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Sodium 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:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6n2t

Go back to Sodium Binding Sites List in 6n2t
Sodium 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 Sodium with other atoms in the Na 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:Na403

b:41.3
occ:1.00
 OP1 P:DG9 2.3 43.3 1.0
O A:THR101 2.4 42.5 1.0
O P:HOH102 2.4 44.2 1.0
O A:ILE106 2.7 47.3 1.0
O A:HOH536 2.7 40.5 1.0
O A:VAL103 2.7 42.0 1.0
P P:DG9 3.3 37.8 1.0
OP2 P:DG9 3.4 40.8 1.0
C A:VAL103 3.5 42.3 1.0
C A:THR101 3.6 38.8 1.0
CA A:SER104 3.7 38.8 1.0
C A:ILE106 3.7 45.6 1.0
N A:GLY105 3.8 36.8 1.0
N A:SER104 3.9 44.9 1.0
N A:ILE106 4.0 41.8 1.0
C A:SER104 4.1 42.8 1.0
CA A:THR101 4.3 35.8 1.0
O3' P:DC8 4.3 42.6 1.0
N A:VAL103 4.4 44.9 1.0
CA A:ILE106 4.4 43.1 1.0
O5' P:DG9 4.4 44.5 1.0
C A:ARG102 4.5 47.0 1.0
N A:ARG102 4.6 39.4 1.0
CA A:VAL103 4.6 41.0 1.0
N A:GLY107 4.6 41.7 1.0
C A:GLY105 4.7 44.5 1.0
CA A:ARG102 4.7 44.2 1.0
CA A:GLY105 4.8 39.0 1.0
O A:ARG102 4.8 48.0 1.0
CA A:GLY107 4.9 40.9 1.0
CB A:THR101 4.9 43.6 1.0
CB A:ILE106 4.9 45.7 1.0
C5' P:DG9 4.9 38.4 1.0
CB A:SER104 5.0 35.9 1.0

Sodium binding site 2 out of 2 in 6n2t

Go back to Sodium Binding Sites List in 6n2t
Sodium 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 Sodium with other atoms in the Na 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:Na404

b:68.1
occ:1.00
 O A:VAL65 2.2 64.9 1.0
O A:LYS60 2.4 64.6 1.0
O A:LEU62 2.9 62.2 1.0
OP1 D:DC3 2.9 58.4 1.0
OP2 D:DC3 3.2 57.9 1.0
C A:VAL65 3.4 59.4 1.0
P D:DC3 3.5 67.5 1.0
C A:LYS60 3.6 65.6 1.0
CG A:LYS60 3.9 65.3 1.0
C A:LEU62 4.0 56.9 1.0
CA A:LYS60 4.3 62.8 1.0
N A:GLY66 4.3 58.6 1.0
CA A:GLY66 4.3 58.6 1.0
N A:VAL65 4.4 60.7 1.0
CA A:VAL65 4.4 59.6 1.0
N A:LEU62 4.6 57.2 1.0
CA A:PRO63 4.6 55.6 1.0
C A:LYS61 4.6 55.8 1.0
N A:LYS61 4.7 65.6 1.0
O5' D:DC3 4.7 66.2 1.0
CB A:LYS60 4.7 65.5 1.0
O3' D:DT2 4.7 64.9 1.0
CD A:LYS60 4.8 66.0 1.0
CE A:LYS60 4.8 66.1 1.0
CB A:VAL65 4.8 55.6 1.0
N A:PRO63 4.8 52.6 1.0
N A:GLY64 4.9 56.2 1.0
CA A:LYS61 4.9 62.5 1.0
O A:LYS61 5.0 60.7 1.0
CA A:LEU62 5.0 56.2 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 8 12:08:15 2024

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