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

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-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 Chcl-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 Chcl-R/S Isomers, Beta, Gamma Dttp Analogue, PDB code: 6ctl 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) 22.20 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.862, 79.699, 55.119, 90.00, 107.66, 90.00
R / Rfree (%) 17.9 / 22.5

Other elements in 6ctl:

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

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 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 Dttp Analogue (pdb code 6ctl). 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 Dttp Analogue, PDB code: 6ctl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctl

Go back to Sodium Binding Sites List in 6ctl
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 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 Chcl-R/S Isomers, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:28.0
occ:1.00
 OD2 A:ASP190 2.1 24.2 1.0
OD1 A:ASP192 2.1 23.9 1.0
OD2 A:ASP256 2.2 25.7 1.0
O P:HOH107 2.3 25.0 1.0
O1A A:FDJ406 2.3 25.6 1.0
CG A:ASP190 3.0 20.1 1.0
CG A:ASP192 3.1 22.6 1.0
OD1 A:ASP190 3.2 23.3 1.0
CG A:ASP256 3.3 26.6 1.0
PA A:FDJ406 3.5 24.1 1.0
OD2 A:ASP192 3.5 24.6 1.0
MG A:MG401 3.5 23.0 1.0
O2A A:FDJ406 3.8 26.9 1.0
O5' A:FDJ406 3.8 26.3 1.0
C3' P:DOC10 3.9 28.1 1.0
CB A:ASP256 3.9 26.3 1.0
C5' A:FDJ406 4.2 24.6 1.0
OD1 A:ASP256 4.3 25.6 1.0
CB A:ASP190 4.4 23.8 1.0
CB A:ASP192 4.4 24.3 1.0
C5' P:DOC10 4.4 27.3 1.0
C4' P:DOC10 4.5 31.4 1.0
O1G A:FDJ406 4.5 24.2 1.0
OP1 P:DOC10 4.5 29.4 1.0
O A:HOH657 4.6 31.9 1.0
O A:MET191 4.7 27.6 1.0
NH2 A:ARG254 4.8 26.0 1.0
O3A A:FDJ406 4.9 26.9 1.0
O5' P:DOC10 4.9 28.7 1.0
N A:ASP256 5.0 24.9 1.0
CA A:ASP192 5.0 24.5 1.0

Sodium binding site 2 out of 3 in 6ctl

Go back to Sodium Binding Sites List in 6ctl
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 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 Chcl-R/S Isomers, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:29.2
occ:1.00
 O A:THR101 2.3 28.8 1.0
OP1 P:DG9 2.4 27.1 1.0
O A:ILE106 2.4 26.9 1.0
O A:VAL103 2.4 26.8 1.0
O P:HOH105 2.5 33.0 1.0
O A:HOH690 2.6 31.3 1.0
C A:VAL103 3.4 28.0 1.0
C A:THR101 3.4 27.1 1.0
C A:ILE106 3.4 24.6 1.0
P P:DG9 3.4 28.4 1.0
OP2 P:DG9 3.6 29.6 1.0
N A:ILE106 3.7 26.4 1.0
O A:HOH669 3.7 38.3 1.0
N A:GLY105 3.8 24.6 1.0
CA A:SER104 3.9 26.6 1.0
CA A:THR101 4.0 28.7 1.0
N A:SER104 4.0 23.1 1.0
CA A:ILE106 4.1 22.3 1.0
N A:VAL103 4.2 24.8 1.0
C A:SER104 4.2 26.7 1.0
O3' P:DC8 4.3 23.7 1.0
N A:GLY107 4.4 26.2 1.0
C A:ARG102 4.4 28.3 1.0
CA A:VAL103 4.4 28.1 1.0
N A:ARG102 4.4 26.5 1.0
C A:GLY105 4.5 26.0 1.0
CB A:ILE106 4.5 26.4 1.0
CB A:THR101 4.5 29.3 1.0
CA A:GLY107 4.6 26.0 1.0
O5' P:DG9 4.7 31.4 1.0
CA A:ARG102 4.7 30.8 1.0
CA A:GLY105 4.7 29.1 1.0
O A:ARG102 4.8 27.6 1.0
O A:LEU100 4.9 26.0 1.0
O A:HOH707 4.9 50.5 1.0

Sodium binding site 3 out of 3 in 6ctl

Go back to Sodium Binding Sites List in 6ctl
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 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 Chcl-R/S Isomers, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:37.1
occ:1.00
 O A:HOH622 2.2 42.9 1.0
O A:LEU62 2.3 35.2 1.0
O A:LYS60 2.4 42.1 1.0
O A:VAL65 2.4 36.4 1.0
O D:HOH102 2.5 36.6 1.0
OP1 D:DC3 2.6 35.6 1.0
C A:LEU62 3.4 35.9 1.0
C A:LYS60 3.5 38.4 1.0
C A:VAL65 3.5 37.1 1.0
P D:DC3 3.7 36.2 1.0
OP2 D:DC3 3.8 35.6 1.0
O D:HOH109 3.8 45.2 1.0
N A:VAL65 3.9 35.0 1.0
CA A:PRO63 4.0 33.6 1.0
C A:LYS61 4.1 40.9 1.0
N A:PRO63 4.1 37.7 1.0
N A:LEU62 4.1 37.8 1.0
N A:GLY64 4.2 38.0 1.0
CA A:VAL65 4.2 34.7 1.0
O A:LYS61 4.2 44.2 1.0
CA A:LYS60 4.2 37.3 1.0
CA A:LEU62 4.4 36.3 1.0
CG A:LYS60 4.4 36.0 1.0
C A:PRO63 4.5 34.0 1.0
N A:LYS61 4.5 35.4 1.0
CB A:VAL65 4.5 34.7 1.0
CA A:LYS61 4.6 37.9 1.0
N A:GLY66 4.6 36.2 1.0
O3' D:DT2 4.6 34.2 1.0
O5' D:DC3 4.8 41.6 1.0
CA A:GLY66 4.9 33.4 1.0
C A:GLY64 4.9 32.4 1.0
CB A:LYS60 4.9 39.6 1.0
O A:ALA59 4.9 34.7 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 06:43:35 2024

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