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

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

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template O6MG and Incoming Ttp:
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 Ttp, PDB code: 4mfa 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) 30.00 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.971, 79.662, 55.001, 90.00, 106.68, 90.00
R / Rfree (%) 21.2 / 28.3

Other elements in 4mfa:

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

Sodium binding site 1 out of 2 in 4mfa

Go back to Sodium Binding Sites List in 4mfa
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 Ttp


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 Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:21.0
occ:1.00
 O A:THR101 2.2 26.4 1.0
O A:ILE106 2.3 14.3 1.0
O P:HOH208 2.4 23.2 1.0
OP1 P:DG9 2.4 19.1 1.0
O A:VAL103 2.5 22.2 1.0
O P:HOH201 2.6 20.2 1.0
C A:VAL103 3.2 22.8 1.0
C A:THR101 3.3 23.8 1.0
O A:HOH501 3.3 21.0 1.0
C A:ILE106 3.4 15.4 1.0
P P:DG9 3.6 18.8 1.0
N A:ILE106 3.6 16.8 1.0
OP2 P:DG9 3.8 19.8 1.0
N A:SER104 3.9 19.3 1.0
CA A:SER104 3.9 18.6 1.0
CA A:THR101 3.9 21.0 1.0
N A:VAL103 3.9 21.8 1.0
N A:GLY105 4.0 16.6 1.0
CA A:ILE106 4.1 15.6 1.0
C A:ARG102 4.1 22.9 1.0
CA A:VAL103 4.2 21.0 1.0
N A:ARG102 4.3 22.5 1.0
C A:SER104 4.3 16.9 1.0
N A:GLY107 4.4 16.9 1.0
CB A:THR101 4.4 19.6 1.0
CB A:ILE106 4.5 15.9 1.0
CA A:ARG102 4.5 21.8 1.0
O3' P:DC8 4.5 18.4 1.0
C A:GLY105 4.6 17.6 1.0
O A:ARG102 4.6 26.1 1.0
CA A:GLY107 4.6 18.8 1.0
O5' P:DG9 4.8 22.4 1.0
O A:LEU100 4.9 20.4 1.0
CA A:GLY105 4.9 17.6 1.0

Sodium binding site 2 out of 2 in 4mfa

Go back to Sodium Binding Sites List in 4mfa
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 Ttp


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 Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:41.7
occ:1.00
 O D:HOH102 2.1 26.9 1.0
O A:LEU62 2.3 40.5 1.0
O A:LYS60 2.5 37.4 1.0
O A:VAL65 2.6 32.4 1.0
OP1 D:DC3 2.8 35.4 1.0
C A:LEU62 3.4 37.3 1.0
C A:LYS60 3.5 35.3 1.0
C A:VAL65 3.7 27.6 1.0
P D:DC3 3.8 29.9 1.0
OP2 D:DC3 3.9 27.1 1.0
N A:VAL65 3.9 29.4 1.0
C A:LYS61 3.9 33.5 1.0
N A:LEU62 3.9 33.6 1.0
N A:GLY64 4.0 36.8 1.0
CA A:PRO63 4.0 38.2 1.0
O A:LYS61 4.1 38.0 1.0
N A:PRO63 4.2 41.6 1.0
CA A:VAL65 4.3 27.0 1.0
N A:LYS61 4.3 32.9 1.0
CA A:LEU62 4.4 33.4 1.0
CA A:LYS61 4.4 34.1 1.0
C A:PRO63 4.4 36.3 1.0
CA A:LYS60 4.5 33.6 1.0
CB A:VAL65 4.5 27.8 1.0
O3' D:DT2 4.6 29.9 1.0
CG A:LYS60 4.7 35.0 1.0
N A:GLY66 4.8 23.4 1.0
C A:GLY64 4.8 32.3 1.0
O A:ALA59 4.9 34.5 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 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy