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Sodium in PDB 6pkz: Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

Enzymatic activity of Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

All present enzymatic activity of Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 6pkz 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) 19.64 / 2.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.609, 78.555, 54.776, 90.00, 106.83, 90.00
R / Rfree (%) 17.5 / 24.9

Other elements in 6pkz:

The structure of Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp (pdb code 6pkz). 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 N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 6pkz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6pkz

Go back to Sodium Binding Sites List in 6pkz
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


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 N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:12.7
occ:1.00
O A:THR101 2.1 20.0 1.0
OP1 P:DG9 2.4 16.1 1.0
O A:ILE106 2.5 17.9 1.0
O A:VAL103 2.7 13.2 1.0
O P:HOH101 2.8 17.3 1.0
O A:HOH539 3.0 18.9 1.0
C A:THR101 3.3 17.6 1.0
P P:DG9 3.4 17.2 1.0
C A:VAL103 3.5 14.2 1.0
C A:ILE106 3.6 15.5 1.0
OP2 P:DG9 3.7 17.3 1.0
CA A:SER104 3.7 14.8 1.0
N A:SER104 3.9 17.0 1.0
CA A:THR101 4.0 16.4 1.0
N A:ILE106 4.1 15.1 1.0
N A:GLY105 4.1 16.4 1.0
C A:ARG102 4.2 15.3 1.0
N A:ARG102 4.3 13.5 1.0
C A:SER104 4.4 15.4 1.0
N A:VAL103 4.4 13.2 1.0
O5' P:DG9 4.4 16.8 1.0
CA A:ILE106 4.4 13.0 1.0
CA A:ARG102 4.5 14.7 1.0
CB A:THR101 4.5 17.6 1.0
O A:ARG102 4.5 14.4 1.0
N A:GLY107 4.6 16.4 1.0
CA A:VAL103 4.6 14.2 1.0
O3' P:DC8 4.7 18.2 1.0
CA A:GLY107 4.8 15.3 1.0
CB A:ILE106 4.8 17.1 1.0
CB A:SER104 4.9 15.8 1.0
C A:GLY105 5.0 15.6 1.0

Sodium binding site 2 out of 2 in 6pkz

Go back to Sodium Binding Sites List in 6pkz
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp


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 N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:30.2
occ:1.00
O A:LYS60 2.5 29.8 1.0
OP1 D:DC3 2.9 25.4 1.0
O A:VAL65 2.9 24.4 1.0
O A:LEU62 3.3 27.1 1.0
OP2 D:DC3 3.6 20.0 1.0
C A:LYS60 3.7 23.2 1.0
P D:DC3 3.7 21.9 1.0
C A:VAL65 4.1 21.9 1.0
C A:LEU62 4.2 25.2 1.0
CG A:LYS60 4.2 19.7 1.0
C A:LYS61 4.3 23.4 1.0
O A:LYS61 4.5 25.7 1.0
N A:LEU62 4.5 24.1 1.0
CA A:LYS60 4.6 23.3 1.0
CA A:LYS61 4.6 21.9 1.0
N A:LYS61 4.6 23.5 1.0
CA A:PRO63 4.7 21.1 1.0
N A:GLY64 4.8 23.8 1.0
N A:VAL65 4.8 23.0 1.0
N A:PRO63 4.8 24.3 1.0
O5' D:DC3 4.9 20.8 1.0
O3' D:DT2 4.9 24.0 1.0
NZ A:LYS60 4.9 28.3 1.0
CA A:GLY66 4.9 19.8 1.0
N A:GLY66 5.0 19.3 1.0
CB A:LYS60 5.0 21.2 1.0

Reference:

M.C.Koag, S.Lee. Structure of Human Dna Polymerase Beta N279A Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp To Be Published.
Page generated: Tue Oct 8 12:43:44 2024

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