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

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp 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 Dctp Analogue, PDB code: 6ctv 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) 23.62 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.666, 79.251, 55.337, 90.00, 107.75, 90.00
R / Rfree (%) 18 / 22

Other elements in 6ctv:

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

Fluorine (F) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 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 CF2, Beta, Gamma Dctp Analogue (pdb code 6ctv). 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 Dctp Analogue, PDB code: 6ctv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctv

Go back to Sodium Binding Sites List in 6ctv
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 Dctp 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 Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:24.3
occ:1.00
 OD1 A:ASP192 2.2 19.2 1.0
OD2 A:ASP256 2.3 30.4 1.0
OD2 A:ASP190 2.3 27.0 1.0
O1A A:FFJ406 2.5 16.8 1.0
O A:HOH560 2.7 37.2 1.0
CG A:ASP190 3.0 20.4 1.0
OD1 A:ASP190 3.1 19.4 1.0
CG A:ASP192 3.2 17.8 1.0
MG A:MG402 3.4 19.1 1.0
OD2 A:ASP192 3.4 18.5 1.0
CG A:ASP256 3.5 25.3 1.0
PA A:FFJ406 3.6 20.4 1.0
O5' A:FFJ406 3.9 21.2 1.0
C3' P:2DA10 3.9 25.6 1.0
CB A:ASP256 4.0 24.2 1.0
O2A A:FFJ406 4.1 21.3 1.0
C5' A:FFJ406 4.2 20.5 1.0
C5' P:2DA10 4.3 29.3 1.0
CB A:ASP190 4.4 20.8 1.0
C4' P:2DA10 4.4 29.0 1.0
OD1 A:ASP256 4.5 24.3 1.0
O A:HOH597 4.5 33.5 1.0
CB A:ASP192 4.5 19.3 1.0
O A:MET191 4.6 18.9 1.0
O2G A:FFJ406 4.6 23.2 1.0
O5' P:2DA10 4.7 30.7 1.0
NH2 A:ARG254 4.7 23.3 1.0
OP1 P:2DA10 4.7 23.6 1.0
O A:HOH742 4.8 34.4 1.0
C A:MET191 4.9 22.3 1.0
CA A:ASP192 5.0 21.5 1.0

Sodium binding site 2 out of 3 in 6ctv

Go back to Sodium Binding Sites List in 6ctv
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 Dctp 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 Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:27.9
occ:1.00
 O P:HOH104 2.4 31.8 1.0
O A:THR101 2.4 24.2 1.0
O A:VAL103 2.4 21.2 1.0
O A:ILE106 2.5 20.9 1.0
OP1 P:DG9 2.5 24.5 1.0
O A:HOH761 2.6 27.8 1.0
C A:THR101 3.3 23.0 1.0
C A:VAL103 3.4 20.6 1.0
C A:ILE106 3.4 22.8 1.0
P P:DG9 3.5 25.8 1.0
OP2 P:DG9 3.7 25.8 1.0
N A:ILE106 3.7 24.0 1.0
N A:GLY105 3.9 23.2 1.0
O A:HOH684 3.9 39.2 1.0
CA A:THR101 3.9 26.1 1.0
CA A:SER104 3.9 20.6 1.0
CA A:ILE106 4.0 21.2 1.0
N A:SER104 4.1 19.4 1.0
N A:VAL103 4.1 24.1 1.0
C A:SER104 4.3 21.3 1.0
C A:ARG102 4.3 26.7 1.0
N A:ARG102 4.3 21.8 1.0
CA A:VAL103 4.4 22.9 1.0
N A:GLY107 4.4 20.6 1.0
O3' P:DC8 4.4 24.3 1.0
CB A:ILE106 4.5 24.5 1.0
CB A:THR101 4.5 25.6 1.0
C A:GLY105 4.5 20.9 1.0
CA A:ARG102 4.6 24.7 1.0
CA A:GLY107 4.7 23.9 1.0
O5' P:DG9 4.7 26.2 1.0
O A:ARG102 4.7 25.4 1.0
CA A:GLY105 4.7 26.1 1.0
O A:LEU100 4.8 22.4 1.0
O A:HOH757 5.0 47.6 1.0

Sodium binding site 3 out of 3 in 6ctv

Go back to Sodium Binding Sites List in 6ctv
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 Dctp 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 Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:30.2
occ:1.00
 O A:VAL65 2.3 27.5 1.0
O A:LYS60 2.4 28.4 1.0
O A:LEU62 2.4 28.6 1.0
O D:HOH104 2.5 31.4 1.0
O A:HOH697 2.6 34.2 1.0
OP1 D:DC3 2.6 28.4 1.0
C A:VAL65 3.4 21.6 1.0
C A:LEU62 3.5 26.8 1.0
C A:LYS60 3.5 29.1 1.0
P D:DC3 3.6 29.0 1.0
OP2 D:DC3 3.8 25.4 1.0
N A:VAL65 3.9 23.5 1.0
N A:LEU62 4.0 24.4 1.0
CA A:VAL65 4.1 25.1 1.0
O D:HOH109 4.1 40.9 1.0
C A:LYS61 4.1 33.5 1.0
CA A:LYS60 4.2 25.6 1.0
CA A:PRO63 4.2 32.4 1.0
N A:PRO63 4.3 31.6 1.0
N A:GLY64 4.3 28.2 1.0
CB A:VAL65 4.3 25.1 1.0
CG A:LYS60 4.4 32.4 1.0
CA A:LEU62 4.4 26.8 1.0
O A:LYS61 4.4 34.7 1.0
N A:LYS61 4.5 29.4 1.0
O3' D:DT2 4.5 29.4 1.0
N A:GLY66 4.5 27.4 1.0
CA A:LYS61 4.6 29.3 1.0
C A:PRO63 4.7 30.3 1.0
CA A:GLY66 4.8 28.4 1.0
O5' D:DC3 4.9 28.0 1.0
C A:GLY64 4.9 27.6 1.0
CB A:LYS60 4.9 28.2 1.0
O A:ALA59 5.0 27.9 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 06:45:35 2024

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