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Sodium in PDB 4phe: Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with T 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 Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 4phe 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) 20.00 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.535, 79.093, 54.796, 90.00, 105.78, 90.00
R / Rfree (%) 21.6 / 26.1

Other elements in 4phe:

The structure of Structure of Human Dna Polymerase Beta Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp 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 T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp (pdb code 4phe). 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 T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp, PDB code: 4phe:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4phe

Go back to Sodium Binding Sites List in 4phe
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with T 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 Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:18.0
occ:1.00
 O A:THR101 2.3 19.5 1.0
OP1 P:DG9 2.3 18.9 1.0
O A:VAL103 2.4 18.1 1.0
O A:ILE106 2.5 20.3 1.0
O A:HOH529 2.6 21.8 1.0
C A:THR101 3.3 17.7 1.0
C A:VAL103 3.3 19.8 1.0
C A:ILE106 3.4 17.1 1.0
P P:DG9 3.4 19.7 1.0
O A:HOH551 3.7 28.8 1.0
OP2 P:DG9 3.7 16.7 1.0
N A:ILE106 3.7 16.1 1.0
CA A:SER104 3.9 20.5 1.0
N A:GLY105 3.9 16.7 1.0
CA A:THR101 3.9 18.9 1.0
N A:SER104 3.9 21.0 1.0
CA A:ILE106 4.0 16.5 1.0
N A:VAL103 4.1 16.3 1.0
C A:SER104 4.3 17.5 1.0
C A:ARG102 4.3 21.2 1.0
N A:ARG102 4.3 21.6 1.0
N A:GLY107 4.4 18.9 1.0
CA A:VAL103 4.4 16.9 1.0
CB A:THR101 4.5 20.3 1.0
CB A:ILE106 4.5 16.7 1.0
O3' P:DC8 4.5 19.6 1.0
O5' P:DG9 4.5 21.6 1.0
C A:GLY105 4.6 15.6 1.0
CA A:GLY107 4.6 17.9 1.0
CA A:ARG102 4.6 19.7 1.0
O A:ARG102 4.8 20.8 1.0
CA A:GLY105 4.8 17.4 1.0
O A:LEU100 4.9 18.8 1.0

Sodium binding site 2 out of 2 in 4phe

Go back to Sodium Binding Sites List in 4phe
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with T 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 Complexed with T in the Template Base Paired with Incoming Non-Hydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:33.4
occ:1.00
 O A:VAL65 2.4 31.0 1.0
O D:HOH109 2.4 29.3 1.0
O A:LYS60 2.5 30.6 1.0
OP1 D:DC3 2.5 27.1 1.0
O A:LEU62 2.6 29.4 1.0
C A:VAL65 3.5 22.5 1.0
P D:DC3 3.6 26.9 1.0
C A:LYS60 3.6 29.8 1.0
C A:LEU62 3.6 28.0 1.0
OP2 D:DC3 3.8 22.7 1.0
N A:VAL65 3.9 20.9 1.0
CA A:VAL65 4.2 23.4 1.0
N A:GLY64 4.3 28.8 1.0
CA A:PRO63 4.3 27.2 1.0
C A:LYS61 4.3 26.6 1.0
N A:PRO63 4.3 28.6 1.0
O A:LYS61 4.4 33.7 1.0
N A:LEU62 4.4 25.3 1.0
CA A:LYS60 4.4 24.6 1.0
CG A:LYS60 4.4 32.2 1.0
CB A:VAL65 4.5 24.9 1.0
N A:GLY66 4.5 19.9 1.0
O3' D:DT2 4.6 25.3 1.0
N A:LYS61 4.6 29.2 1.0
CA A:LEU62 4.6 23.6 1.0
C A:PRO63 4.7 32.6 1.0
CA A:LYS61 4.8 27.7 1.0
CA A:GLY66 4.8 18.7 1.0
O5' D:DC3 4.8 23.2 1.0
C A:GLY64 4.9 27.6 1.0

Reference:

M.C.Koag, S.Lee. The Spontaneous Base Substitution Mechanisms of Human Dna Polymerase Beta To Be Published.
Page generated: Mon Oct 7 17:43:30 2024

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