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Magnesium in PDB 4mf8: Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp, PDB code: 4mf8 was solved by M.C.Koag, K.Min, A.F.Monzingo, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.036, 79.721, 54.989, 90.00, 107.38, 90.00
R / Rfree (%) 20.9 / 27.2

Other elements in 4mf8:

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp (pdb code 4mf8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp, PDB code: 4mf8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4mf8

Go back to Magnesium Binding Sites List in 4mf8
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:38.2
occ:1.00
 OG A:SER171 2.4 29.2 1.0
O A:HOH527 2.7 24.2 1.0
O A:HOH514 2.8 25.1 1.0
CB A:SER171 3.5 27.4 1.0
N A:SER171 4.3 24.4 1.0
CA A:SER171 4.4 26.6 1.0
OD1 A:ASP170 4.9 22.8 1.0

Magnesium binding site 2 out of 2 in 4mf8

Go back to Magnesium Binding Sites List in 4mf8
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:48.5
occ:1.00
 O P:HOH202 2.0 32.1 1.0
OP1 P:DC11 2.5 46.5 1.0
O3 A:PO4404 3.1 73.1 1.0
O2 A:PO4404 3.7 61.0 1.0
P P:DC11 3.8 38.8 1.0
P A:PO4404 3.9 61.0 1.0
OD1 A:ASP190 3.9 23.2 1.0
OD2 A:ASP192 4.1 33.8 1.0
O4 A:PO4404 4.1 61.8 1.0
CA A:GLY179 4.1 24.6 1.0
O5' P:DC11 4.3 41.9 1.0
O3' P:DA10 4.3 37.6 1.0
OD2 A:ASP190 4.4 19.2 1.0
CB A:ASP192 4.4 25.5 1.0
O A:HOH542 4.6 15.6 1.0
CG A:ASP190 4.6 20.1 1.0
CG A:ASP192 4.7 30.9 1.0
O A:PHE272 4.9 21.0 1.0
N A:GLY179 4.9 24.8 1.0

Reference:

M.C.Koag, K.Min, A.F.Monzingo, S.Lee. Structures of Human Dna Polymerase Beta Inserting Bases Opposite Templating O6MG To Be Published.
Page generated: Mon Aug 11 20:22:10 2025

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