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Magnesium in PDB 6ctu: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, 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 Cfcl, Beta, Gamma Dctp Analogue, PDB code: 6ctu 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) 23.72 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.810, 79.636, 55.483, 90.00, 107.78, 90.00
R / Rfree (%) 17.1 / 20.6

Other elements in 6ctu:

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

Fluorine (F) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue (pdb code 6ctu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue, PDB code: 6ctu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ctu

Go back to Magnesium Binding Sites List in 6ctu
Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:42.4
occ:1.00
O T:HOH230 1.9 33.1 1.0
O D:HOH212 2.2 35.4 1.0
O T:HOH254 2.2 37.8 1.0
O A:HOH736 4.3 25.5 1.0
O T:HOH205 4.3 32.8 1.0
O T:HOH249 4.5 41.6 1.0
OE1 A:GLU288 4.5 36.2 1.0
O D:HOH205 4.5 29.1 1.0
O2 D:DC3 4.6 31.9 1.0
N3 T:DA4 4.6 29.0 1.0
O4' T:DC5 4.7 30.0 1.0
C4' T:DC5 4.7 31.0 1.0
C5' T:DC5 4.9 29.7 1.0

Magnesium binding site 2 out of 2 in 6ctu

Go back to Magnesium Binding Sites List in 6ctu
Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:14.9
occ:1.00
O1A A:VC6404 2.0 12.3 1.0
OD2 A:ASP192 2.0 15.2 1.0
OD1 A:ASP190 2.1 18.2 1.0
O A:HOH527 2.1 16.3 1.0
O1B A:VC6404 2.1 14.0 1.0
O2G A:VC6404 2.2 16.9 1.0
CG A:ASP192 3.1 14.2 1.0
CG A:ASP190 3.2 19.9 1.0
PB A:VC6404 3.2 16.2 1.0
PA A:VC6404 3.3 16.1 1.0
PG A:VC6404 3.3 24.4 1.0
OD1 A:ASP192 3.5 15.4 1.0
O3G A:VC6404 3.6 21.9 1.0
NA A:NA401 3.6 19.9 1.0
O3A A:VC6404 3.6 15.9 1.0
OD2 A:ASP190 3.7 24.7 1.0
C3B A:VC6404 3.9 21.6 1.0
O A:ASP190 4.0 17.1 1.0
O5' A:VC6404 4.1 14.2 1.0
C5' A:VC6404 4.1 17.8 1.0
C A:ASP190 4.2 17.5 1.0
O A:HOH647 4.3 15.9 1.0
N A:ASP190 4.4 16.1 1.0
CB A:ASP192 4.4 15.7 1.0
O2A A:VC6404 4.4 15.0 1.0
CB A:ASP190 4.4 16.6 1.0
CA A:GLY179 4.4 10.8 1.0
O2B A:VC6404 4.5 14.6 1.0
O1G A:VC6404 4.6 30.6 1.0
CA A:ASP190 4.6 14.2 1.0
N A:SER180 4.7 17.7 1.0
N A:ASP192 4.8 16.7 1.0
N A:MET191 4.8 14.4 1.0
CL1 A:VC6404 4.9 23.8 1.0
C A:MET191 5.0 13.8 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 Sep 30 22:44:09 2024

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