Zinc in PDB 9icv: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2

Protein crystallography data

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2, PDB code: 9icv was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.972, 57.628, 48.334, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / n/a

Other elements in 9icv:

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 (pdb code 9icv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2, PDB code: 9icv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 9icv

Go back to Zinc Binding Sites List in 9icv
Zinc binding site 1 out of 3 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn339

b:30.0
occ:0.51
OD2 A:ASP192 2.5 31.0 1.0
OD1 A:ASP190 2.5 41.0 1.0
O3G A:DTP338 2.6 36.0 0.5
OP2 P:DA8 2.8 0.0 1.0
ZN A:ZN340 3.2 30.0 0.5
CG A:ASP190 3.3 33.8 1.0
O1G A:DTP338 3.3 36.7 0.5
OP1 P:DA8 3.4 0.0 1.0
P P:DA8 3.5 0.0 1.0
PG A:DTP338 3.5 40.3 0.5
O A:ASP190 3.5 28.6 1.0
O A:HOH662 3.6 53.4 1.0
CG A:ASP192 3.6 35.9 1.0
O2B A:DTP338 3.8 90.9 0.5
OD2 A:ASP190 3.8 43.7 1.0
O A:HOH522 4.0 64.5 1.0
OD1 A:ASP192 4.1 46.9 1.0
O3B A:DTP338 4.2 63.8 0.5
C A:ASP190 4.3 16.8 1.0
CB A:ASP190 4.4 20.9 1.0
N A:ASP190 4.4 21.8 1.0
O3' P:DG7 4.4 98.5 1.0
O A:HOH502 4.5 5.6 1.0
PB A:DTP338 4.5 85.0 0.5
O P:HOH660 4.5 59.8 1.0
O3A A:DTP338 4.6 88.8 0.5
CA A:ASP190 4.6 16.5 1.0
CB A:ASP192 4.8 26.4 1.0
O2G A:DTP338 4.8 39.8 0.5
O5' P:DA8 4.8 0.0 1.0
N A:ASP192 5.0 12.3 1.0

Zinc binding site 2 out of 3 in 9icv

Go back to Zinc Binding Sites List in 9icv
Zinc binding site 2 out of 3 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn340

b:30.0
occ:0.54
OD1 A:ASP192 2.7 46.9 1.0
OD2 A:ASP256 2.8 36.8 1.0
OD2 A:ASP190 3.1 43.7 1.0
OD2 A:ASP192 3.2 31.0 1.0
ZN A:ZN339 3.2 30.0 0.5
CG A:ASP192 3.2 35.9 1.0
O3' P:DG7 3.3 98.5 1.0
OP2 P:DA8 3.3 0.0 1.0
CG A:ASP190 3.4 33.8 1.0
OD1 A:ASP190 3.7 41.0 1.0
P P:DA8 3.8 0.0 1.0
CG A:ASP256 3.8 27.4 1.0
O A:HOH658 3.9 44.1 1.0
OP1 P:DA8 4.2 0.0 1.0
CB A:ASP256 4.2 17.3 1.0
CB A:ASP190 4.2 20.9 1.0
C3' P:DG7 4.4 98.2 1.0
C4' P:DG7 4.5 95.8 1.0
CB A:ASP192 4.5 26.4 1.0
O A:MET191 4.6 15.4 1.0
OD1 A:ASP256 4.6 31.2 1.0
CA A:ASP192 4.8 12.6 1.0
C A:MET191 4.9 12.7 1.0
O A:ASP190 4.9 28.6 1.0
O P:HOH660 5.0 59.8 1.0
N A:ASP192 5.0 12.3 1.0
O5' P:DG7 5.0 77.4 1.0

Zinc binding site 3 out of 3 in 9icv

Go back to Zinc Binding Sites List in 9icv
Zinc binding site 3 out of 3 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and ZNCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn343

b:30.0
occ:0.69
ND1 A:HIS51 2.1 43.8 1.0
CG A:HIS51 2.9 45.0 1.0
CE1 A:HIS51 3.0 46.8 1.0
CB A:HIS51 3.3 42.8 1.0
CA A:HIS51 3.9 36.3 1.0
CD2 A:HIS51 3.9 51.1 1.0
NE2 A:HIS51 3.9 51.4 1.0
O A:PRO50 4.4 50.3 1.0
N A:LYS52 4.7 31.4 1.0
C A:HIS51 4.8 33.1 1.0
N A:HIS51 4.9 39.4 1.0

Reference:

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566
Page generated: Wed Dec 16 14:05:25 2020

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