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Magnesium in PDB 4ph5: Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position, PDB code: 4ph5 was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.613, 80.377, 55.294, 90.00, 107.61, 90.00
R / Rfree (%) 19.1 / 26.1

Other elements in 4ph5:

The structure of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position 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 A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position (pdb code 4ph5). 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 A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position, PDB code: 4ph5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4ph5

Go back to Magnesium Binding Sites List in 4ph5
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position


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 A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:28.6
occ:1.00
OD1 A:ASP190 2.2 27.8 1.0
OD2 A:ASP192 2.2 25.4 1.0
OP1 P:DC11 2.3 26.8 1.0
O1 A:PO4405 2.4 38.7 1.0
CG A:ASP190 3.1 27.8 1.0
O3 A:PO4405 3.2 25.4 1.0
CG A:ASP192 3.3 25.4 1.0
P A:PO4405 3.3 52.3 1.0
O A:HOH540 3.4 26.7 1.0
OD2 A:ASP190 3.5 32.4 1.0
P P:DC11 3.6 31.9 1.0
OD1 A:ASP192 3.7 32.9 1.0
O A:ASP190 3.7 27.9 1.0
O4 A:PO4405 3.9 36.1 1.0
MG A:MG402 4.0 30.8 1.0
C5' P:DC11 4.0 25.4 1.0
O5' P:DC11 4.1 29.4 1.0
O A:HOH541 4.2 20.9 1.0
C A:ASP190 4.2 23.5 1.0
CA A:GLY179 4.4 22.9 1.0
CB A:ASP190 4.4 24.0 1.0
N A:ASP190 4.5 25.3 1.0
OP2 P:DC11 4.5 28.0 1.0
CB A:ASP192 4.5 21.9 1.0
N A:SER180 4.6 21.5 1.0
O2 A:PO4405 4.6 29.8 1.0
CA A:ASP190 4.6 18.8 1.0
O3' P:DC10 4.7 32.0 1.0
OG A:SER180 4.9 31.5 1.0

Magnesium binding site 2 out of 2 in 4ph5

Go back to Magnesium Binding Sites List in 4ph5
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position


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 A Nicked Dna Containing A Ac at N-1 Position and Gc at N Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:30.8
occ:1.00
OD2 A:ASP190 2.0 32.4 1.0
OD2 A:ASP256 2.1 29.0 1.0
OD1 A:ASP192 2.3 32.9 1.0
O3' P:DC10 2.4 32.0 1.0
OP1 P:DC11 2.5 26.8 1.0
P P:DC11 3.0 31.9 1.0
CG A:ASP190 3.1 27.8 1.0
CG A:ASP256 3.1 25.0 1.0
CG A:ASP192 3.3 25.4 1.0
C3' P:DC10 3.6 28.3 1.0
OD2 A:ASP192 3.7 25.4 1.0
OD1 A:ASP190 3.7 27.8 1.0
C4' P:DC10 3.8 31.4 1.0
CB A:ASP256 3.9 23.9 1.0
MG A:MG401 4.0 28.6 1.0
OP2 P:DC11 4.0 28.0 1.0
OD1 A:ASP256 4.1 26.1 1.0
C5' P:DC10 4.1 30.4 1.0
O5' P:DC11 4.1 29.4 1.0
C5' P:DC11 4.3 25.4 1.0
O A:MET191 4.3 21.3 1.0
CB A:ASP190 4.3 24.0 1.0
C2' P:DC10 4.6 27.7 1.0
O5' P:DC10 4.6 30.5 1.0
CB A:ASP192 4.6 21.9 1.0
NH2 A:ARG254 4.8 25.0 1.0
N A:ASP256 4.9 20.4 1.0
C A:MET191 4.9 22.6 1.0
CE1 A:PHE272 4.9 43.6 1.0

Reference:

M.C.Koag, S.Lee. The Spontaneous Base Substitution Mechanisms of Human Dna Polymerase Beta To Be Published.
Page generated: Mon Dec 14 19:19:47 2020

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