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Magnesium in PDB 6ctm: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), 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 Chcl(R-Isomer), Beta, Gamma Dttp Analogue, PDB code: 6ctm 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) 23.69 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.404, 76.853, 54.961, 90.00, 103.76, 90.00
R / Rfree (%) 18.6 / 25.8

Other elements in 6ctm:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 2 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 Chcl(R-Isomer), Beta, Gamma Dttp Analogue (pdb code 6ctm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), Beta, Gamma Dttp Analogue, PDB code: 6ctm:

Magnesium binding site 1 out of 1 in 6ctm

Go back to Magnesium Binding Sites List in 6ctm
Magnesium binding site 1 out of 1 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl(R-Isomer), Beta, Gamma Dttp 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 Chcl(R-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:24.6
occ:1.00
 O1B A:FDJ402 2.0 23.2 1.0
OD1 A:ASP190 2.0 22.6 1.0
O A:HOH548 2.1 23.1 1.0
OD2 A:ASP192 2.1 21.3 1.0
O1A A:FDJ402 2.1 19.5 1.0
O1G A:FDJ402 2.1 24.6 1.0
PB A:FDJ402 3.2 22.2 1.0
CG A:ASP192 3.2 26.5 1.0
CG A:ASP190 3.2 23.1 1.0
PG A:FDJ402 3.2 23.9 1.0
PA A:FDJ402 3.4 22.9 1.0
O3G A:FDJ402 3.5 25.3 1.0
OD1 A:ASP192 3.6 23.8 1.0
O3A A:FDJ402 3.6 20.4 1.0
OD2 A:ASP190 3.7 28.4 1.0
C3B A:FDJ402 3.8 24.6 1.0
O A:ASP190 3.9 23.5 1.0
NA A:NA403 4.0 47.1 1.0
N A:ASP190 4.1 21.6 1.0
C5' A:FDJ402 4.2 25.1 1.0
C A:ASP190 4.2 24.1 1.0
O5' A:FDJ402 4.3 25.0 1.0
CB A:ASP190 4.4 19.2 1.0
N A:SER180 4.4 30.1 1.0
O2A A:FDJ402 4.4 23.5 1.0
CA A:GLY179 4.4 25.3 1.0
O A:HOH553 4.4 21.2 1.0
O2B A:FDJ402 4.5 22.1 1.0
CB A:ASP192 4.5 22.0 1.0
CA A:ASP190 4.5 22.7 1.0
O2G A:FDJ402 4.5 24.7 1.0
OG A:SER180 4.6 24.2 1.0
N A:ASP192 4.9 21.9 1.0
N A:MET191 5.0 20.6 1.0
C A:GLY179 5.0 25.4 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: Mon Sep 30 22:43:30 2024

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