAL75 4.5 24.0 1.0
CA A:GLY74 4.6 23.6 1.0
N A:THR66 4.8 22.4 1.0
CA A:PRO72 4.8 20.6 1.0
O A:CYS76 4.9 21.1 1.0
C A:CYS76 4.9 21.8 1.0
C A:GLY74 5.0 25.5 1.0
CB A:PRO72 5.0 22.1 1.0
CB A:THR66 5.0 23.3 1.0

Zinc binding site 2 out of 4 in 1njf

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Zinc binding site 2 out of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:43.7
occ:1.00
SG B:CYS73 2.3 32.3 1.0
SG B:CYS76 2.4 33.3 1.0
SG B:CYS64 2.4 24.5 1.0
SG B:CYS79 2.6 32.1 1.0
CB B:CYS76 3.3 35.3 1.0
CB B:CYS73 3.4 31.5 1.0
CB B:CYS79 3.5 32.6 1.0
N B:CYS73 3.5 27.8 1.0
CB B:CYS64 3.6 28.8 1.0
N B:GLY74 3.8 32.5 1.0
CA B:CYS73 3.8 30.3 1.0
CA B:CYS64 3.9 28.8 1.0
N B:CYS76 3.9 32.9 1.0
N B:GLU65 4.0 31.5 1.0
CA B:CYS76 4.2 35.3 1.0
C B:CYS73 4.3 31.6 1.0
C B:CYS64 4.4 30.9 1.0
N B:CYS79 4.5 34.1 1.0
C B:PRO72 4.5 27.1 1.0
CA B:CYS79 4.6 34.8 1.0
N B:VAL75 4.6 32.5 1.0
O B:CYS76 4.8 37.0 1.0
C B:CYS76 4.8 36.8 1.0
CA B:GLY74 4.9 31.7 1.0
CG2 B:THR66 4.9 27.8 1.0
CA B:PRO72 4.9 25.6 1.0
N B:THR66 4.9 33.1 1.0

Zinc binding site 3 out of 4 in 1njf

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Zinc binding site 3 out of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:46.5
occ:1.00
SG C:CYS73 2.4 33.9 1.0
SG C:CYS76 2.4 39.5 1.0
SG C:CYS79 2.5 32.2 1.0
SG C:CYS64 2.5 31.4 1.0
CB C:CYS79 3.4 30.4 1.0
CB C:CYS76 3.4 37.1 1.0
CB C:CYS64 3.4 27.3 1.0
N C:CYS73 3.6 37.5 1.0
CB C:CYS73 3.7 36.4 1.0
N C:GLY74 3.8 37.5 1.0
CA C:CYS64 3.8 28.5 1.0
N C:CYS76 3.9 38.4 1.0
CA C:CYS73 4.0 36.8 1.0
N C:GLU65 4.0 32.2 1.0
CA C:CYS76 4.2 36.1 1.0
N C:CYS79 4.3 28.8 1.0
C C:CYS73 4.3 36.5 1.0
C C:CYS64 4.3 29.9 1.0
CA C:CYS79 4.4 30.3 1.0
N C:VAL75 4.4 38.8 1.0
C C:PRO72 4.6 36.6 1.0
CG2 C:THR66 4.7 39.6 1.0
CA C:GLY74 4.7 36.9 1.0
O C:CYS76 4.7 32.4 1.0
C C:CYS76 4.8 34.6 1.0
CA C:PRO72 4.9 35.7 1.0
N C:THR66 5.0 39.0 1.0

Zinc binding site 4 out of 4 in 1njf

Go back to Zinc Binding Sites List in 1njf
Zinc binding site 4 out of 4 in the Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nucleotide Bound Form of An Isolated E. Coli Clamp Loader Gamma Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:48.8
occ:1.00
SG D:CYS79 2.3 25.7 1.0
SG D:CYS64 2.4 24.1 1.0
SG D:CYS73 2.5 29.9 1.0
SG D:CYS76 2.6 26.4 1.0
CB D:CYS64 3.4 25.5 1.0
CB D:CYS79 3.4 26.7 1.0
CB D:CYS76 3.4 27.3 1.0
N D:CYS73 3.5 32.2 1.0
CB D:CYS73 3.6 30.1 1.0
CA D:CYS64 3.7 26.4 1.0
N D:GLY74 3.7 31.6 1.0
CA D:CYS73 3.9 31.9 1.0
N D:GLU65 4.0 30.0 1.0
N D:CYS76 4.1 30.5 1.0
C D:CYS73 4.3 32.3 1.0
C D:CYS64 4.3 28.0 1.0
CA D:CYS76 4.3 28.6 1.0
O D:HOH417 4.4 22.4 1.0
N D:CYS79 4.4 24.2 1.0
C D:PRO72 4.4 30.7 1.0
CA D:CYS79 4.5 25.9 1.0
N D:VAL75 4.6 31.6 1.0
CG2 D:THR66 4.7 37.1 1.0
CA D:PRO72 4.7 30.9 1.0
CA D:GLY74 4.7 30.7 1.0
CB D:PRO72 4.8 31.5 1.0
N D:THR66 4.9 33.9 1.0
N D:CYS64 4.9 23.1 1.0
O D:CYS76 4.9 26.8 1.0
C D:CYS76 5.0 27.5 1.0

Reference:

M.Podobnik, T.F.Weitze, M.O'donnell, J.Kuriyan. Nucleotide-Induced Conformational Changes in An Isolated Escherichia Coli Dna Polymerase III Clamp Loader Subunit Structure V. 11 253 2003.
ISSN: ISSN 0969-2126
PubMed: 12623013
DOI: 10.1016/S0969-2126(03)00027-3
Page generated: Wed Dec 16 02:58:36 2020

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