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Magnesium in PDB 4b9v: Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair.

Enzymatic activity of Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair.

All present enzymatic activity of Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair.:
2.7.7.7;

Protein crystallography data

The structure of Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair., PDB code: 4b9v was solved by T.H.Gehrke, U.Lischke, S.Arnold, S.Schneider, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.02 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.901, 94.035, 105.341, 90.00, 90.00, 90.00
R / Rfree (%) 18.682 / 21.529

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair. (pdb code 4b9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair., PDB code: 4b9v:

Magnesium binding site 1 out of 1 in 4b9v

Go back to Magnesium Binding Sites List in 4b9v
Magnesium binding site 1 out of 1 in the Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the High Fidelity Dna Polymerase I with Extending From An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1883

b:43.8
occ:1.00
 O A:TYR654 2.7 20.8 1.0
OD2 A:ASP653 2.8 37.4 1.0
OD2 A:ASP830 2.9 36.0 1.0
O1 A:SO41882 3.1 25.2 0.5
O A:HOH2159 3.2 42.4 1.0
O2 A:SO41882 3.3 31.8 0.5
O A:HOH2119 3.7 23.5 1.0
CG A:ASP653 3.8 28.9 1.0
S A:SO41882 3.8 34.5 0.5
CG A:ASP830 3.9 30.2 1.0
C A:TYR654 3.9 19.9 1.0
O A:HOH2118 3.9 45.0 1.0
CB A:ASP653 4.0 23.6 1.0
OD1 A:ASP830 4.2 31.4 1.0
O4 A:SO41882 4.4 29.0 0.5
CA A:SER655 4.5 19.7 1.0
N A:SER655 4.6 19.7 1.0
N A:GLN656 4.8 17.2 1.0
N A:TYR654 4.8 17.4 1.0
C A:ASP653 4.9 19.1 1.0
OD1 A:ASP653 4.9 32.4 1.0
CA A:TYR654 5.0 18.5 1.0

Reference:

T.H.Gehrke, U.Lischke, K.L.Gasteiger, S.Schneider, S.Arnold, H.C.Muller, D.S.Stephenson, H.Zipse, T.Carell. Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-Dna Lesions. Nat.Chem.Biol. V. 9 455 2013.
ISSN: ISSN 1552-4450
PubMed: 23685671
DOI: 10.1038/NCHEMBIO.1254
Page generated: Mon Aug 11 06:54:12 2025

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