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Sodium in PDB 5j0p: Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus

Enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus

All present enzymatic activity of Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus, PDB code: 5j0p was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.140, 79.620, 54.570, 90.00, 105.55, 90.00
R / Rfree (%) 24.9 / 32

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus (pdb code 5j0p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus, PDB code: 5j0p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5j0p

Go back to Sodium Binding Sites List in 5j0p
Sodium binding site 1 out of 2 in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:24.3
occ:1.00
O A:THR101 2.3 22.5 1.0
O A:ILE106 2.3 21.5 1.0
OP1 P:DG9 2.5 22.7 1.0
O P:HOH103 2.5 24.4 1.0
O A:HOH566 2.6 28.3 1.0
O A:VAL103 2.6 21.4 1.0
C A:THR101 3.3 24.6 1.0
C A:ILE106 3.3 20.3 1.0
P P:DG9 3.5 19.9 1.0
C A:VAL103 3.6 24.1 1.0
OP2 P:DG9 3.6 23.3 1.0
CA A:THR101 3.7 24.9 1.0
N A:ILE106 3.7 20.4 1.0
O A:HOH534 3.8 28.5 1.0
CA A:ILE106 4.0 19.5 1.0
CA A:SER104 4.1 21.1 1.0
N A:GLY105 4.1 20.9 1.0
CB A:THR101 4.2 26.0 1.0
N A:SER104 4.2 23.4 1.0
N A:GLY107 4.2 21.8 1.0
N A:VAL103 4.3 23.5 1.0
CA A:GLY107 4.4 23.0 1.0
N A:ARG102 4.4 24.1 1.0
C A:SER104 4.4 21.2 1.0
CB A:ILE106 4.4 19.1 1.0
C A:ARG102 4.4 24.2 1.0
CA A:VAL103 4.6 25.2 1.0
O5' P:DG9 4.6 21.7 1.0
O3' P:DC8 4.6 23.3 1.0
C A:GLY105 4.7 19.8 1.0
CA A:ARG102 4.8 24.9 1.0
O A:ARG102 4.8 24.4 1.0
O A:LEU100 4.8 28.0 1.0

Sodium binding site 2 out of 2 in 5j0p

Go back to Sodium Binding Sites List in 5j0p
Sodium binding site 2 out of 2 in the Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:44.7
occ:1.00
O A:LYS60 2.1 36.7 1.0
O A:VAL65 2.1 28.5 1.0
O A:LEU62 2.5 31.4 1.0
O A:HOH620 2.9 37.9 1.0
O D:HOH105 2.9 31.6 1.0
C A:LYS60 3.1 35.5 1.0
OP1 D:DC3 3.2 34.7 1.0
C A:VAL65 3.2 26.0 1.0
C A:LEU62 3.5 29.1 1.0
N A:VAL65 3.6 23.8 1.0
CA A:LYS60 3.7 34.8 1.0
CA A:VAL65 3.8 23.5 1.0
CB A:VAL65 3.9 22.3 1.0
N A:LEU62 4.0 32.6 1.0
OP2 D:DC3 4.0 33.7 1.0
P D:DC3 4.0 33.1 1.0
N A:GLY64 4.2 24.7 1.0
N A:LYS61 4.2 35.7 1.0
CG A:LYS60 4.2 39.7 1.0
C A:LYS61 4.2 34.3 1.0
CA A:PRO63 4.3 26.6 1.0
N A:PRO63 4.4 27.8 1.0
N A:GLY66 4.4 26.3 1.0
CA A:LEU62 4.4 30.2 1.0
O A:ALA59 4.5 31.0 1.0
CA A:LYS61 4.6 35.5 1.0
CB A:LYS60 4.6 34.6 1.0
C A:PRO63 4.6 26.8 1.0
CG1 A:VAL65 4.7 24.1 1.0
C A:GLY64 4.7 26.1 1.0
O3' D:DT2 4.7 29.9 1.0
O A:LYS61 4.7 35.9 1.0
CA A:GLY66 4.7 24.6 1.0
N A:LYS60 4.9 32.2 1.0

Reference:

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006
Page generated: Tue Dec 15 11:06:54 2020

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