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Sodium in PDB 6cto: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue, PDB code: 6cto 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) 19.79 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.784, 79.168, 55.494, 90.00, 107.10, 90.00
R / Rfree (%) 17.9 / 23.2

Other elements in 6cto:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue (pdb code 6cto). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue, PDB code: 6cto:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6cto

Go back to Sodium Binding Sites List in 6cto
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:24.0
occ:1.00
 O A:THR101 2.3 25.0 1.0
OP1 P:DG9 2.3 22.0 1.0
O P:HOH206 2.4 28.9 1.0
O A:ILE106 2.5 21.9 1.0
O A:HOH681 2.6 23.8 1.0
O A:VAL103 2.6 21.4 1.0
C A:THR101 3.3 19.1 1.0
P P:DG9 3.3 23.9 1.0
C A:ILE106 3.5 21.0 1.0
C A:VAL103 3.5 23.8 1.0
OP2 P:DG9 3.5 24.8 1.0
N A:ILE106 3.8 18.9 1.0
O A:HOH673 3.8 49.0 1.0
CA A:THR101 3.9 22.0 1.0
N A:GLY105 3.9 18.2 1.0
CA A:SER104 4.0 21.4 1.0
N A:SER104 4.1 20.3 1.0
CA A:ILE106 4.1 21.8 1.0
C A:SER104 4.3 19.1 1.0
N A:VAL103 4.3 18.6 1.0
N A:ARG102 4.4 21.2 1.0
CB A:THR101 4.4 24.6 1.0
O3' P:DC8 4.4 20.2 1.0
C A:ARG102 4.4 25.2 1.0
N A:GLY107 4.4 19.6 1.0
O5' P:DG9 4.5 23.9 1.0
CA A:VAL103 4.6 24.4 1.0
CB A:ILE106 4.6 23.1 1.0
C A:GLY105 4.6 18.4 1.0
CA A:ARG102 4.6 26.0 1.0
CA A:GLY107 4.7 25.0 1.0
O A:ARG102 4.8 26.6 1.0
CA A:GLY105 4.8 21.4 1.0
O A:HOH697 4.8 37.5 1.0
O A:LEU100 4.9 19.9 1.0

Sodium binding site 2 out of 3 in 6cto

Go back to Sodium Binding Sites List in 6cto
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:31.6
occ:1.00
 O A:VAL65 2.3 30.4 1.0
O A:LEU62 2.3 33.6 1.0
OP1 D:DC3 2.4 27.9 1.0
O A:LYS60 2.5 31.9 1.0
O A:HOH672 2.6 35.5 1.0
O D:HOH202 2.9 43.4 1.0
C A:LEU62 3.4 32.6 1.0
C A:VAL65 3.4 29.4 1.0
P D:DC3 3.5 34.0 1.0
C A:LYS60 3.6 29.6 1.0
OP2 D:DC3 3.7 24.8 1.0
N A:VAL65 3.8 28.0 1.0
CA A:PRO63 3.9 29.1 1.0
N A:GLY64 4.0 27.9 1.0
N A:PRO63 4.0 34.8 1.0
CA A:VAL65 4.1 28.9 1.0
C A:LYS61 4.2 32.2 1.0
N A:LEU62 4.2 26.0 1.0
O A:LYS61 4.3 32.2 1.0
C A:PRO63 4.3 34.7 1.0
CA A:LYS60 4.3 30.3 1.0
N A:GLY66 4.4 29.2 1.0
CA A:LEU62 4.4 29.4 1.0
CB A:VAL65 4.4 27.2 1.0
O3' D:DT2 4.4 32.0 1.0
CG A:LYS60 4.6 31.9 1.0
N A:LYS61 4.6 31.3 1.0
C A:GLY64 4.7 31.3 1.0
O5' D:DC3 4.7 37.1 1.0
CA A:GLY66 4.7 27.9 1.0
CA A:LYS61 4.7 31.2 1.0
O A:ALA59 4.9 26.7 1.0
CA A:GLY64 4.9 33.1 1.0

Sodium binding site 3 out of 3 in 6cto

Go back to Sodium Binding Sites List in 6cto
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.9
occ:1.00
 OD1 A:ASP192 2.2 18.6 1.0
OD2 A:ASP190 2.3 28.9 1.0
OD2 A:ASP256 2.4 35.9 1.0
O1A A:VT7405 2.5 20.5 1.0
C3' P:DOC10 3.1 36.5 1.0
CG A:ASP192 3.2 19.0 1.0
CG A:ASP190 3.2 26.3 1.0
PA A:VT7405 3.4 26.8 1.0
OD1 A:ASP190 3.4 22.6 1.0
OD2 A:ASP192 3.4 18.9 1.0
C4' P:DOC10 3.5 42.8 1.0
C5' P:DOC10 3.5 41.7 1.0
CG A:ASP256 3.5 33.0 1.0
O5' A:VT7405 3.6 21.4 1.0
MG A:MG401 3.7 20.2 1.0
O5' P:DOC10 3.8 48.0 1.0
O2A A:VT7405 3.8 23.6 1.0
C5' A:VT7405 4.0 21.3 1.0
O A:HOH656 4.1 26.2 1.0
CB A:ASP256 4.1 26.1 1.0
CB A:ASP192 4.5 18.9 1.0
C2' P:DOC10 4.5 33.9 1.0
OD1 A:ASP256 4.5 31.5 1.0
CB A:ASP190 4.6 16.1 1.0
O A:HOH711 4.7 37.4 1.0
O P:HOH215 4.7 37.2 1.0
NH2 A:ARG254 4.7 37.6 1.0
O1G A:VT7405 4.8 21.8 1.0
O3A A:VT7405 4.9 26.0 1.0
O A:MET191 4.9 21.8 1.0
O4' P:DOC10 5.0 41.1 1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418
Page generated: Tue Dec 15 12:06:09 2020

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