Zinc in PDB 9icg: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)

Protein crystallography data

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9icg 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 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.890, 57.600, 48.430, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / n/a

Other elements in 9icg:

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) (pdb code 9icg). 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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9icg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 9icg

Go back to Zinc Binding Sites List in 9icg
Zinc binding site 1 out of 3 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn339

b:30.0
occ:0.51
O1A A:DCP338 1.8 79.9 0.5
OD1 A:ASP190 2.3 52.4 1.0
O1G A:DCP338 2.5 9.9 0.5
OD1 A:ASP192 2.9 44.9 1.0
O2B A:DCP338 3.1 0.0 0.5
PA A:DCP338 3.2 59.9 0.5
O3G A:DCP338 3.3 68.0 0.5
PG A:DCP338 3.4 35.5 0.5
O A:ASP190 3.4 22.3 1.0
CG A:ASP190 3.5 55.1 1.0
O3A A:DCP338 3.7 83.3 0.5
O3B A:DCP338 3.7 76.0 0.5
PB A:DCP338 3.7 94.0 0.5
ZN A:ZN340 3.8 30.0 0.4
O5' A:DCP338 3.9 64.6 0.5
CG A:ASP192 4.1 41.7 1.0
C A:ASP190 4.2 17.3 1.0
N A:ASP190 4.2 29.5 1.0
O A:HOH502 4.2 1.0 1.0
O2A A:DCP338 4.4 81.9 0.5
O A:HOH654 4.4 50.4 1.0
OD2 A:ASP190 4.4 66.9 1.0
CB A:ASP190 4.5 42.7 1.0
CA A:ASP190 4.5 29.8 1.0
O A:HOH522 4.7 56.5 1.0
O2G A:DCP338 4.8 75.7 0.5
OD2 A:ASP192 4.9 47.9 1.0

Zinc binding site 2 out of 3 in 9icg

Go back to Zinc Binding Sites List in 9icg
Zinc binding site 2 out of 3 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn340

b:30.0
occ:0.41
OD1 A:ASP190 3.1 52.4 1.0
CG A:ASP190 3.2 55.1 1.0
OD2 A:ASP190 3.2 66.9 1.0
OD1 A:ASP192 3.2 44.9 1.0
OD2 A:ASP192 3.3 47.9 1.0
O3' P:DG7 3.4 0.0 1.0
CG A:ASP192 3.5 41.7 1.0
OD2 A:ASP256 3.6 33.7 1.0
O1A A:DCP338 3.7 79.9 0.5
ZN A:ZN339 3.8 30.0 0.5
CG A:ASP256 4.0 27.8 1.0
CB A:ASP190 4.1 42.7 1.0
C4' P:DG7 4.1 0.0 1.0
C3' P:DG7 4.3 0.0 1.0
OD1 A:ASP256 4.5 28.5 1.0
C5' P:DG7 4.5 0.0 1.0
O5' P:DG7 4.5 0.0 1.0
CB A:ASP256 4.6 15.3 1.0
PA A:DCP338 4.7 59.9 0.5
O A:MET191 4.8 18.5 1.0
CB A:ASP192 4.8 30.5 1.0

Zinc binding site 3 out of 3 in 9icg

Go back to Zinc Binding Sites List in 9icg
Zinc binding site 3 out of 3 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar)


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 (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn343

b:30.0
occ:0.85
ND1 A:HIS51 1.8 33.4 1.0
CE1 A:HIS51 2.8 33.0 1.0
CG A:HIS51 2.9 36.6 1.0
CB A:HIS51 3.3 33.7 1.0
CA A:HIS51 3.9 30.3 1.0
NE2 A:HIS51 4.0 33.6 1.0
CD2 A:HIS51 4.0 35.4 1.0
C A:HIS51 4.6 23.0 1.0
N A:LYS52 4.7 20.2 1.0
O A:PRO50 4.7 55.1 1.0

Reference:

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I
Page generated: Thu Oct 31 15:39:41 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy