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Magnesium 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:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2hpm

Go back to Magnesium Binding Sites List in 2hpm
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1223

b:0.7
occ:1.00
 OD1 A:ASP465 2.2 0.3 1.0
CE A:LYS616 3.1 0.8 1.0
NZ A:LYS616 3.2 0.5 1.0
CG A:ASP465 3.2 1.0 1.0
OD2 A:ASP463 3.3 0.1 1.0
CG A:ASP463 3.4 0.2 1.0
CB A:ASP463 3.5 0.4 1.0
N A:ASP618 3.6 0.7 1.0
OD2 A:ASP465 3.6 1.0 1.0
CA A:MET617 3.9 0.4 1.0
OD2 A:ASP618 4.0 0.8 1.0
CG A:ASP618 4.0 0.2 1.0
C A:MET617 4.1 0.7 1.0
OD1 A:ASP463 4.1 0.9 1.0
CB A:ASP618 4.2 0.0 1.0
CD A:LYS616 4.4 0.8 1.0
O A:LYS616 4.4 0.7 1.0
CB A:ASP465 4.5 0.0 1.0
OD1 A:ASP618 4.5 0.3 1.0
CA A:ASP463 4.5 0.7 1.0
N A:MET617 4.5 1.0 1.0
CA A:ASP618 4.5 0.1 1.0
N A:ASP465 4.7 0.3 1.0
C A:LYS616 4.7 0.3 1.0
CA A:ASP465 4.7 0.1 1.0
C A:ASP463 4.7 0.3 1.0
N A:ILE464 4.8 0.7 1.0
C A:ILE464 4.8 0.7 1.0
O A:ILE464 4.8 0.6 1.0
CG A:LYS616 4.9 0.7 1.0

Magnesium binding site 2 out of 2 in 2hpm

Go back to Magnesium Binding Sites List in 2hpm
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1224

b:62.3
occ:1.00
 OE1 A:GLU149 2.2 0.6 1.0
OD2 A:ASP169 2.7 94.7 1.0
OD1 A:ASP169 2.8 98.7 1.0
CG A:ASP169 3.1 0.8 1.0
CD A:GLU149 3.4 0.6 1.0
CD A:ARG129 3.5 0.2 1.0
CG A:ARG129 3.7 0.7 1.0
CD2 A:LEU96 3.9 0.5 1.0
CD1 A:LEU96 4.0 0.8 1.0
OE2 A:GLU149 4.2 0.1 1.0
CG A:GLU149 4.3 0.6 1.0
CD1 A:LEU132 4.4 0.3 1.0
NE A:ARG129 4.4 0.8 1.0
CG2 A:VAL75 4.5 98.7 1.0
CG A:LEU96 4.5 0.7 1.0
CG1 A:VAL75 4.6 0.1 1.0
CB A:ASP169 4.7 1.0 1.0
CB A:LEU96 4.9 0.9 1.0
CB A:VAL75 5.0 0.1 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: Tue Aug 13 23:56:50 2024

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