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

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ttp:
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 Ttp, PDB code: 4mfa 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) 30.00 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.971, 79.662, 55.001, 90.00, 106.68, 90.00
R / Rfree (%) 21.2 / 28.3

Other elements in 4mfa:

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ttp 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 Ttp (pdb code 4mfa). 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 Ttp, PDB code: 4mfa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4mfa

Go back to Magnesium Binding Sites List in 4mfa
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 Ttp


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 Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:41.1
occ:1.00
OG A:SER171 2.3 24.0 1.0
O A:HOH513 2.4 21.6 1.0
CB A:SER171 3.5 22.7 1.0
O A:HOH521 3.6 34.7 1.0
N A:SER171 4.1 20.9 1.0
CA A:SER171 4.3 22.7 1.0
OD1 A:ASP170 4.8 21.4 1.0
C A:SER171 5.0 22.4 1.0

Magnesium binding site 2 out of 2 in 4mfa

Go back to Magnesium Binding Sites List in 4mfa
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 Ttp


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 Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:42.9
occ:1.00
OP1 P:DT11 1.7 74.7 1.0
OD2 A:ASP190 2.1 27.3 1.0
P P:DT11 3.0 71.9 1.0
CG A:ASP190 3.3 27.5 1.0
OP2 P:DT11 3.6 76.6 1.0
OD2 A:ASP256 3.6 22.3 1.0
OD1 A:ASP190 3.7 30.2 1.0
O3' P:DA10 4.0 64.8 1.0
OD2 A:ASP192 4.0 35.9 1.0
C5' P:DA10 4.1 43.4 1.0
O5' P:DT11 4.2 76.3 1.0
CG A:ASP256 4.4 19.4 1.0
C4' P:DA10 4.5 48.6 1.0
CB A:ASP190 4.5 22.1 1.0
CG A:ASP192 4.6 30.7 1.0
OP1 P:DA10 4.6 32.7 1.0
C3' P:DA10 4.7 54.6 1.0
NH2 A:ARG258 4.8 26.8 1.0
C5' P:DT11 4.8 65.9 1.0
O A:HOH514 4.9 22.9 1.0
CB A:ASP192 4.9 26.0 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 20:22:29 2025

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