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Sodium in PDB 6ctp: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2, 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 CH2, Beta, Gamma Dttp Analogue, PDB code: 6ctp 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) 19.82 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.276, 78.923, 55.352, 90.00, 106.98, 90.00
R / Rfree (%) 22.5 / 29

Other elements in 6ctp:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 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 CH2, Beta, Gamma Dttp Analogue (pdb code 6ctp). 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 CH2, Beta, Gamma Dttp Analogue, PDB code: 6ctp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctp

Go back to Sodium Binding Sites List in 6ctp
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2, 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 CH2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na102

b:34.6
occ:1.00
 O A:HOH549 2.2 40.0 1.0
O A:THR101 2.3 41.8 1.0
OP1 P:DG9 2.3 34.7 1.0
O A:ILE106 2.4 32.8 1.0
O A:VAL103 2.5 33.1 1.0
C A:THR101 3.3 36.3 1.0
C A:VAL103 3.4 32.6 1.0
O A:HOH521 3.4 61.9 1.0
P P:DG9 3.4 36.4 1.0
C A:ILE106 3.5 35.6 1.0
OP2 P:DG9 3.7 37.1 1.0
N A:ILE106 3.7 29.4 1.0
CA A:SER104 3.8 29.2 1.0
N A:GLY105 3.8 29.1 1.0
CA A:THR101 3.9 36.0 1.0
N A:SER104 3.9 29.9 1.0
CA A:ILE106 4.1 31.4 1.0
N A:VAL103 4.2 30.0 1.0
C A:SER104 4.2 33.2 1.0
C A:ARG102 4.2 33.6 1.0
N A:ARG102 4.4 33.0 1.0
O3' P:DC8 4.4 33.9 1.0
CA A:VAL103 4.4 35.5 1.0
N A:GLY107 4.5 31.4 1.0
CB A:THR101 4.5 33.5 1.0
O5' P:DG9 4.5 37.4 1.0
CA A:ARG102 4.5 36.5 1.0
C A:GLY105 4.6 33.5 1.0
O A:ARG102 4.6 28.1 1.0
CB A:ILE106 4.6 31.4 1.0
CA A:GLY107 4.7 30.6 1.0
CA A:GLY105 4.8 30.6 1.0
O A:LEU100 4.8 32.7 1.0

Sodium binding site 2 out of 3 in 6ctp

Go back to Sodium Binding Sites List in 6ctp
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2, 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 CH2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na102

b:66.9
occ:1.00
 O A:LEU62 2.3 60.0 1.0
O A:VAL65 2.4 58.9 1.0
OP1 D:DC3 2.4 59.6 1.0
O A:LYS60 2.7 58.3 1.0
O D:HOH202 2.7 58.0 1.0
C A:VAL65 3.3 55.0 1.0
C A:LEU62 3.4 61.2 1.0
P D:DC3 3.5 67.3 1.0
N A:VAL65 3.6 61.4 1.0
CG1 A:VAL65 3.6 61.6 1.0
C A:LYS60 3.7 58.8 1.0
OP2 D:DC3 3.8 70.3 1.0
CA A:PRO63 3.9 60.1 1.0
CA A:VAL65 3.9 52.8 1.0
N A:GLY64 4.0 59.1 1.0
N A:PRO63 4.1 66.0 1.0
C A:PRO63 4.2 60.6 1.0
N A:LEU62 4.3 56.9 1.0
C A:LYS61 4.3 60.5 1.0
N A:GLY66 4.4 53.0 1.0
CB A:VAL65 4.4 55.5 1.0
CD A:LYS60 4.4 52.3 1.0
CA A:LYS60 4.4 56.9 1.0
O A:LYS61 4.5 71.9 1.0
CA A:LEU62 4.5 61.7 1.0
O3' D:DT2 4.5 63.0 1.0
O5' D:DC3 4.6 63.9 1.0
C A:GLY64 4.6 58.0 1.0
N A:LYS61 4.7 57.9 1.0
CA A:GLY66 4.8 49.6 1.0
CA A:LYS61 4.8 59.9 1.0
CA A:GLY64 4.9 60.6 1.0
CG A:LYS60 4.9 60.5 1.0
CE A:LYS60 4.9 62.7 1.0

Sodium binding site 3 out of 3 in 6ctp

Go back to Sodium Binding Sites List in 6ctp
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CH2, 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 CH2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:40.5
occ:1.00
 OD1 A:ASP192 2.1 32.6 1.0
OD2 A:ASP190 2.2 39.2 1.0
OD2 A:ASP256 2.3 45.9 1.0
O2A A:TTE401 2.4 35.8 1.0
CG A:ASP190 3.0 36.4 1.0
CG A:ASP192 3.1 29.5 1.0
OD1 A:ASP190 3.1 36.1 1.0
PA A:TTE401 3.2 34.4 1.0
C3' P:DOC10 3.2 47.9 1.0
OD2 A:ASP192 3.4 29.6 1.0
O5' A:TTE401 3.4 35.5 1.0
CG A:ASP256 3.4 40.3 1.0
O1A A:TTE401 3.6 35.8 1.0
MG A:MG403 3.8 38.7 1.0
C5' P:DOC10 3.8 53.2 1.0
C4' P:DOC10 3.8 56.8 1.0
C5' A:TTE401 3.9 33.6 1.0
CB A:ASP256 4.1 40.3 1.0
O5' P:DOC10 4.2 56.1 1.0
OD1 A:ASP256 4.4 44.9 1.0
CB A:ASP192 4.4 32.7 1.0
CB A:ASP190 4.4 36.3 1.0
C2' P:DOC10 4.5 48.2 1.0
O3G A:TTE401 4.7 35.1 1.0
O3A A:TTE401 4.7 35.9 1.0
O A:MET191 5.0 34.2 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: Mon Aug 18 04:09:59 2025

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