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Sodium in PDB 6e3x: Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp, PDB code: 6e3x was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.74 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.964, 78.948, 54.823, 90.00, 106.53, 90.00
R / Rfree (%) 19.2 / 26.6

Other elements in 6e3x:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp (pdb code 6e3x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp, PDB code: 6e3x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6e3x

Go back to Sodium Binding Sites List in 6e3x
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:35.1
occ:1.00
 O A:LYS60 2.5 40.7 1.0
OP1 D:DC3 2.6 25.8 1.0
O A:VAL65 2.8 30.1 1.0
O A:LEU62 3.2 30.6 1.0
P D:DC3 3.5 25.4 1.0
OP2 D:DC3 3.6 21.9 1.0
C A:LYS60 3.7 31.8 1.0
C A:VAL65 3.8 28.0 1.0
C A:LEU62 4.1 28.8 1.0
CG A:LYS60 4.4 27.5 1.0
N A:VAL65 4.4 28.0 1.0
C A:LYS61 4.4 28.8 1.0
N A:LEU62 4.5 29.4 1.0
CA A:LYS60 4.5 29.5 1.0
CA A:VAL65 4.6 25.8 1.0
N A:LYS61 4.6 28.5 1.0
O5' D:DC3 4.6 25.8 1.0
N A:GLY66 4.6 24.4 1.0
O3' D:DT2 4.7 25.6 1.0
CA A:PRO63 4.7 29.2 1.0
CA A:GLY66 4.7 25.4 1.0
CA A:LYS61 4.7 30.1 1.0
N A:GLY64 4.7 28.5 1.0
O A:LYS61 4.7 30.3 1.0
N A:PRO63 4.7 31.8 1.0
NZ A:LYS60 4.8 31.6 1.0
CA A:LEU62 5.0 26.1 1.0
CB A:VAL65 5.0 28.1 1.0

Sodium binding site 2 out of 2 in 6e3x

Go back to Sodium Binding Sites List in 6e3x
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:17.2
occ:1.00
 OP1 P:DG9 2.3 22.4 1.0
O A:THR101 2.3 17.5 1.0
O A:VAL103 2.4 21.0 1.0
O A:ILE106 2.5 20.5 1.0
O P:HOH102 2.6 17.7 1.0
O A:HOH555 2.7 22.1 1.0
C A:VAL103 3.2 21.2 1.0
O A:HOH501 3.3 24.7 1.0
C A:THR101 3.3 18.4 1.0
P P:DG9 3.5 19.1 1.0
C A:ILE106 3.5 20.5 1.0
CA A:SER104 3.7 19.1 1.0
N A:SER104 3.7 21.7 1.0
OP2 P:DG9 3.9 26.5 1.0
N A:ILE106 3.9 20.7 1.0
N A:GLY105 4.0 22.9 1.0
CA A:THR101 4.0 17.6 1.0
N A:VAL103 4.0 15.6 1.0
C A:ARG102 4.1 21.2 1.0
C A:SER104 4.2 22.2 1.0
CA A:VAL103 4.2 19.3 1.0
CA A:ILE106 4.2 21.9 1.0
N A:ARG102 4.3 18.9 1.0
O A:ARG102 4.5 18.6 1.0
CA A:ARG102 4.5 19.4 1.0
N A:GLY107 4.5 17.2 1.0
O5' P:DG9 4.5 24.6 1.0
O3' P:DC8 4.5 22.3 1.0
CB A:THR101 4.6 22.1 1.0
CB A:ILE106 4.7 23.1 1.0
C A:GLY105 4.8 22.1 1.0
CA A:GLY107 4.8 16.9 1.0
O A:LEU100 4.9 22.9 1.0
CB A:SER104 4.9 22.2 1.0
CA A:GLY105 5.0 21.7 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp To Be Published.
Page generated: Tue Dec 15 12:09:19 2020

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