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Zinc in PDB 3glf: Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna

Enzymatic activity of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna

All present enzymatic activity of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna, PDB code: 3glf was solved by K.R.Simonetta, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.97 / 3.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.264, 219.947, 273.150, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna (pdb code 3glf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna, PDB code: 3glf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3glf

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Zinc binding site 1 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn418

b:0.2
occ:1.00
SG B:CYS79 2.3 0.8 1.0
SG B:CYS76 2.3 0.1 1.0
SG B:CYS73 2.3 0.8 1.0
SG B:CYS64 2.4 0.4 1.0
CB B:CYS79 3.3 0.7 1.0
CB B:CYS64 3.6 1.0 1.0
CB B:CYS76 3.7 0.9 1.0
N B:CYS73 3.7 0.1 1.0
CB B:CYS73 3.7 0.6 1.0
N B:GLY74 4.0 0.7 1.0
CA B:CYS64 4.0 0.4 1.0
CA B:CYS73 4.1 0.8 1.0
N B:GLU65 4.1 0.3 1.0
N B:CYS76 4.2 0.8 1.0
CA B:CYS79 4.4 0.8 1.0
N B:CYS79 4.4 0.2 1.0
C B:CYS73 4.5 0.9 1.0
CA B:CYS76 4.5 0.3 1.0
CG2 B:THR66 4.6 0.7 1.0
C B:CYS64 4.6 0.6 1.0
N B:VAL75 4.7 0.1 1.0
C B:PRO72 4.8 0.7 1.0
CA B:GLY74 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 3glf

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Zinc binding site 2 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn419

b:0.3
occ:1.00
SG C:CYS79 2.3 0.8 1.0
SG C:CYS76 2.3 0.8 1.0
SG C:CYS73 2.3 0.5 1.0
SG C:CYS64 2.4 0.7 1.0
CB C:CYS79 3.2 0.8 1.0
CB C:CYS64 3.4 0.1 1.0
CB C:CYS76 3.5 0.1 1.0
N C:CYS73 3.7 0.6 1.0
CB C:CYS73 3.7 0.0 1.0
CA C:CYS64 3.8 0.8 1.0
N C:GLU65 4.0 0.4 1.0
N C:CYS76 4.1 0.1 1.0
CA C:CYS73 4.1 0.3 1.0
N C:GLY74 4.1 0.3 1.0
N C:CYS79 4.2 0.8 1.0
CA C:CYS79 4.2 0.5 1.0
C C:CYS64 4.3 0.8 1.0
CA C:CYS76 4.3 0.2 1.0
C C:CYS73 4.4 0.2 1.0
N C:VAL75 4.5 0.5 1.0
O C:CYS76 4.6 0.7 1.0
CG2 C:THR66 4.6 0.0 1.0
C C:PRO72 4.8 0.2 1.0
C C:CYS76 4.8 0.4 1.0
CA C:GLY74 5.0 0.2 1.0

Zinc binding site 3 out of 8 in 3glf

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Zinc binding site 3 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn420

b:0.4
occ:1.00
SG D:CYS79 2.3 0.5 1.0
SG D:CYS76 2.3 0.1 1.0
SG D:CYS73 2.3 0.6 1.0
SG D:CYS64 2.4 0.1 1.0
N D:CYS73 3.5 0.3 1.0
CB D:CYS64 3.5 0.4 1.0
N D:GLY74 3.6 0.9 1.0
CB D:CYS73 3.6 0.8 1.0
CB D:CYS79 3.6 0.9 1.0
CA D:CYS73 3.9 0.2 1.0
CB D:CYS76 3.9 0.3 1.0
CA D:CYS64 4.1 0.4 1.0
CG2 D:THR66 4.1 0.8 1.0
N D:CYS76 4.2 0.5 1.0
N D:VAL75 4.3 0.2 1.0
C D:CYS73 4.3 0.4 1.0
N D:GLU65 4.3 0.7 1.0
C D:PRO72 4.5 0.6 1.0
CA D:GLY74 4.6 0.8 1.0
C D:CYS64 4.6 1.0 1.0
N D:CYS79 4.6 0.8 1.0
CA D:CYS76 4.7 0.1 1.0
CA D:CYS79 4.7 0.9 1.0
OG1 D:THR66 4.8 0.2 1.0
CA D:PRO72 4.9 0.3 1.0
CB D:PRO72 4.9 0.3 1.0
C D:GLY74 4.9 0.9 1.0
N D:THR66 4.9 0.1 1.0

Zinc binding site 4 out of 8 in 3glf

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Zinc binding site 4 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn421

b:0.4
occ:1.00
SG E:CYS59 2.3 0.6 1.0
SG E:CYS62 2.3 0.5 1.0
SG E:CYS65 2.3 0.4 1.0
SG E:CYS50 2.3 0.2 1.0
CB E:CYS65 3.1 0.1 1.0
CB E:CYS50 3.1 0.3 1.0
CB E:CYS62 3.5 0.3 1.0
N E:CYS59 3.6 0.1 1.0
CB E:CYS59 3.8 0.6 1.0
CA E:CYS50 3.8 0.9 1.0
N E:GLY60 4.0 0.2 1.0
CA E:CYS59 4.1 0.2 1.0
N E:CYS62 4.2 0.1 1.0
CA E:CYS65 4.2 0.3 1.0
N E:CYS65 4.2 0.6 1.0
N E:GLN51 4.3 0.9 1.0
C E:CYS50 4.4 0.4 1.0
CA E:CYS62 4.4 0.8 1.0
C E:SER58 4.5 0.4 1.0
N E:GLN52 4.5 0.5 1.0
C E:CYS59 4.6 0.9 1.0
CA E:SER58 4.7 0.0 1.0
N E:HIS61 4.8 0.2 1.0
CB E:SER58 4.8 0.9 1.0
CA E:GLY60 4.9 0.1 1.0
O E:CYS62 5.0 0.7 1.0

Zinc binding site 5 out of 8 in 3glf

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Zinc binding site 5 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn422

b:0.8
occ:1.00
SG G:CYS79 2.3 0.7 1.0
SG G:CYS76 2.3 0.1 1.0
SG G:CYS73 2.3 0.6 1.0
SG G:CYS64 2.4 0.2 1.0
CB G:CYS79 3.3 0.5 1.0
CB G:CYS76 3.5 0.0 1.0
CB G:CYS64 3.6 0.4 1.0
CB G:CYS73 3.7 0.9 1.0
N G:CYS73 3.7 0.1 1.0
N G:GLY74 4.0 0.3 1.0
N G:GLU65 4.1 0.1 1.0
CA G:CYS64 4.1 0.7 1.0
N G:CYS76 4.1 0.0 1.0
CA G:CYS73 4.1 0.8 1.0
CA G:CYS76 4.3 0.6 1.0
N G:CYS79 4.4 0.2 1.0
CA G:CYS79 4.4 0.6 1.0
C G:CYS73 4.5 0.8 1.0
CG2 G:THR66 4.5 0.6 1.0
C G:CYS64 4.6 0.7 1.0
N G:VAL75 4.7 0.1 1.0
C G:PRO72 4.9 0.9 1.0
O G:CYS76 4.9 0.3 1.0
C G:CYS76 5.0 0.9 1.0

Zinc binding site 6 out of 8 in 3glf

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Zinc binding site 6 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn423

b:0.7
occ:1.00
SG H:CYS79 2.3 97.6 1.0
SG H:CYS76 2.3 0.2 1.0
SG H:CYS73 2.3 0.1 1.0
SG H:CYS64 2.4 94.1 1.0
CB H:CYS79 3.3 97.2 1.0
CB H:CYS64 3.4 90.8 1.0
N H:CYS73 3.6 0.2 1.0
CB H:CYS76 3.6 0.8 1.0
CB H:CYS73 3.7 0.5 1.0
CA H:CYS64 3.7 90.8 1.0
N H:GLU65 3.9 0.2 1.0
CA H:CYS73 4.0 0.7 1.0
N H:GLY74 4.1 0.6 1.0
N H:CYS76 4.2 0.1 1.0
C H:CYS64 4.2 94.8 1.0
C H:CYS73 4.3 0.1 1.0
N H:CYS79 4.3 98.5 1.0
CA H:CYS79 4.4 95.8 1.0
CA H:CYS76 4.4 0.5 1.0
CG2 H:THR66 4.5 0.4 1.0
N H:VAL75 4.7 98.7 1.0
C H:PRO72 4.7 0.7 1.0
O H:CYS76 4.7 0.4 1.0
CA H:PRO72 5.0 0.0 1.0
C H:CYS76 5.0 1.0 1.0
N H:CYS64 5.0 88.1 1.0

Zinc binding site 7 out of 8 in 3glf

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Zinc binding site 7 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn424

b:99.2
occ:1.00
SG I:CYS79 2.3 0.7 1.0
SG I:CYS76 2.3 0.6 1.0
SG I:CYS64 2.4 82.5 1.0
SG I:CYS73 2.4 0.9 1.0
CB I:CYS64 3.4 78.8 1.0
N I:CYS73 3.6 0.9 1.0
CB I:CYS79 3.6 0.4 1.0
N I:GLY74 3.7 0.5 1.0
CB I:CYS73 3.8 0.1 1.0
CB I:CYS76 3.8 0.2 1.0
CA I:CYS64 4.0 78.0 1.0
CG2 I:THR66 4.0 95.4 1.0
CA I:CYS73 4.1 0.2 1.0
N I:GLU65 4.1 0.5 1.0
N I:CYS76 4.1 0.5 1.0
N I:VAL75 4.4 93.7 1.0
C I:CYS73 4.4 0.9 1.0
C I:CYS64 4.5 80.8 1.0
N I:CYS79 4.6 0.6 1.0
CA I:CYS76 4.6 0.0 1.0
C I:PRO72 4.6 82.5 1.0
CA I:GLY74 4.7 0.8 1.0
CA I:CYS79 4.7 0.1 1.0
N I:THR66 4.8 92.4 1.0
OG1 I:THR66 4.9 92.9 1.0

Zinc binding site 8 out of 8 in 3glf

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Zinc binding site 8 out of 8 in the Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn425

b:0.3
occ:1.00
SG J:CYS59 2.3 0.8 1.0
SG J:CYS62 2.3 0.1 1.0
SG J:CYS65 2.3 0.6 1.0
SG J:CYS50 2.3 0.4 1.0
CB J:CYS65 3.0 0.9 1.0
CB J:CYS50 3.2 0.2 1.0
CB J:CYS62 3.4 0.9 1.0
N J:CYS59 3.7 0.8 1.0
CB J:CYS59 3.8 0.3 1.0
CA J:CYS50 3.9 0.5 1.0
N J:GLY60 3.9 0.8 1.0
N J:CYS62 4.1 0.0 1.0
CA J:CYS65 4.2 0.6 1.0
CA J:CYS59 4.2 0.1 1.0
N J:CYS65 4.2 0.5 1.0
N J:GLN51 4.2 0.3 1.0
CA J:CYS62 4.3 0.5 1.0
C J:CYS50 4.4 1.0 1.0
N J:GLN52 4.5 0.2 1.0
C J:CYS59 4.6 0.7 1.0
C J:SER58 4.6 0.9 1.0
N J:HIS61 4.7 0.8 1.0
CA J:SER58 4.8 0.4 1.0
CB J:SER58 4.9 0.9 1.0
CA J:GLY60 4.9 0.4 1.0
O J:CYS62 4.9 0.1 1.0
C J:CYS62 4.9 0.3 1.0

Reference:

K.R.Simonetta, S.L.Kazmirski, E.R.Goedken, A.J.Cantor, B.A.Kelch, R.Mcnally, S.N.Seyedin, D.L.Makino, M.O'donnell, J.Kuriyan. The Mechanism of Atp-Dependent Primer-Template Recognition By A Clamp Loader Complex. Cell(Cambridge,Mass.) V. 137 659 2009.
ISSN: ISSN 0092-8674
PubMed: 19450514
DOI: 10.1016/J.CELL.2009.03.044
Page generated: Sat Sep 26 10:17:31 2020
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