Atomistry » Magnesium » PDB 3gx3-3hd1 » 3h4d
Atomistry »
  Magnesium »
    PDB 3gx3-3hd1 »
      3h4d »

Magnesium in PDB 3h4d: Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp

Enzymatic activity of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp, PDB code: 3h4d was solved by R.Jain, D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.68 / 2.20
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.915, 97.915, 203.392, 90.00, 90.00, 120.00
R / Rfree (%) 25.4 / 27

Other elements in 3h4d:

The structure of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp (pdb code 3h4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp, PDB code: 3h4d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3h4d

Go back to Magnesium Binding Sites List in 3h4d
Magnesium binding site 1 out of 2 in the Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg871

b:64.0
occ:1.00
O1A T:DGT875 2.1 45.8 0.7
OD2 A:ASP34 2.2 26.6 1.0
O A:LEU35 2.3 27.9 1.0
O2B T:DGT875 2.7 40.4 0.7
O1G T:DGT875 2.8 42.3 0.7
MG A:MG872 2.9 58.6 1.0
OD2 A:ASP126 3.0 33.3 1.0
CG A:ASP126 3.2 33.3 1.0
PA T:DGT875 3.4 46.6 0.7
C A:LEU35 3.4 26.3 1.0
CG A:ASP34 3.4 27.4 1.0
OD1 A:ASP126 3.5 36.6 1.0
PB T:DGT875 3.6 47.3 0.7
N A:LEU35 3.6 26.4 1.0
O3A T:DGT875 3.7 45.5 0.7
O A:HOH452 3.8 45.6 1.0
CA A:LEU35 3.9 27.9 1.0
C5' T:DGT875 4.0 47.5 0.7
CB A:ASP126 4.0 29.8 1.0
OD1 A:ASP34 4.0 28.4 1.0
PG T:DGT875 4.1 44.4 0.7
O5' T:DGT875 4.1 45.2 0.7
O3B T:DGT875 4.2 42.6 0.7
C A:ASP34 4.2 25.4 1.0
O A:HOH475 4.3 39.6 1.0
CB A:LEU35 4.5 29.4 1.0
O2A T:DGT875 4.5 48.9 0.7
N A:ASP36 4.6 26.3 1.0
CB A:ASP34 4.6 25.3 1.0
CA A:ASP34 4.6 24.4 1.0
O A:ASP126 4.7 26.5 1.0
O1B T:DGT875 4.8 41.2 0.7
N A:CYS37 4.9 24.5 1.0
O A:ASP34 4.9 25.5 1.0
CA A:ASP36 4.9 26.4 1.0
O3G T:DGT875 4.9 40.7 0.7
CG A:GLU127 5.0 22.4 1.0
C A:ASP36 5.0 25.9 1.0

Magnesium binding site 2 out of 2 in 3h4d

Go back to Magnesium Binding Sites List in 3h4d
Magnesium binding site 2 out of 2 in the Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Human Dna Polymerase Iota with Template U/T and Incoming Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg872

b:58.6
occ:1.00
O1A T:DGT875 2.0 45.8 0.7
OE2 A:GLU127 2.4 26.6 1.0
MG A:MG871 2.9 64.0 1.0
OD2 A:ASP34 3.0 26.6 1.0
PA T:DGT875 3.0 46.6 0.7
OD1 A:ASP126 3.1 36.6 1.0
OD1 A:ASP34 3.1 28.4 1.0
O2A T:DGT875 3.2 48.9 0.7
CD A:GLU127 3.2 26.4 1.0
CG A:ASP34 3.3 27.4 1.0
CG A:GLU127 3.3 22.4 1.0
C3' P:DOC873 3.4 37.8 1.0
O A:HOH475 3.5 39.6 1.0
OD2 A:ASP126 3.6 33.3 1.0
CG A:ASP126 3.7 33.3 1.0
O5' T:DGT875 4.1 45.2 0.7
O3A T:DGT875 4.2 45.5 0.7
O1G T:DGT875 4.2 42.3 0.7
OE1 A:GLU127 4.4 25.5 1.0
O A:HOH6 4.4 26.9 1.0
C2' P:DOC873 4.5 36.5 1.0
C4' P:DOC873 4.5 40.2 1.0
CB A:ASP34 4.7 25.3 1.0
CB A:GLU127 4.8 22.4 1.0
C5' T:DGT875 4.8 47.5 0.7
O2B T:DGT875 5.0 40.4 0.7

Reference:

R.Jain, D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Replication Across Template T/U By Human Dna Polymerase-Iota. Structure V. 17 974 2009.
ISSN: ISSN 0969-2126
PubMed: 19604477
DOI: 10.1016/J.STR.2009.04.011
Page generated: Mon Dec 14 08:13:07 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy