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Sodium in PDB 6mq8: Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine

Enzymatic activity of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine

All present enzymatic activity of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine:
2.7.7.7;

Protein crystallography data

The structure of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine, PDB code: 6mq8 was solved by M.A.Hawkins, H.Jung, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 1.97
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.539, 98.539, 81.664, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 20.8

Other elements in 6mq8:

The structure of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine (pdb code 6mq8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine, PDB code: 6mq8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6mq8

Go back to Sodium Binding Sites List in 6mq8
Sodium binding site 1 out of 2 in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:51.1
occ:1.00
O A:HOH876 2.4 39.8 1.0
O A:ASP358 2.9 30.9 1.0
HA A:ASP358 3.0 37.1 1.0
CA A:ASP358 3.7 30.9 1.0
C A:ASP358 3.7 30.1 1.0
HB3 A:ASP358 4.0 39.2 1.0
O A:HOH823 4.2 40.2 1.0
CB A:ASP358 4.3 32.7 1.0
O A:HOH902 4.4 42.5 1.0
O A:ASN357 4.4 31.3 1.0
OD1 A:ASP358 4.5 34.9 1.0
CG A:ASP358 4.7 40.8 1.0
N A:ASP358 4.9 30.8 1.0
N A:ASN359 5.0 27.2 1.0

Sodium binding site 2 out of 2 in 6mq8

Go back to Sodium Binding Sites List in 6mq8
Sodium binding site 2 out of 2 in the Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Structure of Dna Polymerase Eta in Complex with Templating Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:38.6
occ:1.00
OP2 P:DT8 2.1 30.1 1.0
O P:HOH221 2.2 41.3 1.0
O5' P:DT8 2.4 28.0 1.0
H3' P:DA7 2.6 36.1 1.0
P P:DT8 2.7 36.4 1.0
O P:HOH207 2.8 29.5 1.0
O A:HOH896 2.8 39.2 1.0
H2' P:DA7 3.0 32.3 1.0
H2'' P:DA7 3.1 32.3 1.0
C3' P:DA7 3.1 30.1 1.0
H6 P:DT8 3.1 25.4 1.0
C2' P:DA7 3.2 26.9 1.0
O3' P:DA7 3.3 36.4 1.0
H3' P:DT8 3.3 27.0 1.0
H2' P:DT8 3.5 25.6 1.0
C5' P:DT8 3.7 26.0 1.0
C3' P:DT8 4.0 22.5 1.0
C6 P:DT8 4.1 21.1 1.0
OP1 P:DT8 4.1 31.2 1.0
H5' P:DT8 4.2 31.2 1.0
C2' P:DT8 4.2 21.3 1.0
H73 P:DT8 4.2 30.1 1.0
C4' P:DT8 4.2 21.9 1.0
O4' P:DT8 4.2 20.3 1.0
H72 P:DT8 4.3 30.1 1.0
H5'' P:DT8 4.3 31.2 1.0
HZ3 A:LYS224 4.5 29.7 1.0
C4' P:DA7 4.6 30.0 1.0
C7 P:DT8 4.6 25.0 1.0
HE2 A:LYS224 4.6 35.2 1.0
C1' P:DT8 4.7 22.4 1.0
C1' P:DA7 4.7 26.5 1.0
C5 P:DT8 4.8 22.3 1.0
N1 P:DT8 4.9 22.3 1.0
O P:HOH220 4.9 36.9 1.0
O A:HOH715 5.0 17.9 1.0
O5' P:DA7 5.0 22.6 1.0

Reference:

M.A.Hawkins, J.Hunmin, S.Lee. Structural Analysis of Translesion Synthesis Across Hypoxanthine Lesion Using Human Dna Polymerase Eta To Be Published.
Page generated: Tue Dec 15 12:36:37 2020

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