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Magnesium in PDB 6n2t: Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Hydroxymethyl-Dc (5-Hmc) at the Templating Position

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

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

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Hydroxymethyl-Dc (5-Hmc) at the Templating Position, PDB code: 6n2t 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) 28.90 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.476, 79.089, 55.556, 90.00, 106.61, 90.00
R / Rfree (%) 19.8 / 29.1

Other elements in 6n2t:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Hydroxymethyl-Dc (5-Hmc) 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- Hydroxymethyl-Dc (5-Hmc) at the Templating Position (pdb code 6n2t). 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- Hydroxymethyl-Dc (5-Hmc) at the Templating Position, PDB code: 6n2t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6n2t

Go back to Magnesium Binding Sites List in 6n2t
Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Hydroxymethyl-Dc (5-Hmc) 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- Hydroxymethyl-Dc (5-Hmc) at the Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:42.7
occ:1.00
 O1A A:1GC405 2.0 38.2 1.0
O2B A:1GC405 2.0 45.8 1.0
OD2 A:ASP192 2.0 45.9 1.0
O1G A:1GC405 2.2 47.5 1.0
OD1 A:ASP190 2.3 35.6 1.0
O A:HOH527 2.6 45.2 1.0
PB A:1GC405 2.9 41.2 1.0
PA A:1GC405 3.1 40.0 1.0
CG A:ASP192 3.1 43.2 1.0
C3A A:1GC405 3.2 35.9 1.0
PG A:1GC405 3.3 40.4 1.0
CG A:ASP190 3.3 37.0 1.0
O3B A:1GC405 3.4 51.0 1.0
MG A:MG402 3.5 40.0 1.0
OD1 A:ASP192 3.6 40.0 1.0
OD2 A:ASP190 3.8 35.3 1.0
C5' A:1GC405 3.9 39.8 1.0
O5' A:1GC405 3.9 47.0 1.0
O1B A:1GC405 4.2 50.0 1.0
O2A A:1GC405 4.3 47.0 1.0
O3G A:1GC405 4.3 47.3 1.0
O A:ASP190 4.3 40.4 1.0
CA A:GLY179 4.3 42.8 1.0
OG A:SER180 4.4 50.4 1.0
O2G A:1GC405 4.4 50.8 1.0
CB A:ASP192 4.4 39.0 1.0
N A:SER180 4.5 41.5 1.0
O P:HOH103 4.5 38.6 1.0
N A:ASP190 4.6 34.4 1.0
CB A:ASP190 4.6 40.3 1.0
C A:ASP190 4.7 44.7 1.0
CA A:ASP190 4.9 38.3 1.0
O A:HOH537 4.9 57.2 1.0
O3' P:DC10 4.9 47.4 1.0

Magnesium binding site 2 out of 2 in 6n2t

Go back to Magnesium Binding Sites List in 6n2t
Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 5- Hydroxymethyl-Dc (5-Hmc) 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- Hydroxymethyl-Dc (5-Hmc) at the Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:40.0
occ:1.00
 OD1 A:ASP192 2.0 40.0 1.0
OD2 A:ASP190 2.1 35.3 1.0
O P:HOH103 2.2 38.6 1.0
OD2 A:ASP256 2.2 38.0 1.0
O1A A:1GC405 2.3 38.2 1.0
O3' P:DC10 2.3 47.4 1.0
CG A:ASP192 2.9 43.2 1.0
CG A:ASP190 3.0 37.0 1.0
OD2 A:ASP192 3.2 45.9 1.0
OD1 A:ASP190 3.3 35.6 1.0
CG A:ASP256 3.3 46.2 1.0
PA A:1GC405 3.4 40.0 1.0
C3' P:DC10 3.5 46.5 1.0
MG A:MG401 3.5 42.7 1.0
O2A A:1GC405 3.7 47.0 1.0
CB A:ASP256 3.9 44.8 1.0
O5' A:1GC405 4.0 47.0 1.0
C5' A:1GC405 4.1 39.8 1.0
C4' P:DC10 4.1 44.5 1.0
C5' P:DC10 4.2 40.6 1.0
CB A:ASP192 4.3 39.0 1.0
OD1 A:ASP256 4.3 47.5 1.0
OP1 P:DC10 4.4 46.5 1.0
CB A:ASP190 4.4 40.3 1.0
O5' P:DC10 4.6 44.9 1.0
C2' P:DC10 4.7 44.9 1.0
O1G A:1GC405 4.9 47.5 1.0
O A:MET191 4.9 47.0 1.0
C3A A:1GC405 4.9 35.9 1.0
CA A:ASP192 5.0 34.6 1.0
O A:HOH537 5.0 57.2 1.0
P P:DC10 5.0 44.4 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 12:24:32 2024

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