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Sodium in PDB 7mz8: Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) at N-1 of the Template Base Paired with Incoming Dttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) at N-1 of 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) 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 3-Deaza-3- Methyladenine (3DMEA) at N-1 of the Template Base Paired with Incoming Dttp, PDB code: 7mz8 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) 19.71 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.498, 78.827, 54.578, 90, 108.07, 90
R / Rfree (%) 20.1 / 26.3

Other elements in 7mz8:

The structure of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) at N-1 of the Template Base Paired with Incoming Dttp 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 Complexed with 3-Deaza-3- Methyladenine (3DMEA) at N-1 of the Template Base Paired with Incoming Dttp (pdb code 7mz8). 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) at N-1 of the Template Base Paired with Incoming Dttp, PDB code: 7mz8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7mz8

Go back to Sodium Binding Sites List in 7mz8
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) 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 3-Deaza-3- Methyladenine (3DMEA) at N-1 of the Template Base Paired with Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:28.1
occ:1.00
 OP1 P:DG9 2.2 34.7 1.0
O A:THR101 2.3 29.6 1.0
O A:HOH536 2.5 30.9 1.0
O P:HOH101 2.6 29.9 1.0
O A:ILE106 2.8 33.3 1.0
O A:VAL103 2.8 31.9 1.0
P P:DG9 3.2 23.8 1.0
C A:THR101 3.4 30.2 1.0
OP2 P:DG9 3.4 29.3 1.0
C A:VAL103 3.6 28.5 1.0
C A:ILE106 3.7 31.4 1.0
CA A:SER104 3.7 26.8 1.0
N A:SER104 3.9 30.8 1.0
N A:GLY105 4.1 34.6 1.0
CA A:THR101 4.1 25.1 1.0
N A:ILE106 4.1 28.5 1.0
O5' P:DG9 4.2 35.4 1.0
C A:ARG102 4.3 33.0 1.0
C A:SER104 4.3 32.6 1.0
N A:ARG102 4.4 28.8 1.0
O3' P:DC8 4.4 26.8 1.0
CA A:ILE106 4.4 27.3 1.0
N A:VAL103 4.4 20.2 1.0
CB A:THR101 4.5 30.5 1.0
O A:ARG102 4.5 30.9 1.0
N A:GLY107 4.6 28.1 1.0
CA A:ARG102 4.6 27.3 1.0
CA A:VAL103 4.7 24.4 1.0
CA A:GLY107 4.8 30.4 1.0
C A:GLY105 4.9 31.4 1.0
CB A:ILE106 4.9 29.7 1.0
CB A:SER104 4.9 27.5 1.0

Sodium binding site 2 out of 2 in 7mz8

Go back to Sodium Binding Sites List in 7mz8
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) 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 3-Deaza-3- Methyladenine (3DMEA) 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:56.7
occ:1.00
 O A:LYS60 2.5 45.6 1.0
O A:VAL65 2.5 36.5 1.0
OP1 D:DC3 2.9 44.8 1.0
O A:LEU62 3.1 41.6 1.0
OP2 D:DC3 3.6 40.4 1.0
C A:LYS60 3.7 40.9 1.0
C A:VAL65 3.7 35.7 1.0
P D:DC3 3.7 35.6 1.0
C A:LEU62 4.1 43.8 1.0
N A:VAL65 4.4 38.0 1.0
C A:LYS61 4.5 42.8 1.0
CA A:LYS60 4.5 44.8 1.0
N A:LEU62 4.5 41.7 1.0
CA A:VAL65 4.6 33.8 1.0
CG A:LYS60 4.6 40.0 1.0
N A:GLY66 4.6 34.2 1.0
CA A:GLY66 4.6 34.3 1.0
N A:LYS61 4.6 36.3 1.0
CA A:LYS61 4.7 44.2 1.0
O A:LYS61 4.7 38.4 1.0
N A:GLY64 4.8 42.8 1.0
O3' D:DT2 4.8 39.5 1.0
NZ A:LYS60 4.8 47.2 1.0
CA A:PRO63 4.9 42.7 1.0
N A:PRO63 4.9 47.9 1.0
CB A:VAL65 4.9 36.9 1.0
CA A:LEU62 5.0 40.7 1.0
O5' D:DC3 5.0 40.3 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna To Be Published.
Page generated: Tue Oct 8 18:03:00 2024

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