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Sodium in PDB 6cr5: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2-Beta, Gamma Datp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2-Beta, Gamma Datp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2-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 CH2-Beta, Gamma Datp Analogue, PDB code: 6cr5 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) 31.66 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.603, 78.909, 55.528, 90.00, 107.16, 90.00
R / Rfree (%) 17.8 / 23.2

Other elements in 6cr5:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2-Beta, Gamma Datp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

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 CH2-Beta, Gamma Datp Analogue (pdb code 6cr5). 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 CH2-Beta, Gamma Datp Analogue, PDB code: 6cr5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6cr5

Go back to Sodium Binding Sites List in 6cr5
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2-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 CH2-Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:20.5
occ:1.00
 OP1 P:DG9 2.3 21.0 1.0
O A:ILE106 2.3 15.6 1.0
O A:THR101 2.4 25.7 1.0
O P:HOH102 2.5 21.9 1.0
O A:VAL103 2.5 19.6 1.0
O P:HOH110 3.0 24.9 1.0
P P:DG9 3.3 24.0 1.0
C A:ILE106 3.4 20.9 1.0
C A:THR101 3.4 19.1 1.0
C A:VAL103 3.4 19.3 1.0
OP2 P:DG9 3.6 18.7 1.0
N A:ILE106 3.7 18.7 1.0
O A:HOH589 3.8 30.2 1.0
CA A:SER104 3.9 22.8 1.0
N A:GLY105 3.9 22.2 1.0
CA A:THR101 4.0 22.4 1.0
CA A:ILE106 4.0 19.4 1.0
N A:SER104 4.0 16.9 1.0
N A:VAL103 4.1 19.4 1.0
C A:SER104 4.3 22.4 1.0
O3' P:DC8 4.3 20.7 1.0
C A:ARG102 4.3 22.8 1.0
N A:ARG102 4.4 21.4 1.0
N A:GLY107 4.4 20.9 1.0
CA A:VAL103 4.4 19.7 1.0
CB A:ILE106 4.5 18.1 1.0
O5' P:DG9 4.5 19.8 1.0
CB A:THR101 4.6 20.4 1.0
C A:GLY105 4.6 21.5 1.0
CA A:ARG102 4.6 23.1 1.0
CA A:GLY107 4.7 19.5 1.0
O A:ARG102 4.8 23.8 1.0
O A:LEU100 4.8 17.4 1.0
CA A:GLY105 4.8 19.9 1.0

Sodium binding site 2 out of 3 in 6cr5

Go back to Sodium Binding Sites List in 6cr5
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2-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 CH2-Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:32.1
occ:1.00
 O A:VAL65 2.3 29.2 1.0
OP1 D:DC3 2.4 31.1 1.0
O A:LEU62 2.5 30.4 1.0
O A:LYS60 2.6 34.2 1.0
O D:HOH102 2.7 34.4 1.0
O A:HOH571 2.9 31.3 1.0
C A:VAL65 3.3 30.5 1.0
P D:DC3 3.3 33.8 1.0
OP2 D:DC3 3.4 23.4 1.0
C A:LEU62 3.5 27.5 1.0
C A:LYS60 3.7 32.4 1.0
N A:VAL65 3.7 27.5 1.0
O D:HOH106 3.8 39.1 1.0
O A:HOH587 3.9 34.3 1.0
CA A:VAL65 4.0 27.4 1.0
N A:GLY64 4.0 29.5 1.0
CA A:PRO63 4.1 29.9 1.0
N A:GLY66 4.2 29.2 1.0
N A:PRO63 4.2 29.8 1.0
O3' D:DT2 4.2 31.7 1.0
N A:LEU62 4.3 27.1 1.0
CA A:LYS60 4.4 27.1 1.0
CB A:VAL65 4.4 27.8 1.0
C A:PRO63 4.4 32.2 1.0
C A:LYS61 4.4 31.6 1.0
CA A:GLY66 4.4 27.5 1.0
CG A:LYS60 4.5 33.0 1.0
CA A:LEU62 4.6 26.0 1.0
O5' D:DC3 4.6 32.1 1.0
O A:LYS61 4.7 33.8 1.0
C A:GLY64 4.7 30.9 1.0
N A:LYS61 4.7 28.2 1.0
CA A:LYS61 4.9 29.5 1.0
CA A:GLY64 4.9 29.2 1.0

Sodium binding site 3 out of 3 in 6cr5

Go back to Sodium Binding Sites List in 6cr5
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2-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 CH2-Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:34.2
occ:1.00
 OD2 A:ASP190 2.1 34.9 1.0
OD1 A:ASP192 2.2 18.2 1.0
OD2 A:ASP256 2.3 34.3 1.0
CG A:ASP190 2.8 27.0 1.0
O1A A:FCJ401 3.1 18.8 1.0
OD1 A:ASP190 3.1 21.8 1.0
CG A:ASP192 3.2 19.0 1.0
C5' P:DOC10 3.3 35.4 1.0
CG A:ASP256 3.4 29.9 1.0
C3' P:DOC10 3.6 31.8 1.0
OD2 A:ASP192 3.6 19.6 1.0
C4' P:DOC10 3.8 31.7 1.0
MG A:MG402 3.9 21.7 1.0
CB A:ASP190 3.9 19.4 1.0
CB A:ASP256 4.0 24.2 1.0
OD1 A:ASP256 4.3 33.9 1.0
PA A:FCJ401 4.3 24.3 1.0
O5' A:FCJ401 4.3 21.4 1.0
CB A:ASP192 4.5 15.8 1.0
NH2 A:ARG254 4.5 33.8 1.0
O A:MET191 4.5 17.4 1.0
C5' A:FCJ401 4.5 18.4 1.0
O5' P:DOC10 4.6 36.2 1.0
O2A A:FCJ401 4.6 24.5 1.0
N A:ASP256 4.6 18.6 1.0
OP1 P:DOC10 4.7 36.7 1.0
C A:MET191 4.7 17.0 1.0
O A:HOH640 4.7 37.4 1.0
CA A:ASP192 4.8 17.5 1.0
N A:MET191 4.9 19.5 1.0
N A:ASP192 4.9 19.7 1.0
C2' P:DOC10 5.0 25.3 1.0
CA A:ASP256 5.0 20.1 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 Oct 8 06:40:08 2024

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