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Zinc in PDB 2hpm: Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III

Enzymatic activity of Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III

All present enzymatic activity of Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III:
2.7.7.7;

Protein crystallography data

The structure of Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III, PDB code: 2hpm was solved by S.Bailey, R.A.Wing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 174.442, 185.724, 125.836, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 31.1

Other elements in 2hpm:

The structure of Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III (pdb code 2hpm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III, PDB code: 2hpm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2hpm

Go back to Zinc Binding Sites List in 2hpm
Zinc binding site 1 out of 2 in the Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1221

b:94.4
occ:1.00
 OD2 A:ASP20 1.9 0.8 1.0
NE2 A:HIS47 1.9 0.1 1.0
NE2 A:HIS214 2.2 1.0 1.0
CE1 A:HIS47 2.8 0.7 1.0
CG A:ASP20 2.9 0.1 1.0
CD2 A:HIS47 2.9 0.3 1.0
CE1 A:HIS214 3.0 0.8 1.0
OD1 A:ASP20 3.2 0.9 1.0
CD2 A:HIS214 3.2 0.4 1.0
ND1 A:HIS47 3.9 0.7 1.0
CG A:HIS47 4.0 0.3 1.0
ND1 A:HIS214 4.0 0.6 1.0
CG A:HIS214 4.2 0.5 1.0
CB A:ASP20 4.3 0.1 1.0
CE1 A:HIS13 4.4 0.8 1.0
ND1 A:HIS13 4.5 0.5 1.0
ZN A:ZN1222 4.6 0.2 1.0
CZ A:PHE244 4.6 0.2 1.0
NE2 A:HIS13 4.8 0.5 1.0

Zinc binding site 2 out of 2 in 2hpm

Go back to Zinc Binding Sites List in 2hpm
Zinc binding site 2 out of 2 in the Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Eubacterial and Eukaryotic Replicative Dna Polymerases Are Not Homologous: X-Ray Structure of Dna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1222

b:0.2
occ:1.00
 OE1 A:GLU72 1.6 0.6 1.0
OD1 A:ASP212 2.3 0.1 1.0
NE2 A:HIS13 2.5 0.5 1.0
CD A:GLU72 2.6 0.5 1.0
NE2 A:HIS11 2.8 0.7 1.0
OD2 A:ASP212 2.8 0.3 1.0
CG A:ASP212 2.9 0.6 1.0
OE2 A:GLU72 2.9 0.1 1.0
CE1 A:HIS13 3.1 0.8 1.0
CE1 A:HIS11 3.2 0.5 1.0
CD2 A:HIS13 3.6 0.2 1.0
CE1 A:HIS47 3.7 0.7 1.0
CD2 A:HIS11 3.9 0.8 1.0
CG A:GLU72 3.9 0.7 1.0
CE1 A:HIS214 4.0 0.8 1.0
SG A:CYS145 4.0 0.2 1.0
NE2 A:HIS47 4.1 0.1 1.0
ND1 A:HIS13 4.2 0.5 1.0
ND1 A:HIS95 4.2 0.0 1.0
ND1 A:HIS11 4.3 0.6 1.0
CB A:CYS145 4.4 0.6 1.0
CB A:ASP212 4.4 0.2 1.0
CG A:HIS13 4.5 0.3 1.0
CB A:GLU72 4.5 0.1 1.0
ND1 A:HIS47 4.5 0.7 1.0
NE2 A:HIS214 4.6 1.0 1.0
ZN A:ZN1221 4.6 94.4 1.0
CE1 A:HIS95 4.6 0.6 1.0
CG A:HIS11 4.7 0.9 1.0

Reference:

S.Bailey, R.A.Wing, T.A.Steitz. The Structure of T. Aquaticus Dna Polymerase III Is Distinct From Eukaryotic Replicative Dna Polymerases. Cell(Cambridge,Mass.) V. 126 893 2006.
ISSN: ISSN 0092-8674
PubMed: 16959569
DOI: 10.1016/J.CELL.2006.07.027
Page generated: Thu Oct 17 00:40:49 2024

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