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Sodium in PDB 6ctk: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, 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 Chf-R/S Isomers, Beta, Gamma Dttp Analogue, PDB code: 6ctk 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) 21.24 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.640, 79.240, 55.382, 90.00, 107.08, 90.00
R / Rfree (%) 17.9 / 24.4

Other elements in 6ctk:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Fluorine (F) 1 atom
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 Chf-R/S Isomers, Beta, Gamma Dttp Analogue (pdb code 6ctk). 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 Chf-R/S Isomers, Beta, Gamma Dttp Analogue, PDB code: 6ctk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctk

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

b:31.9
occ:1.00
 OP1 P:DG9 2.3 27.0 1.0
O A:THR101 2.3 29.0 1.0
O A:ILE106 2.4 27.4 1.0
O P:HOH205 2.4 32.6 1.0
O A:VAL103 2.6 27.8 1.0
O A:HOH673 2.8 31.6 1.0
P P:DG9 3.3 28.1 1.0
C A:THR101 3.3 25.8 1.0
C A:ILE106 3.4 25.8 1.0
OP2 P:DG9 3.5 30.6 1.0
C A:VAL103 3.6 30.1 1.0
N A:ILE106 3.7 25.7 1.0
CA A:THR101 3.9 29.9 1.0
O A:HOH598 3.9 34.6 1.0
N A:GLY105 4.0 29.8 1.0
CA A:SER104 4.0 29.9 1.0
CA A:ILE106 4.0 29.7 1.0
N A:SER104 4.1 25.5 1.0
N A:VAL103 4.3 24.1 1.0
O3' P:DC8 4.3 29.4 1.0
N A:GLY107 4.3 28.5 1.0
C A:SER104 4.4 26.6 1.0
CB A:THR101 4.4 28.1 1.0
N A:ARG102 4.4 27.5 1.0
C A:ARG102 4.4 27.4 1.0
O5' P:DG9 4.5 32.9 1.0
CB A:ILE106 4.5 28.3 1.0
CA A:VAL103 4.6 32.1 1.0
C A:GLY105 4.6 28.4 1.0
CA A:GLY107 4.6 27.3 1.0
CA A:ARG102 4.7 31.1 1.0
O A:ARG102 4.8 30.0 1.0
CA A:GLY105 4.9 27.7 1.0
O A:LEU100 4.9 26.2 1.0

Sodium binding site 2 out of 3 in 6ctk

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

b:43.4
occ:1.00
 O A:LEU62 2.3 39.5 1.0
O A:LYS60 2.4 39.3 1.0
O A:VAL65 2.5 42.4 1.0
O A:HOH536 2.6 45.6 1.0
OP1 D:DC3 2.8 38.5 1.0
O D:HOH202 3.0 38.5 1.0
C A:LEU62 3.2 39.3 1.0
C A:LYS60 3.5 41.1 1.0
C A:VAL65 3.6 41.1 1.0
CA A:PRO63 3.7 41.2 1.0
OP2 D:DC3 3.7 39.8 1.0
P D:DC3 3.7 41.8 1.0
N A:PRO63 3.8 42.0 1.0
N A:VAL65 3.9 33.7 1.0
C A:LYS61 4.0 44.8 1.0
N A:LEU62 4.1 42.5 1.0
N A:GLY64 4.1 41.6 1.0
O A:LYS61 4.2 47.8 1.0
CA A:VAL65 4.2 36.8 1.0
CA A:LEU62 4.3 41.2 1.0
CA A:LYS60 4.3 43.2 1.0
C A:PRO63 4.3 41.4 1.0
N A:LYS61 4.4 40.6 1.0
CB A:VAL65 4.5 35.4 1.0
CA A:LYS61 4.6 44.6 1.0
N A:GLY66 4.6 38.2 1.0
O3' D:DT2 4.6 46.0 1.0
CG A:LYS60 4.7 42.0 1.0
CA A:GLY66 4.9 37.4 1.0
C A:GLY64 4.9 39.9 1.0
O A:ALA59 4.9 35.3 1.0
CB A:PRO63 5.0 45.9 1.0
O5' D:DC3 5.0 40.9 1.0

Sodium binding site 3 out of 3 in 6ctk

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

b:32.5
occ:1.00
 OD1 A:ASP192 2.3 28.1 1.0
OD2 A:ASP190 2.6 39.7 1.0
OD2 A:ASP256 2.8 36.1 1.0
O1A A:FDY401 2.8 28.1 1.0
CG A:ASP190 3.3 32.9 1.0
CG A:ASP192 3.3 26.5 1.0
C3' P:DOC10 3.4 33.8 1.0
OD1 A:ASP190 3.4 32.2 1.0
C5' P:DOC10 3.6 35.4 1.0
OD2 A:ASP192 3.6 24.2 1.0
C4' P:DOC10 3.6 40.4 1.0
MG A:MG402 3.7 28.2 1.0
CG A:ASP256 3.7 33.5 1.0
PA A:FDY401 3.9 29.4 1.0
O5' A:FDY401 4.0 24.7 1.0
C5' A:FDY401 4.2 23.1 1.0
CB A:ASP256 4.3 27.6 1.0
O2A A:FDY401 4.3 29.5 1.0
O5' P:DOC10 4.4 35.6 1.0
C2' P:DOC10 4.6 31.3 1.0
OD1 A:ASP256 4.6 33.4 1.0
CB A:ASP190 4.6 28.2 1.0
O A:HOH578 4.6 34.8 1.0
CB A:ASP192 4.7 28.7 1.0
NH2 A:ARG254 4.7 31.4 1.0
OP1 P:DOC10 4.7 39.1 1.0
O A:HOH633 4.7 39.6 1.0
O A:MET191 4.8 27.8 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 06:43:25 2024

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