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Sodium in PDB 6ctn: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl,Beta-Gamma Dttp Analogue

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl,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 Cfcl,Beta-Gamma Dttp Analogue, PDB code: 6ctn 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) 18.84 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.834, 79.342, 55.527, 90.00, 107.14, 90.00
R / Rfree (%) 18.7 / 23.5

Other elements in 6ctn:

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

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
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 Cfcl,Beta-Gamma Dttp Analogue (pdb code 6ctn). 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 Cfcl,Beta-Gamma Dttp Analogue, PDB code: 6ctn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctn

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

b:19.2
occ:1.00
 O A:THR101 2.3 21.3 1.0
O A:VAL103 2.4 17.4 1.0
OP1 P:DG9 2.4 19.6 1.0
O A:ILE106 2.4 18.5 1.0
O A:HOH763 2.5 21.8 1.0
O P:HOH208 2.6 21.8 1.0
C A:THR101 3.3 19.2 1.0
C A:VAL103 3.4 18.0 1.0
C A:ILE106 3.5 17.6 1.0
P P:DG9 3.5 23.3 1.0
O A:HOH652 3.7 28.6 1.0
N A:ILE106 3.7 16.2 1.0
OP2 P:DG9 3.7 20.0 1.0
CA A:THR101 3.8 19.3 1.0
N A:GLY105 3.9 17.1 1.0
CA A:SER104 4.0 15.7 1.0
N A:VAL103 4.1 18.7 1.0
N A:SER104 4.1 15.7 1.0
CA A:ILE106 4.1 17.7 1.0
C A:ARG102 4.2 20.0 1.0
N A:ARG102 4.3 18.9 1.0
C A:SER104 4.3 16.1 1.0
CA A:VAL103 4.4 19.1 1.0
CB A:THR101 4.4 19.2 1.0
O3' P:DC8 4.4 18.7 1.0
N A:GLY107 4.5 17.0 1.0
CB A:ILE106 4.5 17.4 1.0
CA A:ARG102 4.5 19.5 1.0
C A:GLY105 4.6 20.4 1.0
O5' P:DG9 4.7 20.6 1.0
O A:ARG102 4.7 20.3 1.0
CA A:GLY107 4.7 18.9 1.0
O A:LEU100 4.8 17.0 1.0
CA A:GLY105 4.8 19.8 1.0
O A:HOH828 4.9 37.9 1.0

Sodium binding site 2 out of 3 in 6ctn

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

b:29.1
occ:1.00
 O A:LEU62 2.3 28.5 1.0
O A:LYS60 2.4 30.6 1.0
O A:VAL65 2.4 29.5 1.0
O A:HOH720 2.4 30.4 1.0
O D:HOH202 2.5 31.4 1.0
OP1 D:DC3 2.6 30.0 1.0
C A:LEU62 3.3 29.5 1.0
C A:LYS60 3.5 27.4 1.0
C A:VAL65 3.5 29.5 1.0
P D:DC3 3.7 31.8 1.0
O D:HOH206 3.8 37.4 1.0
N A:VAL65 3.9 26.6 1.0
OP2 D:DC3 4.0 27.2 1.0
N A:LEU62 4.0 28.4 1.0
C A:LYS61 4.1 30.4 1.0
CA A:PRO63 4.1 29.9 1.0
N A:PRO63 4.1 31.0 1.0
N A:GLY64 4.2 30.2 1.0
CA A:VAL65 4.2 28.2 1.0
CA A:LYS60 4.2 24.6 1.0
O A:HOH749 4.3 34.8 1.0
O A:LYS61 4.3 32.1 1.0
CA A:LEU62 4.3 25.7 1.0
CG A:LYS60 4.3 30.4 1.0
N A:LYS61 4.4 27.9 1.0
CB A:VAL65 4.5 27.4 1.0
C A:PRO63 4.5 28.9 1.0
CA A:LYS61 4.5 28.4 1.0
N A:GLY66 4.6 25.9 1.0
O3' D:DT2 4.7 30.6 1.0
CA A:GLY66 4.8 26.6 1.0
C A:GLY64 4.9 28.5 1.0
O A:ALA59 4.9 25.6 1.0
O5' D:DC3 4.9 33.9 1.0
CB A:LYS60 4.9 29.4 1.0

Sodium binding site 3 out of 3 in 6ctn

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

b:25.2
occ:1.00
 OD2 A:ASP190 2.1 24.6 1.0
OD1 A:ASP192 2.2 15.5 1.0
OD2 A:ASP256 2.3 25.5 1.0
O1A A:VT6401 2.5 16.8 1.0
C5' P:DOC10 3.0 37.4 1.0
CG A:ASP190 3.0 21.7 1.0
C3' P:DOC10 3.2 31.4 1.0
CG A:ASP192 3.2 17.3 1.0
OD1 A:ASP190 3.3 19.1 1.0
C4' P:DOC10 3.3 40.0 1.0
CG A:ASP256 3.4 26.9 1.0
PA A:VT6401 3.5 20.7 1.0
OD2 A:ASP192 3.5 15.2 1.0
MG A:MG402 3.7 17.0 1.0
O5' A:VT6401 3.7 19.3 1.0
CB A:ASP256 4.0 21.2 1.0
O2A A:VT6401 4.0 19.4 1.0
C5' A:VT6401 4.1 19.0 1.0
O5' P:DOC10 4.3 42.6 1.0
O A:HOH662 4.4 27.5 1.0
CB A:ASP190 4.4 14.9 1.0
OD1 A:ASP256 4.4 26.6 1.0
OP1 P:DOC10 4.4 45.6 1.0
CB A:ASP192 4.5 14.6 1.0
C2' P:DOC10 4.6 29.5 1.0
O1G A:VT6401 4.7 17.6 1.0
O P:HOH219 4.8 30.4 1.0
O4' P:DOC10 4.8 40.9 1.0
O A:MET191 5.0 17.5 1.0
O3A A:VT6401 5.0 18.4 1.0
NH2 A:ARG254 5.0 32.3 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 Dec 15 12:06:09 2020

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