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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

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