Atomistry » Sodium » PDB 6chr-6ctn » 6ctn
Atomistry »
  Sodium »
    PDB 6chr-6ctn »
      6ctn »

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 Oct 8 06:44:20 2024

Last articles

Cl in 7UY1
Cl in 7UVR
Cl in 7UX4
Cl in 7UVM
Cl in 7UVN
Cl in 7UVH
Cl in 7UVO
Cl in 7UVF
Cl in 7UQC
Cl in 7UQA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy