Sodium in PDB 4mf8: Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp, PDB code: 4mf8 was solved by M.C.Koag, K.Min, A.F.Monzingo, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.036, 79.721, 54.989, 90.00, 107.38, 90.00
R / Rfree (%) 20.9 / 27.2

Other elements in 4mf8:

The structure of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp 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 Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp (pdb code 4mf8). 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 Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp, PDB code: 4mf8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4mf8

Go back to Sodium Binding Sites List in 4mf8
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp


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 Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:29.2
occ:1.00
 O A:ILE106 2.2 17.5 1.0
O A:THR101 2.3 18.9 1.0
OP1 P:DG9 2.3 21.1 1.0
O A:VAL103 2.6 18.1 1.0
O A:HOH502 2.7 15.1 1.0
C A:ILE106 3.3 17.3 1.0
C A:THR101 3.3 19.1 1.0
C A:VAL103 3.4 19.7 1.0
P P:DG9 3.4 22.0 1.0
N A:ILE106 3.5 16.2 1.0
OP2 P:DG9 3.7 24.3 1.0
N A:GLY105 3.8 16.4 1.0
CA A:SER104 3.9 17.2 1.0
N A:SER104 3.9 18.0 1.0
CA A:THR101 3.9 18.1 1.0
CA A:ILE106 3.9 16.7 1.0
N A:VAL103 4.2 20.4 1.0
C A:SER104 4.2 16.6 1.0
N A:GLY107 4.2 18.8 1.0
N A:ARG102 4.4 20.2 1.0
C A:GLY105 4.4 17.1 1.0
O3' P:DC8 4.4 21.7 1.0
CA A:VAL103 4.4 19.5 1.0
C A:ARG102 4.4 21.3 1.0
CB A:THR101 4.4 18.4 1.0
CB A:ILE106 4.5 16.2 1.0
CA A:GLY107 4.5 19.2 1.0
O5' P:DG9 4.6 23.9 1.0
CA A:GLY105 4.7 16.6 1.0
CA A:ARG102 4.7 18.8 1.0
O A:LEU100 4.9 19.4 1.0
O A:ARG102 4.9 20.1 1.0

Sodium binding site 2 out of 2 in 4mf8

Go back to Sodium Binding Sites List in 4mf8
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp


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 Nicked Dna Containing A Mismatched Template O6MG and Incoming Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:36.8
occ:1.00
 O D:HOH104 2.3 22.0 1.0
O A:LYS60 2.3 29.3 1.0
O A:VAL65 2.4 23.6 1.0
O A:LEU62 2.6 26.9 1.0
OP1 D:DC3 3.0 38.2 1.0
C A:LYS60 3.4 28.8 1.0
C A:VAL65 3.5 22.9 1.0
C A:LEU62 3.6 25.1 1.0
OP2 D:DC3 3.7 25.2 1.0
P D:DC3 3.8 27.9 1.0
C A:LYS61 3.9 27.6 1.0
N A:VAL65 4.0 22.7 1.0
O A:LYS61 4.2 29.8 1.0
N A:LEU62 4.2 26.4 1.0
CA A:VAL65 4.2 21.6 1.0
CA A:LYS61 4.2 29.3 1.0
CG A:LYS60 4.3 29.0 1.0
N A:LYS61 4.3 28.0 1.0
CA A:PRO63 4.3 25.5 1.0
CA A:LYS60 4.3 28.9 1.0
N A:PRO63 4.3 24.1 1.0
N A:GLY64 4.4 25.2 1.0
NZ A:LYS60 4.5 35.0 1.0
N A:GLY66 4.6 22.1 1.0
CB A:VAL65 4.6 22.4 1.0
CA A:LEU62 4.6 25.6 1.0
O3' D:DT2 4.7 26.9 1.0
C A:PRO63 4.7 25.7 1.0
CA A:GLY66 4.8 22.1 1.0
CB A:LYS60 4.9 29.1 1.0

Reference:

M.C.Koag, K.Min, A.F.Monzingo, S.Lee. Structures of Human Dna Polymerase Beta Inserting Bases Opposite Templating O6MG To Be Published.
Page generated: Tue Dec 15 06:54:11 2020

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