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Sodium in PDB 6cr8: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp 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 Chcl (R & S Isomers), Beta, Gamma Datp Analogue, PDB code: 6cr8 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) 19.28 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.585, 78.601, 55.473, 90.00, 107.14, 90.00
R / Rfree (%) 19.1 / 24.8

Other elements in 6cr8:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 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 Chcl (R & S Isomers), Beta, Gamma Datp Analogue (pdb code 6cr8). 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 Chcl (R & S Isomers), Beta, Gamma Datp Analogue, PDB code: 6cr8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6cr8

Go back to Sodium Binding Sites List in 6cr8
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp 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 Chcl (R & S Isomers), Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.9
occ:1.00
 OP1 P:DG9 2.3 21.6 1.0
O A:ILE106 2.3 22.8 1.0
O A:THR101 2.4 26.4 1.0
O A:VAL103 2.5 22.6 1.0
O A:HOH709 2.6 25.0 1.0
O P:HOH106 2.6 26.9 1.0
C A:ILE106 3.3 24.2 1.0
C A:THR101 3.4 20.6 1.0
C A:VAL103 3.4 24.0 1.0
P P:DG9 3.4 23.1 1.0
N A:ILE106 3.6 18.4 1.0
OP2 P:DG9 3.6 24.1 1.0
O A:HOH589 3.8 35.1 1.0
CA A:THR101 3.9 19.9 1.0
N A:GLY105 3.9 22.3 1.0
CA A:SER104 3.9 21.2 1.0
CA A:ILE106 4.0 19.7 1.0
N A:SER104 4.0 19.2 1.0
N A:VAL103 4.1 18.1 1.0
C A:SER104 4.2 20.8 1.0
C A:ARG102 4.2 25.0 1.0
O3' P:DC8 4.3 18.8 1.0
CA A:VAL103 4.4 21.9 1.0
N A:GLY107 4.4 20.4 1.0
N A:ARG102 4.4 21.7 1.0
CB A:ILE106 4.5 19.4 1.0
CB A:THR101 4.5 21.7 1.0
C A:GLY105 4.5 23.6 1.0
O5' P:DG9 4.6 23.5 1.0
O A:ARG102 4.6 25.0 1.0
CA A:ARG102 4.6 23.2 1.0
CA A:GLY107 4.7 20.1 1.0
CA A:GLY105 4.8 18.6 1.0
O A:LEU100 4.8 22.8 1.0

Sodium binding site 2 out of 3 in 6cr8

Go back to Sodium Binding Sites List in 6cr8
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp 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 Chcl (R & S Isomers), Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:35.7
occ:1.00
 O A:LEU62 2.3 26.5 1.0
O A:VAL65 2.3 27.6 1.0
O A:HOH615 2.4 31.3 1.0
O A:LYS60 2.5 36.2 1.0
OP1 D:DC3 2.5 29.5 1.0
O D:HOH103 2.8 41.0 1.0
C A:LEU62 3.4 30.9 1.0
C A:VAL65 3.4 27.4 1.0
P D:DC3 3.5 32.6 1.0
C A:LYS60 3.6 35.6 1.0
O D:HOH106 3.6 35.0 1.0
OP2 D:DC3 3.7 26.8 1.0
N A:VAL65 3.8 30.5 1.0
N A:LEU62 4.0 26.9 1.0
CA A:VAL65 4.0 28.3 1.0
N A:GLY64 4.1 31.3 1.0
CA A:PRO63 4.1 33.7 1.0
C A:LYS61 4.1 35.4 1.0
N A:PRO63 4.1 36.2 1.0
CA A:LYS60 4.3 30.4 1.0
O A:LYS61 4.3 35.8 1.0
CA A:LEU62 4.3 29.2 1.0
CB A:VAL65 4.4 27.7 1.0
N A:GLY66 4.4 29.8 1.0
O3' D:DT2 4.5 34.7 1.0
C A:PRO63 4.5 32.8 1.0
CG A:LYS60 4.5 31.2 1.0
N A:LYS61 4.6 28.7 1.0
CA A:LYS61 4.7 30.4 1.0
CA A:GLY66 4.7 25.8 1.0
C A:GLY64 4.7 29.2 1.0
O5' D:DC3 4.8 36.5 1.0
O A:ALA59 4.9 28.6 1.0
CA A:GLY64 4.9 29.2 1.0

Sodium binding site 3 out of 3 in 6cr8

Go back to Sodium Binding Sites List in 6cr8
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp 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 Chcl (R & S Isomers), Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:47.0
occ:1.00
 OD1 A:ASP192 2.3 28.6 1.0
OD2 A:ASP190 2.3 36.4 1.0
OD2 A:ASP256 2.4 40.9 1.0
O1A A:VA4401 2.7 19.6 1.0
C3' P:DOC10 2.8 32.5 1.0
C4' P:DOC10 3.3 34.9 1.0
CG A:ASP192 3.3 24.6 1.0
CG A:ASP190 3.4 28.5 1.0
CG A:ASP256 3.4 32.0 1.0
PA A:VA4401 3.6 33.0 1.0
O5' A:VA4401 3.7 20.6 1.0
OD2 A:ASP192 3.7 20.0 1.0
C5' P:DOC10 3.7 40.4 1.0
C2' P:DOC10 3.9 29.7 1.0
OD1 A:ASP190 3.9 30.2 1.0
MG A:MG402 3.9 27.6 1.0
CB A:ASP256 3.9 24.7 1.0
C5' A:VA4401 4.0 20.3 1.0
O2A A:VA4401 4.0 23.4 1.0
O5' P:DOC10 4.0 43.5 1.0
OD1 A:ASP256 4.5 36.5 1.0
CB A:ASP192 4.6 21.7 1.0
O4' P:DOC10 4.6 32.0 1.0
CB A:ASP190 4.7 21.3 1.0
O A:HOH644 4.7 37.1 1.0
CE1 A:PHE272 4.9 26.1 1.0
C1' P:DOC10 4.9 30.5 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 Oct 8 06:40:57 2024

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