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Zinc in PDB 1xxi: Adp Bound E. Coli Clamp Loader Complex

Enzymatic activity of Adp Bound E. Coli Clamp Loader Complex

All present enzymatic activity of Adp Bound E. Coli Clamp Loader Complex:
2.7.7.7;

Protein crystallography data

The structure of Adp Bound E. Coli Clamp Loader Complex, PDB code: 1xxi was solved by S.L.Kazmirski, 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) 20.00 / 4.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.208, 106.574, 535.829, 90.00, 90.00, 90.00
R / Rfree (%) 36.6 / 36.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Adp Bound E. Coli Clamp Loader Complex (pdb code 1xxi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Adp Bound E. Coli Clamp Loader Complex, PDB code: 1xxi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1xxi

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Zinc binding site 1 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

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

b:0.4
occ:1.00
 SG C:CYS76 2.3 0.3 1.0
SG C:CYS73 2.3 0.3 1.0
SG C:CYS64 2.3 0.3 1.0
SG C:CYS79 2.3 0.3 1.0
O C:CYS73 2.9 0.3 1.0
CB C:CYS76 3.2 0.3 1.0
CB C:CYS64 3.5 0.3 1.0
CB C:CYS79 3.5 0.3 1.0
N C:CYS73 3.8 0.3 1.0
CB C:CYS73 3.8 0.3 1.0
C C:CYS73 3.9 0.3 1.0
CA C:CYS64 4.0 0.3 1.0
CA C:CYS73 4.1 0.3 1.0
OG1 C:THR66 4.1 0.3 1.0
N C:GLU65 4.1 0.3 1.0
CA C:CYS76 4.1 0.3 1.0
N C:CYS76 4.2 0.3 1.0
N C:CYS79 4.3 0.3 1.0
O C:CYS76 4.4 0.3 1.0
CA C:CYS79 4.5 0.3 1.0
C C:CYS64 4.5 0.3 1.0
C C:CYS76 4.7 0.3 1.0
N C:THR66 4.7 0.3 1.0
C C:PRO72 4.8 0.3 1.0
CB C:THR66 4.9 0.3 1.0
O C:LYS60 5.0 0.3 1.0

Zinc binding site 2 out of 8 in 1xxi

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Zinc binding site 2 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Adp Bound E. Coli Clamp Loader Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:43.1
occ:1.00
 SG D:CYS73 2.4 72.7 1.0
SG D:CYS76 2.4 72.7 1.0
SG D:CYS64 2.5 72.7 1.0
SG D:CYS79 2.5 72.7 1.0
CB D:CYS79 3.4 72.7 1.0
CB D:CYS76 3.4 72.7 1.0
CB D:CYS64 3.5 72.7 1.0
N D:CYS73 3.6 72.7 1.0
CB D:CYS73 3.6 72.7 1.0
N D:GLY74 3.7 72.7 1.0
CA D:CYS64 3.8 72.7 1.0
N D:CYS76 3.9 72.7 1.0
CA D:CYS73 4.0 72.7 1.0
N D:GLU65 4.1 72.7 1.0
CA D:CYS76 4.3 72.7 1.0
C D:CYS73 4.3 72.7 1.0
C D:CYS64 4.4 72.7 1.0
N D:CYS79 4.4 72.7 1.0
CA D:CYS79 4.5 72.7 1.0
C D:PRO72 4.5 72.7 1.0
N D:VAL75 4.5 72.7 1.0
CA D:GLY74 4.6 72.7 1.0
N D:THR66 4.8 72.7 1.0
CA D:PRO72 4.8 72.7 1.0
O D:CYS76 4.9 72.7 1.0
C D:CYS76 4.9 72.7 1.0
C D:GLY74 5.0 72.7 1.0
CB D:PRO72 5.0 72.7 1.0
CB D:THR66 5.0 72.7 1.0

Zinc binding site 3 out of 8 in 1xxi

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Zinc binding site 3 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Adp Bound E. Coli Clamp Loader Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:0.6
occ:1.00
 SG B:CYS73 2.4 0.7 1.0
SG B:CYS76 2.4 0.7 1.0
SG B:CYS64 2.5 0.7 1.0
SG B:CYS79 2.5 0.7 1.0
CB B:CYS79 3.4 0.7 1.0
CB B:CYS76 3.4 0.7 1.0
CB B:CYS64 3.5 0.7 1.0
N B:CYS73 3.6 0.7 1.0
CB B:CYS73 3.6 0.7 1.0
N B:GLY74 3.7 0.7 1.0
CA B:CYS64 3.8 0.7 1.0
N B:CYS76 3.9 0.7 1.0
CA B:CYS73 4.0 0.7 1.0
N B:GLU65 4.1 0.7 1.0
CA B:CYS76 4.3 0.7 1.0
C B:CYS73 4.3 0.7 1.0
C B:CYS64 4.4 0.7 1.0
N B:CYS79 4.4 0.7 1.0
CA B:CYS79 4.5 0.7 1.0
C B:PRO72 4.5 0.7 1.0
N B:VAL75 4.5 0.7 1.0
CA B:GLY74 4.6 0.7 1.0
N B:THR66 4.8 0.7 1.0
CA B:PRO72 4.8 0.7 1.0
O B:CYS76 4.9 0.7 1.0
C B:CYS76 4.9 0.7 1.0
C B:GLY74 5.0 0.7 1.0
CB B:PRO72 5.0 0.7 1.0
CB B:THR66 5.0 0.7 1.0

Zinc binding site 4 out of 8 in 1xxi

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Zinc binding site 4 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Adp Bound E. Coli Clamp Loader Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn404

b:0.9
occ:1.00
 SG E:CYS65 2.3 97.8 1.0
SG E:CYS62 2.3 97.8 1.0
SG E:CYS50 2.3 97.8 1.0
SG E:CYS59 2.3 97.8 1.0
CB E:CYS65 3.3 97.8 1.0
CB E:CYS62 3.4 97.8 1.0
CB E:CYS50 3.6 97.8 1.0
N E:CYS59 3.6 97.8 1.0
CB E:CYS59 3.9 97.8 1.0
CA E:CYS50 3.9 97.8 1.0
N E:GLN51 3.9 97.8 1.0
CB E:SER58 4.0 97.8 1.0
N E:GLY60 4.0 97.8 1.0
N E:GLN52 4.1 97.8 1.0
N E:CYS65 4.1 97.8 1.0
N E:CYS62 4.2 97.8 1.0
CA E:CYS59 4.2 97.8 1.0
O E:GLN52 4.3 97.8 1.0
CA E:CYS65 4.3 97.8 1.0
CA E:CYS62 4.3 97.8 1.0
C E:CYS50 4.3 97.8 1.0
C E:GLN52 4.4 97.8 1.0
CA E:SER58 4.5 97.8 1.0
C E:SER58 4.6 97.8 1.0
OG E:SER58 4.6 97.8 1.0
C E:CYS59 4.7 97.8 1.0
CA E:GLN52 4.7 97.8 1.0
O E:CYS62 4.8 97.8 1.0
N E:PRO53 4.8 97.8 1.0
N E:HIS61 4.8 97.8 1.0
C E:CYS62 4.9 97.8 1.0
CA E:GLN51 4.9 97.8 1.0

Zinc binding site 5 out of 8 in 1xxi

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Zinc binding site 5 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Adp Bound E. Coli Clamp Loader Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn405

b:0.9
occ:1.00
 SG H:CYS76 2.3 0.3 1.0
SG H:CYS79 2.3 0.3 1.0
SG H:CYS64 2.3 0.3 1.0
SG H:CYS73 2.3 0.3 1.0
O H:CYS73 2.9 0.3 1.0
CB H:CYS76 3.2 0.3 1.0
CB H:CYS64 3.5 0.3 1.0
CB H:CYS79 3.5 0.3 1.0
N H:CYS73 3.8 0.3 1.0
CB H:CYS73 3.8 0.3 1.0
C H:CYS73 3.9 0.3 1.0
CA H:CYS64 4.0 0.3 1.0
CA H:CYS73 4.1 0.3 1.0
OG1 H:THR66 4.1 0.3 1.0
N H:CYS76 4.1 0.3 1.0
N H:GLU65 4.1 0.3 1.0
CA H:CYS76 4.2 0.3 1.0
N H:CYS79 4.3 0.3 1.0
O H:CYS76 4.4 0.3 1.0
CA H:CYS79 4.5 0.3 1.0
C H:CYS64 4.5 0.3 1.0
C H:CYS76 4.7 0.3 1.0
N H:THR66 4.7 0.3 1.0
C H:PRO72 4.8 0.3 1.0
CB H:THR66 4.9 0.3 1.0
O H:LYS60 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 1xxi

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Zinc binding site 6 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Adp Bound E. Coli Clamp Loader Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn406

b:0.1
occ:1.00
 SG I:CYS64 2.4 0.2 1.0
SG I:CYS73 2.4 0.2 1.0
SG I:CYS76 2.4 0.2 1.0
SG I:CYS79 2.5 0.2 1.0
CB I:CYS76 3.4 0.2 1.0
CB I:CYS79 3.4 0.2 1.0
CB I:CYS64 3.5 0.2 1.0
N I:CYS73 3.6 0.2 1.0
CB I:CYS73 3.6 0.2 1.0
N I:GLY74 3.6 0.2 1.0
CA I:CYS64 3.8 0.2 1.0
N I:CYS76 3.9 0.2 1.0
CA I:CYS73 4.0 0.2 1.0
N I:GLU65 4.1 0.2 1.0
CA I:CYS76 4.2 0.2 1.0
C I:CYS73 4.3 0.2 1.0
C I:CYS64 4.4 0.2 1.0
N I:CYS79 4.4 0.2 1.0
CA I:CYS79 4.5 0.2 1.0
C I:PRO72 4.5 0.2 1.0
N I:VAL75 4.5 0.2 1.0
CA I:GLY74 4.6 0.2 1.0
N I:THR66 4.8 0.2 1.0
CA I:PRO72 4.8 0.2 1.0
O I:CYS76 4.9 0.2 1.0
C I:CYS76 4.9 0.2 1.0
C I:GLY74 5.0 0.2 1.0
CB I:PRO72 5.0 0.2 1.0
CB I:THR66 5.0 0.2 1.0

Zinc binding site 7 out of 8 in 1xxi

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Zinc binding site 7 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Adp Bound E. Coli Clamp Loader Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn407

b:0.2
occ:1.00
 SG G:CYS73 2.4 0.2 1.0
SG G:CYS76 2.4 0.2 1.0
SG G:CYS64 2.5 0.2 1.0
SG G:CYS79 2.5 0.2 1.0
CB G:CYS79 3.4 0.2 1.0
CB G:CYS76 3.4 0.2 1.0
CB G:CYS64 3.5 0.2 1.0
N G:CYS73 3.6 0.2 1.0
CB G:CYS73 3.6 0.2 1.0
N G:GLY74 3.7 0.2 1.0
CA G:CYS64 3.8 0.2 1.0
N G:CYS76 3.9 0.2 1.0
CA G:CYS73 4.0 0.2 1.0
N G:GLU65 4.1 0.2 1.0
CA G:CYS76 4.3 0.2 1.0
C G:CYS73 4.3 0.2 1.0
C G:CYS64 4.4 0.2 1.0
N G:CYS79 4.4 0.2 1.0
CA G:CYS79 4.5 0.2 1.0
C G:PRO72 4.5 0.2 1.0
N G:VAL75 4.5 0.2 1.0
CA G:GLY74 4.6 0.2 1.0
N G:THR66 4.8 0.2 1.0
CA G:PRO72 4.8 0.2 1.0
O G:CYS76 4.9 0.2 1.0
C G:CYS76 4.9 0.2 1.0
C G:GLY74 5.0 0.2 1.0
CB G:PRO72 5.0 0.2 1.0
CB G:THR66 5.0 0.2 1.0

Zinc binding site 8 out of 8 in 1xxi

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Zinc binding site 8 out of 8 in the Adp Bound E. Coli Clamp Loader Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Adp Bound E. Coli Clamp Loader Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn408

b:0.6
occ:1.00
 SG J:CYS65 2.3 0.6 1.0
SG J:CYS62 2.3 0.6 1.0
SG J:CYS50 2.3 0.6 1.0
SG J:CYS59 2.3 0.6 1.0
CB J:CYS65 3.3 0.6 1.0
CB J:CYS62 3.4 0.6 1.0
CB J:CYS50 3.6 0.6 1.0
N J:CYS59 3.6 0.6 1.0
CB J:CYS59 3.9 0.6 1.0
CA J:CYS50 3.9 0.6 1.0
N J:GLN51 3.9 0.6 1.0
CB J:SER58 4.0 0.6 1.0
N J:GLY60 4.0 0.6 1.0
N J:GLN52 4.0 0.6 1.0
N J:CYS65 4.1 0.6 1.0
N J:CYS62 4.2 0.6 1.0
CA J:CYS59 4.2 0.6 1.0
O J:GLN52 4.3 0.6 1.0
CA J:CYS65 4.3 0.6 1.0
CA J:CYS62 4.3 0.6 1.0
C J:CYS50 4.3 0.6 1.0
C J:GLN52 4.4 0.6 1.0
CA J:SER58 4.5 0.6 1.0
C J:SER58 4.6 0.6 1.0
OG J:SER58 4.6 0.6 1.0
C J:CYS59 4.7 0.6 1.0
CA J:GLN52 4.7 0.6 1.0
O J:CYS62 4.8 0.6 1.0
N J:PRO53 4.8 0.6 1.0
N J:HIS61 4.9 0.6 1.0
C J:CYS62 4.9 0.6 1.0
CA J:GLN51 4.9 0.6 1.0

Reference:

S.L.Kazmirski, M.Podobnik, T.F.Weitze, M.O'donnell, J.Kuriyan. Structural Analysis of the Inactive State of the Escherichia Coli Dna Polymerase Clamp-Loader Complex Proc.Natl.Acad.Sci.Usa V. 101 16750 2004.
ISSN: ISSN 0027-8424
PubMed: 15556993
DOI: 10.1073/PNAS.0407904101
Page generated: Wed Oct 16 20:39:59 2024

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