Atomistry » Sodium » PDB 6cto-6d4o » 6ctx
Atomistry »
  Sodium »
    PDB 6cto-6d4o »
      6ctx »

Sodium in PDB 6ctx: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp 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 CBR2, Beta, Gamma Dctp Analogue, PDB code: 6ctx 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) 31.79 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.815, 79.565, 55.502, 90.00, 107.78, 90.00
R / Rfree (%) 17.7 / 22.9

Other elements in 6ctx:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Bromine (Br) 2 atoms
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 CBR2, Beta, Gamma Dctp Analogue (pdb code 6ctx). 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 CBR2, Beta, Gamma Dctp Analogue, PDB code: 6ctx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctx

Go back to Sodium Binding Sites List in 6ctx
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:24.1
occ:1.00
 O P:HOH203 2.4 27.5 1.0
O A:THR101 2.4 23.9 1.0
O A:ILE106 2.5 15.6 1.0
O A:VAL103 2.5 18.9 1.0
OP1 P:DG9 2.6 23.8 1.0
O A:HOH789 2.6 22.5 1.0
C A:THR101 3.3 21.8 1.0
C A:VAL103 3.4 19.2 1.0
C A:ILE106 3.5 20.4 1.0
P P:DG9 3.6 24.8 1.0
OP2 P:DG9 3.7 23.7 1.0
N A:ILE106 3.8 20.8 1.0
CA A:THR101 3.9 25.0 1.0
N A:GLY105 4.0 21.0 1.0
CA A:SER104 4.1 19.8 1.0
CA A:ILE106 4.1 19.9 1.0
N A:VAL103 4.1 22.2 1.0
N A:SER104 4.1 18.0 1.0
N A:ARG102 4.3 18.2 1.0
C A:ARG102 4.3 21.9 1.0
C A:SER104 4.4 17.7 1.0
N A:GLY107 4.4 22.1 1.0
CA A:VAL103 4.4 22.7 1.0
O3' P:DC8 4.5 24.6 1.0
CB A:ILE106 4.5 17.2 1.0
CB A:THR101 4.5 23.1 1.0
CA A:ARG102 4.6 22.9 1.0
C A:GLY105 4.6 22.7 1.0
CA A:GLY107 4.7 20.4 1.0
O A:LEU100 4.8 19.3 1.0
O A:ARG102 4.8 24.2 1.0
O5' P:DG9 4.8 23.6 1.0
CA A:GLY105 4.9 22.9 1.0

Sodium binding site 2 out of 3 in 6ctx

Go back to Sodium Binding Sites List in 6ctx
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:30.4
occ:1.00
 O A:LEU62 2.3 24.0 1.0
O A:VAL65 2.4 24.4 1.0
O A:LYS60 2.5 27.3 1.0
O D:HOH204 2.5 22.9 1.0
O A:HOH742 2.5 29.9 1.0
OP1 D:DC3 2.6 27.1 1.0
C A:LEU62 3.3 25.1 1.0
C A:VAL65 3.5 21.8 1.0
C A:LYS60 3.6 22.4 1.0
P D:DC3 3.6 27.9 1.0
O D:HOH211 3.8 32.6 1.0
OP2 D:DC3 3.8 27.5 1.0
N A:VAL65 3.9 21.5 1.0
N A:LEU62 3.9 25.5 1.0
CA A:PRO63 4.0 26.2 1.0
C A:LYS61 4.0 32.1 1.0
N A:PRO63 4.0 28.4 1.0
CA A:VAL65 4.1 20.7 1.0
N A:GLY64 4.1 23.1 1.0
O A:LYS61 4.2 31.4 1.0
CA A:LEU62 4.2 24.4 1.0
CA A:LYS60 4.3 23.9 1.0
CB A:VAL65 4.4 21.5 1.0
N A:LYS61 4.5 25.8 1.0
C A:PRO63 4.5 25.6 1.0
O3' D:DT2 4.5 29.3 1.0
CG A:LYS60 4.5 28.1 1.0
CA A:LYS61 4.6 27.0 1.0
N A:GLY66 4.6 25.0 1.0
C A:GLY64 4.8 26.4 1.0
O5' D:DC3 4.9 29.9 1.0
O A:ALA59 4.9 24.8 1.0
CA A:GLY66 4.9 23.9 1.0

Sodium binding site 3 out of 3 in 6ctx

Go back to Sodium Binding Sites List in 6ctx
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:23.5
occ:1.00
 OD1 A:ASP192 2.2 19.6 1.0
OD2 A:ASP256 2.3 24.9 1.0
OD2 A:ASP190 2.3 26.9 1.0
O P:HOH206 2.4 33.6 1.0
O1A A:VC9404 2.7 15.4 1.0
CG A:ASP190 3.0 19.7 1.0
OD1 A:ASP190 3.1 17.8 1.0
CG A:ASP192 3.2 15.5 1.0
CG A:ASP256 3.4 19.7 1.0
MG A:MG402 3.6 15.7 1.0
OD2 A:ASP192 3.6 17.0 1.0
PA A:VC9404 3.7 17.9 1.0
O5' A:VC9404 3.9 18.7 1.0
C3' P:2DA10 3.9 20.5 1.0
CB A:ASP256 3.9 21.6 1.0
O2A A:VC9404 4.1 19.0 1.0
C5' P:2DA10 4.2 21.6 1.0
O A:HOH505 4.3 32.0 1.0
C5' A:VC9404 4.3 17.7 1.0
O A:HOH597 4.3 29.3 1.0
CB A:ASP190 4.4 20.1 1.0
C4' P:2DA10 4.4 25.5 1.0
OD1 A:ASP256 4.4 21.6 1.0
CB A:ASP192 4.5 17.3 1.0
OP1 P:2DA10 4.6 21.9 1.0
O A:MET191 4.6 16.7 1.0
O5' P:2DA10 4.7 26.2 1.0
NH2 A:ARG254 4.7 23.4 1.0
O2G A:VC9404 4.7 17.4 1.0
N A:ASP256 4.9 17.6 1.0
C A:MET191 4.9 14.2 1.0
CA A:ASP192 5.0 14.4 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 06:47:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy