Magnesium in PDB 6mq8: Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine

Enzymatic activity of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine

All present enzymatic activity of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine:
2.7.7.7;

Protein crystallography data

The structure of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine, PDB code: 6mq8 was solved by M.A.Hawkins, H.Jung, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 1.97
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.539, 98.539, 81.664, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 20.8

Other elements in 6mq8:

The structure of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine (pdb code 6mq8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine, PDB code: 6mq8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6mq8

Go back to Magnesium Binding Sites List in 6mq8
Magnesium binding site 1 out of 2 in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:15.9
occ:1.00
OD1 A:ASP13 2.0 19.4 1.0
OD2 A:ASP115 2.0 18.4 1.0
O1A A:0KX501 2.0 18.8 1.0
O2B A:0KX501 2.1 16.6 1.0
O2G A:0KX501 2.1 17.4 1.0
O A:MET14 2.2 15.3 1.0
CG A:ASP13 3.0 21.4 1.0
CG A:ASP115 3.1 20.2 1.0
PB A:0KX501 3.1 18.6 1.0
H7 A:0KX501 3.2 22.9 1.0
PA A:0KX501 3.3 20.6 1.0
OD2 A:ASP13 3.3 22.0 1.0
HZ2 A:LYS231 3.3 22.3 1.0
C A:MET14 3.4 16.5 1.0
PG A:0KX501 3.4 18.0 1.0
MG A:MG503 3.4 17.9 0.9
HZ3 A:LYS231 3.5 22.3 1.0
N3A A:0KX501 3.5 19.4 1.0
OD1 A:ASP115 3.6 19.1 1.0
O A:HOH643 3.7 21.2 1.0
O3B A:0KX501 3.7 16.8 1.0
NZ A:LYS231 3.9 18.6 1.0
C5' A:0KX501 3.9 19.1 1.0
N A:MET14 3.9 17.2 1.0
H A:MET14 4.0 20.6 1.0
HB2 A:PHE17 4.0 17.2 1.0
HB2 A:MET14 4.0 19.9 1.0
H A:PHE17 4.1 17.5 1.0
O1G A:0KX501 4.1 17.2 1.0
H6 A:0KX501 4.1 22.9 1.0
HA A:ASP15 4.1 19.9 1.0
HE3 A:LYS231 4.1 27.7 1.0
O5' A:0KX501 4.2 20.4 1.0
CA A:MET14 4.2 15.9 1.0
C A:ASP13 4.2 18.4 1.0
CB A:ASP13 4.3 19.7 1.0
O A:HOH715 4.3 17.9 1.0
H5 A:0KX501 4.3 23.2 1.0
HB2 A:ASP115 4.4 21.8 1.0
CB A:ASP115 4.4 18.1 1.0
H A:CYS16 4.4 20.5 1.0
N A:ASP15 4.4 16.4 1.0
O2A A:0KX501 4.4 18.8 1.0
O1B A:0KX501 4.5 16.2 1.0
HB3 A:ASP13 4.5 23.7 1.0
O3G A:0KX501 4.6 19.3 1.0
O A:ASP13 4.6 16.6 1.0
HZ1 A:LYS231 4.6 22.3 1.0
CE A:LYS231 4.6 23.1 1.0
CA A:ASP15 4.6 16.6 1.0
N A:CYS16 4.6 17.1 1.0
CB A:MET14 4.7 16.6 1.0
CA A:ASP13 4.7 18.7 1.0
HA A:ASP13 4.7 22.5 1.0
HB3 A:ASP115 4.7 21.8 1.0
O A:ASP115 4.8 18.4 1.0
C A:ASP15 4.8 17.4 1.0
N A:PHE17 4.8 14.6 1.0
CB A:PHE17 4.8 14.4 1.0
HB3 A:PHE17 4.9 17.2 1.0
HA A:CYS16 5.0 19.9 1.0
O3' P:DT8 5.0 19.1 1.0
HB2 A:ASP13 5.0 23.7 1.0

Magnesium binding site 2 out of 2 in 6mq8

Go back to Magnesium Binding Sites List in 6mq8
Magnesium binding site 2 out of 2 in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:17.9
occ:0.95
OD2 A:ASP13 2.0 22.0 1.0
OE2 A:GLU116 2.1 22.9 1.0
OD1 A:ASP115 2.1 19.1 1.0
O3' P:DT8 2.2 19.1 1.0
O A:HOH715 2.2 17.9 1.0
O1A A:0KX501 2.2 18.8 1.0
CG A:ASP13 3.0 21.4 1.0
CG A:ASP115 3.0 20.2 1.0
CD A:GLU116 3.1 23.6 1.0
HG A:SER113 3.1 24.9 1.0
PA A:0KX501 3.2 20.6 1.0
OD2 A:ASP115 3.3 18.4 1.0
C3' P:DT8 3.3 22.5 1.0
H3' P:DT8 3.4 27.0 1.0
HB3 A:GLU116 3.4 25.8 1.0
OD1 A:ASP13 3.4 19.4 1.0
MG A:MG502 3.4 15.9 1.0
O2A A:0KX501 3.5 18.8 1.0
H6 A:0KX501 3.7 22.9 1.0
O5' A:0KX501 3.7 20.4 1.0
OE1 A:GLU116 3.8 22.4 1.0
OG A:SER113 3.9 20.8 1.0
H4' P:DT8 4.0 26.3 1.0
HZ3 A:LYS224 4.0 29.7 1.0
HZ2 A:LYS224 4.0 29.7 1.0
C5' A:0KX501 4.0 19.1 1.0
CG A:GLU116 4.1 20.1 1.0
O A:HOH643 4.1 21.2 1.0
H7 A:0KX501 4.1 22.9 1.0
H5'' P:DT8 4.1 31.2 1.0
C4' P:DT8 4.1 21.9 1.0
CB A:GLU116 4.1 21.5 1.0
HG2 A:GLU116 4.3 24.1 1.0
NZ A:LYS224 4.3 24.7 1.0
HZ1 A:LYS224 4.4 29.7 1.0
CB A:ASP13 4.4 19.7 1.0
HB2 A:ASP13 4.4 23.7 1.0
CB A:ASP115 4.4 18.1 1.0
H2'' P:DT8 4.4 25.6 1.0
O A:HOH746 4.5 19.6 1.0
C2' P:DT8 4.5 21.3 1.0
C A:ASP115 4.6 20.4 1.0
O A:ASP115 4.6 18.4 1.0
C5' P:DT8 4.6 26.0 1.0
O2G A:0KX501 4.7 17.4 1.0
H A:ASP115 4.7 22.6 1.0
HB3 A:ASP115 4.7 21.8 1.0
N3A A:0KX501 4.7 19.4 1.0
HA A:ASP13 4.7 22.5 1.0
HB2 A:GLU116 4.8 25.8 1.0
N A:GLU116 4.8 18.4 1.0
O2B A:0KX501 4.8 16.6 1.0
HG3 A:GLU116 4.9 24.1 1.0
O A:HOH795 4.9 23.3 1.0
CB A:SER113 5.0 21.7 1.0
CA A:ASP115 5.0 18.2 1.0
HB3 A:SER113 5.0 26.0 1.0

Reference:

M.A.Hawkins, J.Hunmin, S.Lee. Structural Analysis of Translesion Synthesis Across Hypoxanthine Lesion Using Human Dna Polymerase Eta To Be Published.
Page generated: Mon Dec 14 23:37:52 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy