Atomistry » Magnesium » PDB 4p9d-4pjj » 4ph5
Atomistry »
  Magnesium »
    PDB 4p9d-4pjj »
      4ph5 »

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: Tue Aug 20 01:20:49 2024

Last articles

Ca in 5S5U
Ca in 5S5T
Ca in 5S5S
Ca in 5S5R
Ca in 5S5Q
Ca in 5S5P
Ca in 5S5O
Ca in 5S5N
Ca in 5S5M
Ca in 5S5L
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy