Atomistry » Magnesium » PDB 6mxd-6n6n » 6n2s
Atomistry »
  Magnesium »
    PDB 6mxd-6n6n »
      6n2s »

Magnesium in PDB 6n2s: Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position, PDB code: 6n2s was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.22 / 2.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.066, 79.631, 55.427, 90.00, 106.46, 90.00
R / Rfree (%) 20.2 / 29

Other elements in 6n2s:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position (pdb code 6n2s). 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 Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position, PDB code: 6n2s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6n2s

Go back to Magnesium Binding Sites List in 6n2s
Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:31.7
occ:1.00
 O1G A:1GC405 1.8 28.8 1.0
O1A A:1GC405 1.9 32.0 1.0
OD1 A:ASP190 2.0 28.9 1.0
O2B A:1GC405 2.2 31.5 1.0
OD2 A:ASP192 2.3 33.4 1.0
O A:HOH531 2.4 32.2 1.0
PB A:1GC405 3.0 34.4 1.0
PA A:1GC405 3.1 33.9 1.0
CG A:ASP190 3.1 31.0 1.0
PG A:1GC405 3.1 30.4 1.0
C3A A:1GC405 3.2 32.3 1.0
O3B A:1GC405 3.3 43.5 1.0
CG A:ASP192 3.4 35.8 1.0
OD2 A:ASP190 3.5 28.0 1.0
MG A:MG402 3.6 24.9 1.0
OD1 A:ASP192 3.8 33.4 1.0
O2G A:1GC405 4.0 37.0 1.0
O5' A:1GC405 4.1 35.6 1.0
O2A A:1GC405 4.1 37.7 1.0
C5' A:1GC405 4.1 28.3 1.0
O3G A:1GC405 4.2 40.3 1.0
O A:ASP190 4.2 30.8 1.0
N A:ASP190 4.2 32.6 1.0
OG A:SER180 4.3 37.4 1.0
CB A:ASP190 4.3 30.1 1.0
C A:ASP190 4.4 32.7 1.0
O1B A:1GC405 4.4 42.0 1.0
N A:SER180 4.5 34.8 1.0
O P:HOH102 4.5 25.5 1.0
CA A:ASP190 4.6 33.4 1.0
CA A:GLY179 4.6 30.7 1.0
CB A:ASP192 4.6 31.7 1.0
O A:HOH520 4.7 34.9 1.0
O3' P:DC10 5.0 32.6 1.0

Magnesium binding site 2 out of 2 in 6n2s

Go back to Magnesium Binding Sites List in 6n2s
Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Carboxy-Dc (5-Cac) at the Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:24.9
occ:1.00
 OD2 A:ASP190 1.9 28.0 1.0
O P:HOH102 2.1 25.5 1.0
OD1 A:ASP192 2.1 33.4 1.0
OD2 A:ASP256 2.3 32.3 1.0
O3' P:DC10 2.3 32.6 1.0
O1A A:1GC405 2.5 32.0 1.0
CG A:ASP190 2.9 31.0 1.0
CG A:ASP192 3.1 35.8 1.0
OD1 A:ASP190 3.3 28.9 1.0
CG A:ASP256 3.4 31.2 1.0
OD2 A:ASP192 3.4 33.4 1.0
C3' P:DC10 3.5 31.4 1.0
PA A:1GC405 3.5 33.9 1.0
MG A:MG401 3.6 31.7 1.0
O2A A:1GC405 3.7 37.7 1.0
CB A:ASP256 3.9 33.7 1.0
O5' A:1GC405 4.1 35.6 1.0
C4' P:DC10 4.1 34.4 1.0
C5' P:DC10 4.2 31.3 1.0
C5' A:1GC405 4.2 28.3 1.0
CB A:ASP190 4.3 30.1 1.0
OP1 P:DC10 4.4 41.5 1.0
CB A:ASP192 4.4 31.7 1.0
OD1 A:ASP256 4.4 36.8 1.0
O5' P:DC10 4.5 40.9 1.0
NH2 A:ARG254 4.7 36.9 1.0
C2' P:DC10 4.7 29.5 1.0
O A:MET191 4.8 33.8 1.0
CA A:ASP192 4.9 33.2 1.0

Reference:

M.J.Howard, K.G.Foley, D.D.Shock, V.K.Batra, S.H.Wilson. Molecular Basis For the Faithful Replication of 5-Methylcytosine and Its Oxidized Forms By Dna Polymerase Beta. J.Biol.Chem. V. 294 7194 2019.
ISSN: ESSN 1083-351X
PubMed: 30885943
DOI: 10.1074/JBC.RA118.006809
Page generated: Tue Oct 1 12:24:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy