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Sodium in PDB 7mz2: Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp, PDB code: 7mz2 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) 19.87 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.809, 80.181, 55.414, 90, 107.56, 90
R / Rfree (%) 19.7 / 24.3

Other elements in 7mz2:

The structure of Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp 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 Dza at N-1 of the Template Base Paired with Incoming Dttp (pdb code 7mz2). 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 Dza at N-1 of the Template Base Paired with Incoming Dttp, PDB code: 7mz2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7mz2

Go back to Sodium Binding Sites List in 7mz2
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp


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 Dza at N-1 of the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:13.1
occ:1.00
O A:THR101 2.3 14.5 1.0
OP1 P:DG9 2.4 13.3 1.0
O A:ILE106 2.4 11.2 1.0
O A:VAL103 2.4 8.8 1.0
O P:HOH104 2.5 17.3 1.0
O A:HOH605 2.8 13.1 1.0
C A:THR101 3.3 11.3 1.0
C A:VAL103 3.4 10.4 1.0
C A:ILE106 3.4 10.4 1.0
P P:DG9 3.5 14.4 1.0
OP2 P:DG9 3.6 13.2 1.0
N A:ILE106 3.8 9.4 1.0
CA A:THR101 3.9 12.5 1.0
CA A:SER104 3.9 13.6 1.0
N A:GLY105 3.9 12.5 1.0
N A:SER104 4.0 8.4 1.0
CA A:ILE106 4.0 9.8 1.0
N A:VAL103 4.1 11.5 1.0
N A:ARG102 4.3 10.4 1.0
C A:ARG102 4.3 14.0 1.0
C A:SER104 4.3 12.5 1.0
CA A:VAL103 4.4 12.3 1.0
N A:GLY107 4.4 11.3 1.0
CB A:ILE106 4.4 11.4 1.0
O3' P:DC8 4.4 10.8 1.0
CB A:THR101 4.5 11.2 1.0
CA A:ARG102 4.6 13.2 1.0
C A:GLY105 4.6 11.1 1.0
O5' P:DG9 4.7 18.3 1.0
CA A:GLY107 4.7 10.6 1.0
O A:ARG102 4.8 15.3 1.0
O A:LEU100 4.8 11.7 1.0
CA A:GLY105 4.9 10.2 1.0

Sodium binding site 2 out of 2 in 7mz2

Go back to Sodium Binding Sites List in 7mz2
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp


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 Dza at N-1 of the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:23.4
occ:1.00
O A:HOH592 2.4 19.7 1.0
O A:LEU62 2.5 24.3 1.0
O A:LYS60 2.5 22.6 1.0
O A:VAL65 2.5 20.6 1.0
OP1 D:DC3 2.5 18.0 1.0
C A:LEU62 3.4 24.6 1.0
C A:VAL65 3.5 19.9 1.0
C A:LYS60 3.6 23.2 1.0
P D:DC3 3.6 22.3 1.0
N A:VAL65 3.8 19.1 1.0
OP2 D:DC3 3.8 21.4 1.0
N A:LEU62 4.1 20.8 1.0
N A:GLY64 4.1 16.4 1.0
CA A:VAL65 4.1 18.2 1.0
C A:LYS61 4.1 22.6 1.0
CA A:PRO63 4.2 19.8 1.0
N A:PRO63 4.2 23.8 1.0
CA A:LYS60 4.4 20.6 1.0
O A:LYS61 4.4 22.8 1.0
CA A:LEU62 4.4 17.9 1.0
CB A:VAL65 4.5 16.7 1.0
N A:LYS61 4.5 17.7 1.0
O3' D:DT2 4.5 23.0 1.0
C A:PRO63 4.6 19.3 1.0
CG A:LYS60 4.6 25.0 1.0
N A:GLY66 4.6 17.9 1.0
CA A:LYS61 4.6 21.9 1.0
C A:GLY64 4.8 17.9 1.0
O5' D:DC3 4.8 31.0 1.0
CA A:GLY66 4.9 19.2 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with Dza at N-1 of the Template Base Paired with Incoming Dttp To Be Published.
Page generated: Tue Oct 8 18:02:37 2024

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