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Calcium in PDB 2bq3: Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine

Enzymatic activity of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine

All present enzymatic activity of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine:
2.7.7.7;

Protein crystallography data

The structure of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine, PDB code: 2bq3 was solved by A.Irimia, L.V.Loukachevitch, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.84 / 2.0
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.679, 102.852, 53.178, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 27

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine (pdb code 2bq3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine, PDB code: 2bq3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2bq3

Go back to Calcium Binding Sites List in 2bq3
Calcium binding site 1 out of 3 in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:82.6
occ:1.00
 O A:HOH2065 2.7 65.5 1.0
OD2 A:ASP7 3.0 44.4 1.0
OP1 P:DA14 3.1 66.4 1.0
OE2 A:GLU106 3.2 47.8 1.0
CD A:GLU106 3.5 42.7 1.0
CG A:GLU106 3.5 40.0 1.0
OD1 A:ASP7 3.6 44.4 1.0
CG A:ASP7 3.6 41.6 1.0
OD1 A:ASP105 3.6 42.0 1.0
OD2 A:ASP105 3.7 44.5 1.0
CA A:CA2002 3.7 72.6 1.0
C5' P:DA14 3.8 63.8 1.0
O5' P:DA14 3.9 63.0 1.0
CG A:ASP105 3.9 41.7 1.0
P P:DA14 4.1 64.6 1.0
C3' P:DA14 4.3 63.8 1.0
OE1 A:GLU106 4.3 48.5 1.0
C4' P:DA14 4.6 63.4 1.0
NZ A:LYS159 4.6 61.4 1.0
O A:ASP105 4.9 29.8 1.0
NZ A:LYS152 4.9 49.4 1.0
CB A:ASP7 5.0 37.1 1.0

Calcium binding site 2 out of 3 in 2bq3

Go back to Calcium Binding Sites List in 2bq3
Calcium binding site 2 out of 3 in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:72.6
occ:1.00
 O A:PHE8 2.7 31.5 1.0
OD2 A:ASP105 2.8 44.5 1.0
O A:HOH2065 3.3 65.5 1.0
OD1 A:ASP7 3.5 44.4 1.0
CG A:ASP105 3.6 41.7 1.0
N A:PHE11 3.7 29.4 1.0
CA A:CA2001 3.7 82.6 1.0
N A:TYR10 3.7 30.6 1.0
C A:PHE8 3.9 33.1 1.0
CB A:ASP105 4.1 36.9 1.0
CB A:PHE11 4.2 30.1 1.0
C A:ASP9 4.2 33.5 1.0
CA A:TYR10 4.2 29.6 1.0
C3' P:DA14 4.3 63.8 1.0
O A:HOH2032 4.3 26.6 1.0
C A:TYR10 4.5 30.5 1.0
OD1 A:ASP105 4.5 42.0 1.0
O3' P:DA14 4.5 63.5 1.0
CA A:ASP9 4.5 34.0 1.0
CA A:PHE11 4.6 30.6 1.0
CG A:ASP7 4.6 41.6 1.0
N A:ASP9 4.7 33.4 1.0
C2' P:DA14 4.8 62.4 1.0
O A:HOH2014 4.9 33.7 1.0
N A:PHE8 4.9 32.0 1.0
CA A:PHE8 4.9 32.2 1.0
O A:ASP9 4.9 32.8 1.0
OD2 A:ASP7 5.0 44.4 1.0

Calcium binding site 3 out of 3 in 2bq3

Go back to Calcium Binding Sites List in 2bq3
Calcium binding site 3 out of 3 in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:54.2
occ:1.00
 O A:ALA181 2.5 42.8 1.0
O A:HOH2072 2.5 64.6 1.0
O P:HOH2006 2.6 50.5 1.0
O P:HOH2020 2.7 44.4 1.0
O P:HOH2021 2.7 47.1 1.0
O A:ILE186 3.0 40.9 1.0
C A:ALA181 3.6 44.6 1.0
C A:ILE186 4.2 40.4 1.0
OP2 P:DC13 4.3 44.6 1.0
CA A:ASP182 4.4 42.9 1.0
N A:ASP182 4.5 42.5 1.0
CA A:ALA181 4.5 44.8 1.0
CA A:GLY187 4.7 43.9 1.0
CB A:ALA181 4.7 45.9 1.0
O A:VAL183 4.8 37.8 1.0
OP1 P:DC13 4.8 44.5 1.0
N A:GLY187 4.9 42.3 1.0
C A:ASP182 4.9 40.6 1.0

Reference:

H.Zang, A.K.Goodenough, J.Y.Choi, A.Irimia, L.V.Loukachevitch, I.D.Kozekov, K.C.Angel, C.J.Rizzo, M.Egli, F.P.Guengerich. Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus Dna Polymerase DPO4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine. J.Biol.Chem. V. 280 29750 2005.
ISSN: ISSN 0021-9258
PubMed: 15965231
DOI: 10.1074/JBC.M504756200
Page generated: Fri Jul 12 09:08:47 2024

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