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Sodium in PDB 4f5r: Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

Enzymatic activity of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

All present enzymatic activity of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit:
2.7.7.7;

Protein crystallography data

The structure of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit, PDB code: 4f5r 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) 21.36 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.028, 79.446, 102.090, 90.00, 96.96, 90.00
R / Rfree (%) 21 / 27.8

Other elements in 4f5r:

The structure of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit (pdb code 4f5r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit, PDB code: 4f5r:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4f5r

Go back to Sodium Binding Sites List in 4f5r
Sodium binding site 1 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:22.2
occ:1.00
 OP1 P:DG9 2.3 24.9 1.0
O A:THR101 2.3 20.6 1.0
O A:VAL103 2.4 18.1 1.0
O A:HOH509 2.4 20.6 1.0
O A:ILE106 2.5 19.9 1.0
O P:HOH110 2.5 21.2 1.0
C A:VAL103 3.4 19.9 1.0
C A:ILE106 3.4 17.0 1.0
C A:THR101 3.4 20.4 1.0
P P:DG9 3.4 21.4 1.0
OP2 P:DG9 3.6 21.7 1.0
N A:ILE106 3.7 17.7 1.0
CA A:SER104 3.9 20.8 1.0
N A:GLY105 3.9 19.1 1.0
N A:SER104 4.0 18.0 1.0
CA A:THR101 4.0 18.2 1.0
CA A:ILE106 4.1 17.0 1.0
N A:VAL103 4.2 21.0 1.0
C A:SER104 4.3 23.7 1.0
N A:GLY107 4.3 17.8 1.0
C A:ARG102 4.3 22.9 1.0
O3' P:DC8 4.4 21.8 1.0
CA A:VAL103 4.4 20.4 1.0
N A:ARG102 4.5 20.3 1.0
CB A:THR101 4.5 20.9 1.0
CB A:ILE106 4.6 21.2 1.0
O5' P:DG9 4.6 21.6 1.0
CA A:GLY107 4.6 16.3 1.0
C A:GLY105 4.6 17.2 1.0
CA A:ARG102 4.7 19.8 1.0
O A:ARG102 4.8 17.7 1.0
CA A:GLY105 4.8 20.9 1.0
O A:LEU100 4.9 19.9 1.0

Sodium binding site 2 out of 4 in 4f5r

Go back to Sodium Binding Sites List in 4f5r
Sodium binding site 2 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit


Mono view


Stereo pair view

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

b:33.1
occ:1.00
 O B:HOH582 2.2 42.2 1.0
O B:HOH616 2.3 34.8 1.0
OD1 B:ASP318 2.4 37.7 1.0
O B:HOH617 2.5 51.7 1.0
O B:HOH609 2.5 38.4 1.0
OD2 B:ASP318 2.6 38.3 1.0
CB B:ASP314 2.7 38.9 1.0
CG B:ASP318 2.8 37.3 1.0
OD1 B:ASP314 3.1 44.7 1.0
CG B:ASP314 3.3 44.0 1.0
CA B:ASP314 4.0 40.1 1.0
OG B:SER315 4.1 37.0 1.0
N B:ASP314 4.3 38.6 1.0
CB B:ASP318 4.3 33.4 1.0
C B:ASP314 4.5 41.3 1.0
OD2 B:ASP314 4.5 49.6 1.0
N B:SER315 4.7 34.8 1.0

Sodium binding site 3 out of 4 in 4f5r

Go back to Sodium Binding Sites List in 4f5r
Sodium binding site 3 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na102

b:54.8
occ:1.00
 O T:HOH236 2.2 38.5 1.0
O T:HOH229 2.3 42.6 1.0
O T:HOH237 2.3 46.6 1.0
O T:HOH238 2.4 55.8 1.0
N7 T:DA14 3.8 39.6 1.0
C8 T:DA14 4.2 39.5 1.0
N7 T:DG15 4.5 33.0 1.0
O6 T:DG15 4.6 29.0 1.0
O T:HOH204 4.6 29.7 1.0
O T:HOH211 4.8 35.0 1.0
C5 T:DA14 4.9 35.5 1.0

Sodium binding site 4 out of 4 in 4f5r

Go back to Sodium Binding Sites List in 4f5r
Sodium binding site 4 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na101

b:44.0
occ:1.00
 O G:HOH212 2.2 44.2 1.0
N7 G:DG4 2.2 45.4 1.0
O G:HOH210 2.3 56.4 1.0
O G:HOH211 2.4 50.5 1.0
C8 G:DG4 3.2 43.1 1.0
C5 G:DG4 3.3 39.7 1.0
O6 G:DG4 3.6 41.9 1.0
C6 G:DG4 3.8 37.5 1.0
C2' G:DT3 4.0 47.2 1.0
N9 G:DG4 4.4 45.0 1.0
N6 G:DA5 4.4 40.8 1.0
O G:HOH209 4.5 46.4 1.0
C4 G:DG4 4.5 44.6 1.0
C6 G:DT3 4.6 38.9 1.0
OP2 G:DG4 4.7 47.9 1.0
N1 G:DT3 4.8 43.1 1.0
C1' G:DT3 4.9 47.0 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: Mon Oct 7 15:18:09 2024

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