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Calcium in PDB 2bqu: 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: 2bqu 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) 42.25 / 2.5
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.359, 103.027, 52.987, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 24.8

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 2bqu). 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: 2bqu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2bqu

Go back to Calcium Binding Sites List in 2bqu
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:Ca1343

b:76.7
occ:1.00
 OE1 A:GLU106 2.6 55.9 1.0
OD2 A:ASP7 2.8 36.6 1.0
O3A A:DAD1342 2.9 79.8 1.0
OD2 A:ASP105 3.0 38.4 1.0
OD1 A:ASP7 3.1 36.1 1.0
CA A:CA1344 3.1 49.4 1.0
CG A:ASP7 3.2 38.2 1.0
CG A:GLU106 3.2 48.7 1.0
CD A:GLU106 3.3 51.1 1.0
O5' A:DAD1342 3.4 81.2 1.0
C5' A:DAD1342 3.4 79.3 1.0
OD1 A:ASP105 3.5 39.7 1.0
O A:HOH2090 3.6 50.6 1.0
CG A:ASP105 3.6 39.4 1.0
O2B A:DAD1342 3.6 75.4 1.0
PB A:DAD1342 3.7 75.3 1.0
PA A:DAD1342 3.8 84.0 1.0
O3B A:DAD1342 4.0 68.2 1.0
NZ A:LYS159 4.2 53.2 1.0
O1A A:DAD1342 4.4 82.8 1.0
O A:HOH2035 4.4 38.8 1.0
OE2 A:GLU106 4.5 53.6 1.0
CB A:ASP7 4.6 36.4 1.0
CB A:GLU106 4.7 42.7 1.0
O A:ASP105 4.8 37.1 1.0
C4' A:DAD1342 4.8 76.3 1.0
NZ A:LYS152 4.9 54.3 1.0

Calcium binding site 2 out of 3 in 2bqu

Go back to Calcium Binding Sites List in 2bqu
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:Ca1344

b:49.4
occ:1.00
 OD1 A:ASP7 2.5 36.1 1.0
O A:PHE8 2.6 32.6 1.0
OD2 A:ASP105 2.6 38.4 1.0
O2B A:DAD1342 2.9 75.4 1.0
O1G A:DAD1342 2.9 63.1 1.0
O3B A:DAD1342 3.1 68.2 1.0
CA A:CA1343 3.1 76.7 1.0
PG A:DAD1342 3.3 60.7 1.0
PB A:DAD1342 3.5 75.3 1.0
O A:HOH2005 3.5 31.9 1.0
O A:HOH2086 3.5 47.2 1.0
CG A:ASP7 3.5 38.2 1.0
C A:PHE8 3.7 33.4 1.0
O3G A:DAD1342 3.7 62.6 1.0
CG A:ASP105 3.8 39.4 1.0
OD2 A:ASP7 3.9 36.6 1.0
O3A A:DAD1342 4.0 79.8 1.0
C5' A:DAD1342 4.2 79.3 1.0
NZ A:LYS159 4.2 53.2 1.0
N A:TYR10 4.2 27.9 1.0
N A:PHE8 4.4 34.5 1.0
CA A:ASP9 4.5 30.9 1.0
N A:ASP9 4.5 32.5 1.0
C A:ASP9 4.6 30.4 1.0
C A:ASP7 4.6 35.5 1.0
OD1 A:ASP105 4.6 39.7 1.0
CA A:PHE8 4.6 32.6 1.0
N A:PHE11 4.7 27.6 1.0
O2G A:DAD1342 4.8 63.6 1.0
CB A:ASP105 4.8 39.2 1.0
O A:ASP7 4.8 37.3 1.0
O1B A:DAD1342 4.8 77.5 1.0
CB A:ASP7 4.8 36.4 1.0
CA A:TYR10 4.9 28.1 1.0

Calcium binding site 3 out of 3 in 2bqu

Go back to Calcium Binding Sites List in 2bqu
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:Ca1345

b:51.7
occ:1.00
 O P:HOH2014 2.4 43.6 1.0
O A:HOH2045 2.5 66.0 1.0
O A:ALA181 2.5 52.6 1.0
O P:HOH2015 2.6 41.0 1.0
O P:HOH2006 2.7 45.7 1.0
O A:ILE186 3.0 35.3 1.0
C A:ALA181 3.5 49.3 1.0
N A:ASP182 4.3 47.9 1.0
C A:ILE186 4.3 37.2 1.0
CA A:ASP182 4.3 45.5 1.0
CA A:ALA181 4.3 49.5 1.0
CB A:ALA181 4.4 48.2 1.0
OP1 P:DC13 4.7 36.4 1.0
OD1 A:ASP182 4.8 57.6 1.0
CA A:GLY187 4.9 40.4 1.0
C A:ASP182 4.9 43.1 1.0
O P:HOH2004 5.0 65.4 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 09:09:44 2024

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