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Calcium in PDB 2bqr: 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: 2bqr 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) 42.32 / 2.37
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.528, 103.027, 53.097, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26

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

Calcium binding site 1 out of 3 in 2bqr

Go back to Calcium Binding Sites List in 2bqr
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:89.4
occ:1.00
 OE2 A:GLU106 3.0 61.7 1.0
O A:HOH2029 3.0 58.9 1.0
O5' A:DTP1000 3.1 67.8 1.0
OD2 A:ASP7 3.1 46.5 1.0
O3A A:DTP1000 3.3 74.3 1.0
OD2 A:ASP105 3.3 43.5 1.0
OD1 A:ASP105 3.3 44.4 1.0
CA A:CA2002 3.3 41.1 1.0
O1A A:DTP1000 3.3 73.8 1.0
OD1 A:ASP7 3.4 43.5 1.0
PA A:DTP1000 3.4 71.5 1.0
CG A:GLU106 3.4 54.4 1.0
CD A:GLU106 3.6 59.0 1.0
CG A:ASP7 3.6 43.9 1.0
CG A:ASP105 3.6 43.4 1.0
O P:HOH2018 3.7 89.0 1.0
C5' A:DTP1000 3.9 61.6 1.0
NZ A:LYS159 4.5 62.7 1.0
O A:HOH2071 4.5 54.2 1.0
PB A:DTP1000 4.7 76.2 1.0
OE1 A:GLU106 4.7 60.9 1.0
O A:ASP105 4.8 39.6 1.0
O2B A:DTP1000 4.8 75.3 1.0
O A:HOH2006 4.9 63.2 1.0
O2A A:DTP1000 4.9 76.2 1.0
CB A:GLU106 4.9 47.5 1.0
CB A:ASP7 4.9 41.7 1.0
O3G A:DTP1000 5.0 69.3 1.0
OG A:SER103 5.0 47.6 1.0

Calcium binding site 2 out of 3 in 2bqr

Go back to Calcium Binding Sites List in 2bqr
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:41.1
occ:1.00
 O A:PHE8 2.3 34.5 1.0
OD2 A:ASP105 2.5 43.5 1.0
OD1 A:ASP7 2.5 43.5 1.0
O3A A:DTP1000 2.6 74.3 1.0
O2B A:DTP1000 2.6 75.3 1.0
O3G A:DTP1000 2.8 69.3 1.0
PB A:DTP1000 3.2 76.2 1.0
CA A:CA2001 3.3 89.4 1.0
C A:PHE8 3.5 37.2 1.0
O A:HOH2009 3.6 47.0 1.0
CG A:ASP7 3.6 43.9 1.0
CG A:ASP105 3.6 43.4 1.0
C5' A:DTP1000 3.7 61.6 1.0
O5' A:DTP1000 3.9 67.8 1.0
O3B A:DTP1000 3.9 69.1 1.0
PA A:DTP1000 3.9 71.5 1.0
PG A:DTP1000 3.9 66.0 1.0
N A:PHE8 4.1 37.2 1.0
OD2 A:ASP7 4.1 46.5 1.0
OD1 A:ASP105 4.3 44.4 1.0
CA A:PHE8 4.3 35.9 1.0
N A:TYR10 4.4 32.8 1.0
NZ A:LYS159 4.4 62.7 1.0
N A:ASP9 4.4 36.6 1.0
C A:ASP7 4.4 38.6 1.0
CA A:ASP9 4.5 35.5 1.0
O1B A:DTP1000 4.5 74.9 1.0
C A:ASP9 4.5 35.4 1.0
O A:HOH2072 4.7 51.9 1.0
N A:PHE11 4.7 30.9 1.0
CB A:ASP105 4.7 40.8 1.0
CB A:ASP7 4.8 41.7 1.0
O1A A:DTP1000 4.8 73.8 1.0
O A:ASP105 4.8 39.6 1.0
CB A:PHE8 4.9 34.3 1.0
O A:ASP7 4.9 38.7 1.0
O1G A:DTP1000 4.9 71.8 1.0
CB A:PHE11 4.9 28.3 1.0
O2A A:DTP1000 4.9 76.2 1.0
O2G A:DTP1000 4.9 72.4 1.0
CA A:ASP7 5.0 38.2 1.0

Calcium binding site 3 out of 3 in 2bqr

Go back to Calcium Binding Sites List in 2bqr
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:62.0
occ:1.00
 O A:ALA181 2.4 54.1 1.0
O P:HOH2016 2.5 42.3 1.0
O A:HOH2043 2.5 54.6 1.0
O A:ILE186 2.6 39.4 1.0
O P:HOH2017 2.7 44.3 1.0
O A:HOH2007 2.8 59.5 1.0
O A:HOH2004 2.8 56.7 1.0
C A:ALA181 3.6 53.7 1.0
C A:ILE186 3.8 39.8 1.0
OP1 P:DC13 4.1 37.9 1.0
O A:VAL183 4.4 45.2 1.0
CA A:ASP182 4.5 53.9 1.0
OP2 P:DC13 4.5 39.7 1.0
CA A:ALA181 4.5 53.6 1.0
N A:ASP182 4.5 54.4 1.0
CA A:GLY187 4.5 43.0 1.0
N A:GLY187 4.6 40.9 1.0
C A:ASP182 4.8 51.7 1.0
CB A:ALA181 4.8 52.0 1.0
CA A:ILE186 4.8 40.3 1.0
P P:DC13 4.8 38.5 1.0
CB A:ILE186 4.8 40.4 1.0
N A:VAL183 4.9 49.4 1.0
N A:ILE186 5.0 39.0 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: Tue Jul 8 04:36:14 2025

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