Atomistry » Calcium » PDB 2bir-2bw1 » 2bqr
Atomistry »
  Calcium »
    PDB 2bir-2bw1 »
      2bqr »

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: Fri Jul 12 09:09:43 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy