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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

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