Magnesium 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:

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

Magnesium binding site 1 out of 2 in 6ctx

Go back to Magnesium Binding Sites List in 6ctx
Magnesium binding site 1 out of 2 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 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:41.0
occ:1.00
O T:HOH231 1.9 34.5 1.0
O A:HOH826 2.0 37.6 1.0
O A:HOH587 2.1 41.8 1.0
O T:HOH251 2.2 37.6 1.0
O T:HOH241 2.4 40.2 1.0
O A:HOH745 4.3 28.6 1.0
OE1 A:GLU288 4.4 35.1 1.0
N3 T:DA4 4.4 29.8 1.0
O D:HOH202 4.5 29.6 1.0
O T:HOH204 4.5 32.1 1.0
O D:HOH214 4.6 39.3 1.0
O4' T:DC5 4.6 31.6 1.0
O2 D:DC3 4.6 32.4 1.0
O D:HOH213 4.7 38.0 1.0
C4' T:DC5 4.7 29.2 1.0
C2 T:DA4 4.8 27.6 1.0
C5' T:DC5 4.9 30.1 1.0
N2 T:DG3 4.9 35.0 1.0

Magnesium binding site 2 out of 2 in 6ctx

Go back to Magnesium Binding Sites List in 6ctx
Magnesium binding site 2 out of 2 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 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 CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:15.7
occ:1.00
OD1 A:ASP190 2.0 17.8 1.0
O1A A:VC9404 2.1 15.4 1.0
OD2 A:ASP192 2.1 17.0 1.0
O1B A:VC9404 2.1 19.0 1.0
O2G A:VC9404 2.2 17.4 1.0
O A:HOH526 2.2 18.4 1.0
CG A:ASP190 3.1 19.7 1.0
CG A:ASP192 3.1 15.5 1.0
PB A:VC9404 3.2 19.3 1.0
PG A:VC9404 3.2 24.9 1.0
PA A:VC9404 3.3 17.9 1.0
OD1 A:ASP192 3.4 19.6 1.0
OD2 A:ASP190 3.5 26.9 1.0
O3G A:VC9404 3.6 19.0 1.0
NA A:NA401 3.6 23.5 1.0
O3A A:VC9404 3.7 17.9 1.0
O A:HOH505 3.7 32.0 1.0
C3B A:VC9404 3.8 21.1 1.0
O A:ASP190 4.0 18.3 1.0
C5' A:VC9404 4.2 17.7 1.0
C A:ASP190 4.2 16.6 1.0
O5' A:VC9404 4.2 18.7 1.0
O A:HOH673 4.3 17.2 1.0
CB A:ASP190 4.4 20.1 1.0
N A:ASP190 4.4 16.4 1.0
O2A A:VC9404 4.4 19.0 1.0
CB A:ASP192 4.5 17.3 1.0
CA A:GLY179 4.5 14.5 1.0
CA A:ASP190 4.5 14.5 1.0
O2B A:VC9404 4.6 17.0 1.0
O1G A:VC9404 4.6 26.0 1.0
O P:HOH206 4.7 33.6 1.0
N A:SER180 4.8 19.1 1.0
N A:ASP192 4.8 18.5 1.0
N A:MET191 4.8 14.0 1.0
OG A:SER180 4.9 19.2 1.0
C A:MET191 5.0 14.2 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 Dec 14 22:32:14 2020

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