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Sodium in PDB 6ctr: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf (R & S Isomers), Beta, Gamma Dctp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf (R & S Isomers), Beta, Gamma Dctp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf (R & S Isomers), 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 Chf (R & S Isomers), Beta, Gamma Dctp Analogue, PDB code: 6ctr 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) 23.74 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.810, 79.712, 55.437, 90.00, 107.72, 90.00
R / Rfree (%) 17.2 / 22.2

Other elements in 6ctr:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf (R & S Isomers), Beta, Gamma Dctp Analogue also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 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 Chf (R & S Isomers), Beta, Gamma Dctp Analogue (pdb code 6ctr). 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 Chf (R & S Isomers), Beta, Gamma Dctp Analogue, PDB code: 6ctr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6ctr

Go back to Sodium Binding Sites List in 6ctr
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf (R & S Isomers), 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 Chf (R & S Isomers), Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na401

b:23.8
occ:1.00
 O A:THR101 2.3 25.1 1.0
O A:ILE106 2.4 20.9 1.0
O P:HOH502 2.4 26.1 1.0
O A:VAL103 2.4 20.4 1.0
OP1 P:DG9 2.6 24.9 1.0
O A:HOH791 2.7 29.1 1.0
C A:THR101 3.3 23.4 1.0
C A:VAL103 3.4 19.6 1.0
C A:ILE106 3.4 25.1 1.0
P P:DG9 3.6 26.1 1.0
O A:HOH676 3.7 39.6 1.0
OP2 P:DG9 3.8 25.0 1.0
N A:ILE106 3.8 21.4 1.0
CA A:THR101 3.9 23.8 1.0
CA A:SER104 4.0 21.0 1.0
N A:VAL103 4.1 23.1 1.0
N A:SER104 4.1 19.4 1.0
N A:GLY105 4.1 23.5 1.0
CA A:ILE106 4.1 22.0 1.0
C A:ARG102 4.3 24.0 1.0
N A:ARG102 4.3 23.2 1.0
CA A:VAL103 4.4 22.9 1.0
C A:SER104 4.4 20.2 1.0
N A:GLY107 4.4 21.5 1.0
CB A:THR101 4.5 26.1 1.0
O3' P:DC8 4.5 28.0 1.0
CB A:ILE106 4.5 23.2 1.0
CA A:ARG102 4.5 23.1 1.0
C A:GLY105 4.7 23.4 1.0
CA A:GLY107 4.7 24.1 1.0
O A:HOH588 4.7 36.0 1.0
O A:ARG102 4.8 25.3 1.0
O A:LEU100 4.8 21.0 1.0
O5' P:DG9 4.9 26.7 1.0
CA A:GLY105 4.9 23.5 1.0
O A:HOH783 5.0 38.2 1.0

Sodium binding site 2 out of 3 in 6ctr

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

b:25.3
occ:1.00
 O A:LEU62 2.4 25.7 1.0
O A:LYS60 2.4 27.7 1.0
O A:VAL65 2.4 24.9 1.0
O A:HOH774 2.5 31.4 1.0
O D:HOH208 2.6 32.2 1.0
OP1 D:DC3 2.7 23.7 1.0
C A:LEU62 3.4 23.8 1.0
C A:LYS60 3.4 29.6 1.0
C A:VAL65 3.5 24.8 1.0
P D:DC3 3.7 26.6 1.0
N A:LEU62 3.9 25.0 1.0
OP2 D:DC3 3.9 23.4 1.0
N A:VAL65 3.9 23.9 1.0
C A:LYS61 4.0 28.4 1.0
O D:HOH213 4.0 33.7 1.0
N A:PRO63 4.1 26.5 1.0
CA A:PRO63 4.2 26.8 1.0
CA A:VAL65 4.2 21.8 1.0
CA A:LYS60 4.2 25.0 1.0
N A:GLY64 4.2 24.2 1.0
CA A:LEU62 4.3 24.6 1.0
O A:LYS61 4.3 27.5 1.0
N A:LYS61 4.4 29.1 1.0
CB A:VAL65 4.4 23.0 1.0
CA A:LYS61 4.4 27.3 1.0
CG A:LYS60 4.5 32.3 1.0
C A:PRO63 4.6 24.1 1.0
N A:GLY66 4.6 25.3 1.0
O3' D:DT2 4.6 25.7 1.0
O A:HOH794 4.8 39.2 1.0
O A:ALA59 4.8 25.5 1.0
C A:GLY64 4.9 25.7 1.0
CA A:GLY66 4.9 28.0 1.0
O5' D:DC3 4.9 28.2 1.0
CB A:LYS60 5.0 28.9 1.0

Sodium binding site 3 out of 3 in 6ctr

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

b:20.8
occ:1.00
 OD1 A:ASP192 2.1 19.4 1.0
OD2 A:ASP256 2.2 24.6 1.0
OD2 A:ASP190 2.3 26.1 1.0
O1A A:F3C404 2.5 17.6 0.6
O1A A:FF4405 2.5 17.6 0.4
CG A:ASP190 3.0 21.3 1.0
OD1 A:ASP190 3.1 20.6 1.0
CG A:ASP192 3.1 17.8 1.0
CG A:ASP256 3.4 24.7 1.0
OD2 A:ASP192 3.4 19.4 1.0
MG A:MG402 3.5 17.9 1.0
PA A:F3C404 3.5 19.6 0.6
PA A:FF4405 3.5 19.6 0.4
O5' A:F3C404 3.7 19.8 0.6
O5' A:FF4405 3.7 19.8 0.4
C3' P:2DA10 3.7 20.0 1.0
C5' A:F3C404 4.0 20.3 0.6
C5' A:FF4405 4.0 20.3 0.4
CB A:ASP256 4.0 20.7 1.0
O2A A:F3C404 4.1 19.2 0.6
O2A A:FF4405 4.1 19.2 0.4
C5' P:2DA10 4.2 25.9 1.0
CB A:ASP190 4.4 22.3 1.0
C4' P:2DA10 4.4 28.0 1.0
OD1 A:ASP256 4.4 22.5 1.0
O A:HOH646 4.5 30.6 1.0
CB A:ASP192 4.5 17.1 1.0
O A:MET191 4.7 17.8 1.0
OP1 P:2DA10 4.7 20.4 1.0
O A:HOH677 4.7 28.4 1.0
O5' P:2DA10 4.7 26.4 1.0
O2G A:F3C404 4.8 25.5 0.6
O2G A:FF4405 4.8 25.5 0.4
NH2 A:ARG254 4.9 20.4 1.0
CA A:ASP192 4.9 18.7 1.0
C A:MET191 5.0 18.3 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 06:45:35 2024

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