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Sodium in PDB 7mz3: Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 7mz3 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) 19.76 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.519, 79.031, 54.87, 90, 106.42, 90
R / Rfree (%) 20.4 / 26.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna (pdb code 7mz3). 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) As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 7mz3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7mz3

Go back to Sodium Binding Sites List in 7mz3
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna


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) As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:21.4
occ:1.00
 OP1 P:DG9 2.3 22.5 1.0
O A:THR101 2.3 26.9 1.0
O A:ILE106 2.5 25.8 1.0
O P:HOH102 2.5 19.5 1.0
O A:VAL103 2.5 20.5 1.0
O A:HOH553 2.8 22.8 1.0
O A:HOH501 3.1 17.4 1.0
C A:THR101 3.3 27.2 1.0
C A:VAL103 3.3 21.2 1.0
C A:ILE106 3.4 22.1 1.0
P P:DG9 3.4 23.4 1.0
OP2 P:DG9 3.7 23.8 1.0
CA A:SER104 3.7 21.5 1.0
N A:ILE106 3.7 20.4 1.0
N A:SER104 3.8 22.2 1.0
N A:GLY105 3.9 19.9 1.0
CA A:THR101 3.9 19.2 1.0
CA A:ILE106 4.1 23.1 1.0
N A:VAL103 4.2 17.6 1.0
C A:SER104 4.2 22.0 1.0
C A:ARG102 4.3 25.8 1.0
N A:ARG102 4.3 20.9 1.0
N A:GLY107 4.4 23.0 1.0
CA A:VAL103 4.4 19.6 1.0
O3' P:DC8 4.5 25.7 1.0
O5' P:DG9 4.5 23.3 1.0
CB A:THR101 4.5 22.7 1.0
CB A:ILE106 4.5 25.4 1.0
CA A:ARG102 4.6 27.3 1.0
C A:GLY105 4.6 22.9 1.0
CA A:GLY107 4.7 24.1 1.0
O A:ARG102 4.7 21.9 1.0
CA A:GLY105 4.9 22.5 1.0
O A:LEU100 4.9 25.7 1.0

Sodium binding site 2 out of 2 in 7mz3

Go back to Sodium Binding Sites List in 7mz3
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3- Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna


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) As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:39.7
occ:1.00
 O A:LYS60 2.5 38.5 1.0
O A:VAL65 2.6 28.3 1.0
OP1 D:DC3 2.9 29.4 1.0
O A:LEU62 3.1 35.2 1.0
OP2 D:DC3 3.5 29.2 1.0
P D:DC3 3.7 24.7 1.0
C A:VAL65 3.7 29.5 1.0
C A:LYS60 3.7 34.3 1.0
C A:LEU62 4.1 28.9 1.0
CG A:LYS60 4.2 34.8 1.0
N A:VAL65 4.4 24.3 1.0
NZ A:LYS60 4.5 30.4 1.0
CA A:LYS60 4.5 30.7 1.0
CA A:VAL65 4.5 23.1 1.0
C A:LYS61 4.5 31.4 1.0
N A:LEU62 4.6 30.6 1.0
N A:GLY66 4.6 30.2 1.0
CA A:GLY66 4.7 25.0 1.0
N A:LYS61 4.7 29.5 1.0
O3' D:DT2 4.8 31.8 1.0
CA A:LYS61 4.8 33.3 1.0
O5' D:DC3 4.8 25.6 1.0
CB A:VAL65 4.8 28.5 1.0
CA A:PRO63 4.9 29.7 1.0
O A:LYS61 4.9 35.6 1.0
N A:GLY64 4.9 37.2 1.0
N A:PRO63 4.9 31.2 1.0
CB A:LYS60 5.0 32.4 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 3-Deaza-3-Methyladenine (3DMEA) As the Template Base in A 1-Nucleotide Gapped Dna To Be Published.
Page generated: Tue Oct 8 18:02:39 2024

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