Atomistry » Sodium » PDB 4ehu-4f5q » 4f5p
Atomistry »
  Sodium »
    PDB 4ehu-4f5q »
      4f5p »

Sodium in PDB 4f5p: Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog

Enzymatic activity of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog

All present enzymatic activity of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog, PDB code: 4f5p was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.11 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.380, 79.240, 54.880, 90.00, 105.49, 90.00
R / Rfree (%) 20.3 / 24.5

Other elements in 4f5p:

The structure of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog (pdb code 4f5p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog, PDB code: 4f5p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4f5p

Go back to Sodium Binding Sites List in 4f5p
Sodium binding site 1 out of 2 in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:37.8
occ:1.00
O A:HOH501 2.5 22.1 1.0
O P:HOH101 2.5 20.6 1.0
O A:THR101 2.5 19.4 1.0
O A:HOH629 2.5 44.2 1.0
O A:HOH508 2.6 28.0 1.0
NA A:NA403 3.2 17.6 1.0
C A:THR101 3.5 17.7 1.0
CA A:ARG102 4.1 19.0 1.0
N A:ARG102 4.2 19.8 1.0
CB A:THR101 4.4 20.3 1.0
OG1 A:THR101 4.4 20.6 1.0
O A:HOH552 4.4 25.9 1.0
NZ A:LYS27 4.6 42.5 1.0
CA A:THR101 4.6 17.9 1.0
C A:ARG102 4.6 20.6 1.0
OP1 P:DG9 4.8 17.4 1.0
O A:HOH662 4.8 45.8 1.0
O A:ARG102 4.9 20.3 1.0
O A:HOH570 4.9 31.8 1.0

Sodium binding site 2 out of 2 in 4f5p

Go back to Sodium Binding Sites List in 4f5p
Sodium binding site 2 out of 2 in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:17.6
occ:1.00
O A:THR101 2.3 19.4 1.0
OP1 P:DG9 2.4 17.4 1.0
O A:ILE106 2.4 18.2 1.0
O P:HOH101 2.4 20.6 1.0
O A:VAL103 2.5 19.4 1.0
O A:HOH501 2.5 22.1 1.0
NA A:NA402 3.2 37.8 1.0
C A:THR101 3.3 17.7 1.0
C A:ILE106 3.4 18.2 1.0
C A:VAL103 3.4 21.0 1.0
P P:DG9 3.5 19.2 1.0
OP2 P:DG9 3.8 17.4 1.0
N A:ILE106 3.8 16.8 1.0
CA A:THR101 3.9 17.9 1.0
CA A:SER104 4.0 21.0 1.0
N A:GLY105 4.0 15.6 1.0
N A:SER104 4.1 18.8 1.0
CA A:ILE106 4.2 16.5 1.0
N A:VAL103 4.2 17.1 1.0
C A:SER104 4.3 16.5 1.0
C A:ARG102 4.3 20.6 1.0
CB A:THR101 4.3 20.3 1.0
N A:GLY107 4.4 16.7 1.0
N A:ARG102 4.4 19.8 1.0
CA A:VAL103 4.5 18.2 1.0
O3' P:DC8 4.5 17.8 1.0
CA A:GLY107 4.6 20.6 1.0
CB A:ILE106 4.6 21.2 1.0
CA A:ARG102 4.6 19.0 1.0
O5' P:DG9 4.7 17.7 1.0
C A:GLY105 4.7 14.9 1.0
O A:ARG102 4.8 20.3 1.0
CA A:GLY105 4.9 14.6 1.0
O A:HOH552 4.9 25.9 1.0
O A:LEU100 4.9 20.1 1.0

Reference:

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Structures of Dntp Intermediate States During Dna Polymerase Active Site Assembly. Structure V. 20 1829 2012.
ISSN: ISSN 0969-2126
PubMed: 22959623
DOI: 10.1016/J.STR.2012.08.008
Page generated: Tue Dec 15 06:39:40 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy