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Sodium in PDB 7mz4: Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in 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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp, PDB code: 7mz4 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) 20.09 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.706, 80.183, 54.927, 90, 108.64, 90
R / Rfree (%) 21.6 / 27

Other elements in 7mz4:

The structure of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in 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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp (pdb code 7mz4). 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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp, PDB code: 7mz4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7mz4

Go back to Sodium Binding Sites List in 7mz4
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in 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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:15.8
occ:1.00
 OP1 P:DG9 2.3 16.5 1.0
O A:THR101 2.4 16.8 1.0
O A:ILE106 2.4 17.3 1.0
O A:VAL103 2.5 13.8 1.0
O P:HOH109 2.5 18.9 1.0
O A:HOH594 2.6 16.8 1.0
C A:THR101 3.3 17.1 1.0
C A:ILE106 3.3 16.6 1.0
C A:VAL103 3.4 19.0 1.0
P P:DG9 3.4 19.4 1.0
O A:HOH506 3.5 21.8 1.0
OP2 P:DG9 3.7 17.9 1.0
N A:ILE106 3.8 14.8 1.0
CA A:THR101 3.8 18.9 1.0
N A:GLY105 3.9 18.2 1.0
CA A:SER104 4.0 17.7 1.0
CA A:ILE106 4.0 14.4 1.0
N A:SER104 4.1 17.7 1.0
N A:VAL103 4.2 14.8 1.0
N A:GLY107 4.3 16.2 1.0
N A:ARG102 4.3 19.5 1.0
CB A:THR101 4.3 18.3 1.0
C A:SER104 4.4 16.1 1.0
C A:ARG102 4.4 19.6 1.0
CA A:VAL103 4.5 17.6 1.0
CB A:ILE106 4.5 15.8 1.0
O5' P:DG9 4.5 22.2 1.0
O3' P:DC8 4.5 18.5 1.0
CA A:GLY107 4.5 15.7 1.0
C A:GLY105 4.6 15.4 1.0
CA A:ARG102 4.7 18.5 1.0
O A:LEU100 4.9 17.7 1.0
CA A:GLY105 4.9 18.6 1.0
O A:ARG102 4.9 16.2 1.0

Sodium binding site 2 out of 2 in 7mz4

Go back to Sodium Binding Sites List in 7mz4
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) in 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 3-Deaza-3- Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:33.1
occ:1.00
 O A:LYS60 2.4 23.6 1.0
O A:VAL65 2.4 22.1 1.0
O A:HOH596 2.5 33.4 1.0
O A:LEU62 2.8 23.7 1.0
OP1 D:DC3 2.9 26.9 1.0
C A:LYS60 3.5 24.5 1.0
C A:VAL65 3.5 21.6 1.0
C A:LEU62 3.8 25.0 1.0
P D:DC3 3.8 24.9 1.0
OP2 D:DC3 3.9 22.1 1.0
N A:VAL65 4.1 21.2 1.0
O D:HOH106 4.2 35.0 1.0
CG A:LYS60 4.2 33.8 1.0
CA A:LYS60 4.2 24.1 1.0
C A:LYS61 4.3 27.9 1.0
CA A:VAL65 4.3 21.1 1.0
N A:LEU62 4.3 25.8 1.0
N A:GLY64 4.4 23.2 1.0
CA A:PRO63 4.4 24.7 1.0
N A:PRO63 4.5 25.4 1.0
O A:LYS61 4.5 29.6 1.0
N A:LYS61 4.5 25.6 1.0
N A:GLY66 4.5 24.5 1.0
CB A:VAL65 4.6 24.7 1.0
CA A:LYS61 4.7 25.9 1.0
CA A:LEU62 4.7 24.4 1.0
NZ A:LYS60 4.7 32.9 1.0
CA A:GLY66 4.7 20.6 1.0
O3' D:DT2 4.8 24.4 1.0
C A:PRO63 4.9 26.7 1.0
CB A:LYS60 4.9 28.7 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3-Methyladenine (3DMEA) in the Template Base Paired with Incoming Dttp To Be Published.
Page generated: Tue Oct 8 18:02:39 2024

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