Atomistry » Sodium » PDB 4m04-4mfa » 4mf8
Atomistry »
  Sodium »
    PDB 4m04-4mfa »
      4mf8 »

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: Mon Oct 7 16:59:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy