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Magnesium in PDB 6ctv: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, 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 CF2, Beta, Gamma Dctp Analogue, PDB code: 6ctv 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) 23.62 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.666, 79.251, 55.337, 90.00, 107.75, 90.00
R / Rfree (%) 18 / 22

Other elements in 6ctv:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue also contains other interesting chemical elements:

Fluorine (F) 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 CF2, Beta, Gamma Dctp Analogue (pdb code 6ctv). 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 CF2, Beta, Gamma Dctp Analogue, PDB code: 6ctv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ctv

Go back to Magnesium Binding Sites List in 6ctv
Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, 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 CF2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:47.5
occ:1.00
O A:HOH795 2.0 38.5 1.0
O T:HOH237 2.0 40.1 1.0
O A:HOH798 2.4 38.4 1.0
O T:HOH218 4.3 31.6 1.0
N3 T:DA4 4.4 34.8 1.0
O D:HOH107 4.4 38.5 1.0
O2 D:DC3 4.4 40.1 1.0
O A:HOH673 4.4 27.7 1.0
OE1 A:GLU288 4.6 36.3 1.0
O T:HOH234 4.7 36.1 1.0
O4' T:DC5 4.7 32.1 1.0
N2 T:DG3 4.7 36.3 1.0
C4' T:DC5 4.8 35.2 1.0
C5' T:DC5 4.8 33.1 1.0
C2 T:DA4 4.8 32.9 1.0
C5' D:DG4 4.9 38.7 1.0
O4' D:DG4 5.0 39.4 1.0

Magnesium binding site 2 out of 2 in 6ctv

Go back to Magnesium Binding Sites List in 6ctv
Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, 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 CF2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:19.1
occ:1.00
O1A A:FFJ406 2.0 16.8 1.0
OD2 A:ASP192 2.0 18.5 1.0
OD1 A:ASP190 2.1 19.4 1.0
O2G A:FFJ406 2.1 23.2 1.0
O1B A:FFJ406 2.1 20.0 1.0
O A:HOH520 2.2 24.9 1.0
CG A:ASP192 3.0 17.8 1.0
CG A:ASP190 3.2 20.4 1.0
PB A:FFJ406 3.2 20.7 1.0
PA A:FFJ406 3.2 20.4 1.0
PG A:FFJ406 3.3 26.3 1.0
NA A:NA401 3.4 24.3 1.0
OD1 A:ASP192 3.4 19.2 1.0
O3A A:FFJ406 3.5 24.4 1.0
OD2 A:ASP190 3.6 27.0 1.0
O3G A:FFJ406 3.7 24.7 1.0
C3B A:FFJ406 3.9 23.2 1.0
O A:ASP190 4.0 24.6 1.0
C5' A:FFJ406 4.1 20.5 1.0
O5' A:FFJ406 4.2 21.2 1.0
C A:ASP190 4.3 21.7 1.0
O2A A:FFJ406 4.3 21.3 1.0
O A:HOH607 4.4 17.9 1.0
CB A:ASP192 4.4 19.3 1.0
CA A:GLY179 4.4 17.8 1.0
N A:ASP190 4.4 19.4 1.0
CB A:ASP190 4.5 20.8 1.0
O A:HOH742 4.5 34.4 1.0
O1G A:FFJ406 4.5 25.5 1.0
O2B A:FFJ406 4.5 19.0 1.0
CA A:ASP190 4.6 17.7 1.0
F3B A:FFJ406 4.7 21.2 1.0
N A:SER180 4.7 20.8 1.0
O A:HOH560 4.8 37.2 1.0
N A:ASP192 4.8 22.1 1.0
N A:MET191 4.8 19.0 1.0
F4B A:FFJ406 4.9 24.2 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 Sep 30 22:44:20 2024

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