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Sodium in PDB 6ctx: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Dctp Analogue, PDB code: 6ctx 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) 31.79 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.815, 79.565, 55.502, 90.00, 107.78, 90.00
R / Rfree (%) 17.7 / 22.9

Other elements in 6ctx:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Bromine (Br) 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 CBR2, Beta, Gamma Dctp Analogue (pdb code 6ctx). 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 CBR2, Beta, Gamma Dctp Analogue, PDB code: 6ctx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctx

Go back to Sodium Binding Sites List in 6ctx
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:24.1
occ:1.00
 O P:HOH203 2.4 27.5 1.0
O A:THR101 2.4 23.9 1.0
O A:ILE106 2.5 15.6 1.0
O A:VAL103 2.5 18.9 1.0
OP1 P:DG9 2.6 23.8 1.0
O A:HOH789 2.6 22.5 1.0
C A:THR101 3.3 21.8 1.0
C A:VAL103 3.4 19.2 1.0
C A:ILE106 3.5 20.4 1.0
P P:DG9 3.6 24.8 1.0
OP2 P:DG9 3.7 23.7 1.0
N A:ILE106 3.8 20.8 1.0
CA A:THR101 3.9 25.0 1.0
N A:GLY105 4.0 21.0 1.0
CA A:SER104 4.1 19.8 1.0
CA A:ILE106 4.1 19.9 1.0
N A:VAL103 4.1 22.2 1.0
N A:SER104 4.1 18.0 1.0
N A:ARG102 4.3 18.2 1.0
C A:ARG102 4.3 21.9 1.0
C A:SER104 4.4 17.7 1.0
N A:GLY107 4.4 22.1 1.0
CA A:VAL103 4.4 22.7 1.0
O3' P:DC8 4.5 24.6 1.0
CB A:ILE106 4.5 17.2 1.0
CB A:THR101 4.5 23.1 1.0
CA A:ARG102 4.6 22.9 1.0
C A:GLY105 4.6 22.7 1.0
CA A:GLY107 4.7 20.4 1.0
O A:LEU100 4.8 19.3 1.0
O A:ARG102 4.8 24.2 1.0
O5' P:DG9 4.8 23.6 1.0
CA A:GLY105 4.9 22.9 1.0

Sodium binding site 2 out of 3 in 6ctx

Go back to Sodium Binding Sites List in 6ctx
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:30.4
occ:1.00
 O A:LEU62 2.3 24.0 1.0
O A:VAL65 2.4 24.4 1.0
O A:LYS60 2.5 27.3 1.0
O D:HOH204 2.5 22.9 1.0
O A:HOH742 2.5 29.9 1.0
OP1 D:DC3 2.6 27.1 1.0
C A:LEU62 3.3 25.1 1.0
C A:VAL65 3.5 21.8 1.0
C A:LYS60 3.6 22.4 1.0
P D:DC3 3.6 27.9 1.0
O D:HOH211 3.8 32.6 1.0
OP2 D:DC3 3.8 27.5 1.0
N A:VAL65 3.9 21.5 1.0
N A:LEU62 3.9 25.5 1.0
CA A:PRO63 4.0 26.2 1.0
C A:LYS61 4.0 32.1 1.0
N A:PRO63 4.0 28.4 1.0
CA A:VAL65 4.1 20.7 1.0
N A:GLY64 4.1 23.1 1.0
O A:LYS61 4.2 31.4 1.0
CA A:LEU62 4.2 24.4 1.0
CA A:LYS60 4.3 23.9 1.0
CB A:VAL65 4.4 21.5 1.0
N A:LYS61 4.5 25.8 1.0
C A:PRO63 4.5 25.6 1.0
O3' D:DT2 4.5 29.3 1.0
CG A:LYS60 4.5 28.1 1.0
CA A:LYS61 4.6 27.0 1.0
N A:GLY66 4.6 25.0 1.0
C A:GLY64 4.8 26.4 1.0
O5' D:DC3 4.9 29.9 1.0
O A:ALA59 4.9 24.8 1.0
CA A:GLY66 4.9 23.9 1.0

Sodium binding site 3 out of 3 in 6ctx

Go back to Sodium Binding Sites List in 6ctx
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:23.5
occ:1.00
 OD1 A:ASP192 2.2 19.6 1.0
OD2 A:ASP256 2.3 24.9 1.0
OD2 A:ASP190 2.3 26.9 1.0
O P:HOH206 2.4 33.6 1.0
O1A A:VC9404 2.7 15.4 1.0
CG A:ASP190 3.0 19.7 1.0
OD1 A:ASP190 3.1 17.8 1.0
CG A:ASP192 3.2 15.5 1.0
CG A:ASP256 3.4 19.7 1.0
MG A:MG402 3.6 15.7 1.0
OD2 A:ASP192 3.6 17.0 1.0
PA A:VC9404 3.7 17.9 1.0
O5' A:VC9404 3.9 18.7 1.0
C3' P:2DA10 3.9 20.5 1.0
CB A:ASP256 3.9 21.6 1.0
O2A A:VC9404 4.1 19.0 1.0
C5' P:2DA10 4.2 21.6 1.0
O A:HOH505 4.3 32.0 1.0
C5' A:VC9404 4.3 17.7 1.0
O A:HOH597 4.3 29.3 1.0
CB A:ASP190 4.4 20.1 1.0
C4' P:2DA10 4.4 25.5 1.0
OD1 A:ASP256 4.4 21.6 1.0
CB A:ASP192 4.5 17.3 1.0
OP1 P:2DA10 4.6 21.9 1.0
O A:MET191 4.6 16.7 1.0
O5' P:2DA10 4.7 26.2 1.0
NH2 A:ARG254 4.7 23.4 1.0
O2G A:VC9404 4.7 17.4 1.0
N A:ASP256 4.9 17.6 1.0
C A:MET191 4.9 14.2 1.0
CA A:ASP192 5.0 14.4 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 06:47:12 2024

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