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Calcium in PDB 2v4r: Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine

Enzymatic activity of Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine

All present enzymatic activity of Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine:
2.7.7.7;

Protein crystallography data

The structure of Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine, PDB code: 2v4r was solved by R.L.Eoff, J.B.Stafford, J.Szekely, C.J.Rizzo, M.Egli, F.P.Guengerich, L.J.Marnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.545, 102.537, 52.176, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 27.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine (pdb code 2v4r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine, PDB code: 2v4r:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2v4r

Go back to Calcium Binding Sites List in 2v4r
Calcium binding site 1 out of 3 in the Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1000

b:36.5
occ:1.00
 O A:PHE9 2.4 28.1 1.0
OD2 A:ASP8 2.5 35.0 1.0
OD2 A:ASP106 2.5 35.0 1.0
O3G A:DGT404 2.7 36.4 1.0
O3A A:DGT404 2.8 37.6 1.0
O1B A:DGT404 2.8 31.6 1.0
O1G A:DGT404 3.3 42.0 1.0
CG A:ASP8 3.3 32.8 1.0
PG A:DGT404 3.3 36.0 1.0
PB A:DGT404 3.4 29.3 1.0
CA A:CA1001 3.4 38.0 1.0
OD1 A:ASP8 3.5 35.2 1.0
C A:PHE9 3.5 29.0 1.0
O2A A:DGT404 3.7 44.1 1.0
CG A:ASP106 3.8 34.2 1.0
PA A:DGT404 3.8 39.1 1.0
O3B A:DGT404 3.8 35.4 1.0
N A:PHE9 4.2 29.1 1.0
C5' A:DGT404 4.3 33.6 1.0
N A:TYR11 4.3 27.1 1.0
NZ A:LYS160 4.4 42.3 1.0
OD1 A:ASP106 4.4 35.4 1.0
CA A:PHE9 4.4 29.8 1.0
N A:ASP10 4.4 28.7 1.0
CA A:ASP10 4.5 28.7 1.0
O5' A:DGT404 4.5 40.5 1.0
C A:ASP8 4.5 30.1 1.0
CB A:ASP8 4.6 31.9 1.0
C A:ASP10 4.6 28.8 1.0
O2B A:DGT404 4.7 36.2 1.0
N A:PHE12 4.8 24.1 1.0
CB A:ASP106 4.8 32.1 1.0
O2G A:DGT404 4.9 38.8 1.0
O A:ASP106 5.0 31.5 1.0

Calcium binding site 2 out of 3 in 2v4r

Go back to Calcium Binding Sites List in 2v4r
Calcium binding site 2 out of 3 in the Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:38.0
occ:1.00
 O2A A:DGT404 2.4 44.1 1.0
OD1 A:ASP106 2.6 35.4 1.0
O A:HOH2089 2.8 30.4 1.0
OE2 A:GLU107 2.8 44.1 1.0
O A:HOH2091 2.9 46.9 1.0
OD2 A:ASP106 3.0 35.0 1.0
OD2 A:ASP8 3.0 35.0 1.0
OD1 A:ASP8 3.0 35.2 1.0
CG A:ASP106 3.1 34.2 1.0
CG A:GLU107 3.2 38.5 1.0
CD A:GLU107 3.2 40.1 1.0
CG A:ASP8 3.3 32.8 1.0
CA A:CA1000 3.4 36.5 1.0
PA A:DGT404 3.7 39.1 1.0
O3A A:DGT404 4.1 37.6 1.0
OE1 A:GLU107 4.3 43.6 1.0
C5' A:DGT404 4.3 33.6 1.0
O A:ASP106 4.3 31.5 1.0
CB A:ASP8 4.6 31.9 1.0
O5' A:DGT404 4.6 40.5 1.0
CB A:ASP106 4.6 32.1 1.0
CB A:GLU107 4.6 35.1 1.0
C A:ASP106 4.7 31.3 1.0
O3G A:DGT404 4.7 36.4 1.0
NZ A:LYS160 4.9 42.3 1.0
O1A A:DGT404 4.9 42.8 1.0
OG A:SER104 4.9 37.3 1.0

Calcium binding site 3 out of 3 in 2v4r

Go back to Calcium Binding Sites List in 2v4r
Calcium binding site 3 out of 3 in the Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Non-Productive Complex of the Y-Family Dna Polymerase DPO4 with Dgtp Skipping the M1DG Adduct to Pair with the Next Template Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:57.6
occ:1.00
 O A:ALA182 2.7 47.2 1.0
O P:HOH2020 2.8 56.5 1.0
O A:HOH2050 2.9 58.1 1.0
O A:ILE187 3.3 32.3 1.0
O A:HOH2053 3.3 48.2 1.0
C A:ALA182 3.9 45.1 1.0
OP2 P:DC13 4.4 26.5 1.0
C A:ILE187 4.4 31.0 1.0
CA A:GLY188 4.6 35.0 1.0
CA A:ALA182 4.7 45.5 1.0
OP1 P:DC13 4.7 27.4 1.0
CB A:ALA182 4.7 43.6 1.0
N A:ASP183 4.8 42.8 1.0
CA A:ASP183 4.8 40.4 1.0
N A:GLY188 5.0 32.3 1.0

Reference:

R.L.Eoff, J.B.Stafford, J.Szekely, C.J.Rizzo, M.Egli, F.P.Guengerich, L.J.Marnett. Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family Dna Polymerase DPO4-Catalyzed Bypass of the Malondialdehyde-Deoxyguanosine Adduct. Biochemistry V. 48 7079 2009.
ISSN: ISSN 0006-2960
PubMed: 19492857
DOI: 10.1021/BI9003588
Page generated: Tue Jul 8 08:29:29 2025

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