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Sodium 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:

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- Carboxy-Dc (5-Cac) at the Templating Position (pdb code 6n2s). 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- Carboxy-Dc (5-Cac) at the Templating Position, PDB code: 6n2s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6n2s

Go back to Sodium Binding Sites List in 6n2s
Sodium 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 Sodium with other atoms in the Na 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:Na403

b:42.7
occ:1.00
 O A:HOH502 2.4 34.0 1.0
O A:ARG102 3.4 41.3 1.0
O A:THR101 3.5 30.7 1.0
O A:VAL103 3.6 32.7 1.0
CA A:SER104 3.6 31.1 1.0
OP1 P:DG9 3.6 35.4 1.0
C A:VAL103 3.7 30.8 1.0
N A:SER104 3.7 31.8 1.0
C A:ARG102 3.8 33.0 1.0
CB A:SER104 4.3 29.9 1.0
N A:VAL103 4.4 34.2 1.0
CA A:ARG102 4.4 31.8 1.0
O5' P:DG9 4.5 46.3 1.0
P P:DG9 4.5 37.2 1.0
OG A:SER104 4.5 32.9 1.0
O A:HOH515 4.6 38.6 1.0
C A:THR101 4.6 31.9 1.0
CA A:VAL103 4.6 31.1 1.0
C A:SER104 4.7 32.4 1.0
N A:GLY105 4.8 33.0 1.0
OP2 P:DG9 4.9 34.9 1.0

Sodium binding site 2 out of 2 in 6n2s

Go back to Sodium Binding Sites List in 6n2s
Sodium 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 Sodium with other atoms in the Na 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:Na404

b:39.9
occ:1.00
 O A:LYS60 2.2 46.6 1.0
O D:HOH103 2.3 40.3 1.0
O A:VAL65 2.3 42.3 1.0
O A:LEU62 2.4 43.8 1.0
OP1 D:DC3 2.8 41.4 1.0
C A:LYS60 3.4 45.9 1.0
C A:VAL65 3.5 41.7 1.0
C A:LEU62 3.5 46.1 1.0
OP2 D:DC3 3.7 53.9 1.0
P D:DC3 3.7 50.8 1.0
O A:LYS61 4.0 49.7 1.0
CG A:LYS60 4.0 49.6 1.0
C A:LYS61 4.0 47.2 1.0
N A:VAL65 4.1 40.7 1.0
CA A:LYS60 4.1 48.5 1.0
CA A:VAL65 4.2 40.7 1.0
CA A:PRO63 4.3 40.0 1.0
N A:LEU62 4.3 49.6 1.0
N A:PRO63 4.3 43.2 1.0
N A:LYS61 4.4 49.9 1.0
N A:GLY66 4.5 46.3 1.0
CA A:LYS61 4.5 49.9 1.0
CB A:VAL65 4.5 45.0 1.0
CA A:LEU62 4.5 41.2 1.0
N A:GLY64 4.7 46.8 1.0
CB A:LYS60 4.7 48.5 1.0
CA A:GLY66 4.7 47.0 1.0
O3' D:DT2 4.8 51.7 1.0
C A:PRO63 4.8 43.5 1.0
NZ A:LYS60 4.8 55.1 1.0
O5' D:DC3 4.9 49.0 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 Dec 15 12:37:47 2020

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