Atomistry » Magnesium » PDB 2xbp-2xnd » 2xca
Atomistry »
  Magnesium »
    PDB 2xbp-2xnd »
      2xca »

Magnesium in PDB 2xca: Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form

Enzymatic activity of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form

All present enzymatic activity of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form, PDB code: 2xca was solved by A.Irimia, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.13 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.443, 103.909, 52.707, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form (pdb code 2xca). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form, PDB code: 2xca:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2xca

Go back to Magnesium Binding Sites List in 2xca
Magnesium binding site 1 out of 4 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3000

b:20.0
occ:1.00
 OD1 A:ASP105 2.1 28.2 1.0
OD1 A:ASP7 2.1 25.8 1.0
O A:HOH2006 2.2 30.8 1.0
OE2 A:GLU106 2.3 30.9 1.0
O A:HOH2070 2.3 30.1 1.0
O1A A:DGT1000 2.4 24.2 1.0
CG A:ASP105 2.8 26.7 1.0
OD2 A:ASP105 2.9 25.8 1.0
CG A:ASP7 3.1 23.6 1.0
CD A:GLU106 3.1 30.5 1.0
OD2 A:ASP7 3.4 21.0 1.0
PA A:DGT1000 3.6 25.4 1.0
OG A:SER103 3.7 24.1 1.0
MG A:MG3001 3.7 22.4 1.0
CG A:GLU106 3.8 29.0 1.0
O2A A:DGT1000 3.8 26.3 1.0
O5' A:DGT1000 3.8 22.7 1.0
C5' A:DGT1000 3.9 23.1 1.0
CB A:GLU106 3.9 27.6 1.0
OE1 A:GLU106 3.9 31.9 1.0
O A:ASP105 4.1 26.6 1.0
C A:ASP105 4.1 27.0 1.0
CB A:ASP105 4.2 24.8 1.0
CB A:ASP7 4.4 24.6 1.0
N A:GLU106 4.5 27.3 1.0
O A:HOH2154 4.5 36.7 1.0
O2G A:DGT1000 4.5 29.6 1.0
CA A:ASP105 4.6 24.7 1.0
NZ A:LYS152 4.7 38.3 1.0
CA A:GLU106 4.8 29.4 1.0
O A:HOH2069 4.8 44.1 1.0
CB A:SER103 4.8 21.3 1.0
O2B A:DGT1000 4.8 26.6 1.0
N A:ASP105 4.8 22.9 1.0
O A:HOH2155 4.9 30.0 1.0
CA A:ASP7 5.0 25.6 1.0
O A:HOH2156 5.0 32.8 1.0

Magnesium binding site 2 out of 4 in 2xca

Go back to Magnesium Binding Sites List in 2xca
Magnesium binding site 2 out of 4 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:22.4
occ:1.00
 O A:PHE8 2.0 32.4 1.0
O2B A:DGT1000 2.1 26.6 1.0
O2G A:DGT1000 2.2 29.6 1.0
O1A A:DGT1000 2.2 24.2 1.0
OD2 A:ASP7 2.2 21.0 1.0
OD2 A:ASP105 2.3 25.8 1.0
NZ A:LYS159 3.2 35.0 1.0
C A:PHE8 3.2 28.7 1.0
PG A:DGT1000 3.2 28.6 1.0
CG A:ASP7 3.2 23.6 1.0
PB A:DGT1000 3.3 24.2 1.0
O3G A:DGT1000 3.5 30.6 1.0
PA A:DGT1000 3.5 25.4 1.0
CG A:ASP105 3.5 26.7 1.0
O3B A:DGT1000 3.6 26.7 1.0
MG A:MG3000 3.7 20.0 1.0
OD1 A:ASP7 3.8 25.8 1.0
O3A A:DGT1000 3.8 26.9 1.0
N A:PHE8 3.8 27.0 1.0
O A:HOH2154 3.9 36.7 1.0
C5' A:DGT1000 4.0 23.1 1.0
CA A:PHE8 4.0 27.1 1.0
C A:ASP7 4.1 26.4 1.0
N A:ASP9 4.1 28.9 1.0
OD1 A:ASP105 4.2 28.2 1.0
CA A:ASP9 4.2 27.6 1.0
CE A:LYS159 4.2 39.8 1.0
N A:TYR10 4.3 25.0 1.0
O5' A:DGT1000 4.3 22.7 1.0
CB A:ASP7 4.3 24.6 1.0
C A:ASP9 4.4 26.7 1.0
O A:HOH2006 4.4 30.8 1.0
O A:ASP7 4.5 25.7 1.0
O1G A:DGT1000 4.6 31.1 1.0
N A:PHE11 4.6 26.0 1.0
O1B A:DGT1000 4.6 23.2 1.0
CB A:PHE8 4.6 24.6 1.0
CB A:ASP105 4.6 24.8 1.0
CA A:ASP7 4.7 25.6 1.0
CB A:PHE11 4.7 26.2 1.0
O2A A:DGT1000 4.7 26.3 1.0
O A:ASP105 4.9 26.6 1.0

Magnesium binding site 3 out of 4 in 2xca

Go back to Magnesium Binding Sites List in 2xca
Magnesium binding site 3 out of 4 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:68.5
occ:1.00
 O A:HOH2139 2.0 59.2 1.0
O A:HOH2137 2.1 68.1 1.0
O P:HOH2013 2.2 82.0 1.0
O A:HOH2138 2.3 69.8 1.0
OP2 P:DA10 2.5 50.5 1.0
OD1 A:ASP294 2.6 43.8 1.0
OD2 A:ASP294 3.2 45.2 1.0
CG A:ASP294 3.2 42.2 1.0
OP1 P:DA10 3.2 50.7 1.0
P P:DA10 3.3 48.0 1.0
O3' P:DG9 4.5 47.8 1.0
O5' P:DA10 4.5 47.2 1.0
O A:ILE295 4.6 40.5 1.0
C3' P:DG9 4.7 48.0 1.0
CB A:ASP294 4.7 40.1 1.0
N A:ILE295 4.9 37.7 1.0

Magnesium binding site 4 out of 4 in 2xca

Go back to Magnesium Binding Sites List in 2xca
Magnesium binding site 4 out of 4 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dgtp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:55.2
occ:1.00
 O A:HOH2095 2.1 62.7 1.0
O A:HOH2097 2.1 66.9 1.0
O A:HOH2039 2.9 48.5 1.0
OP1 P:DOC13 3.0 37.2 1.0
O A:HOH2092 3.1 48.1 1.0
O P:HOH2017 3.1 60.0 1.0
O A:VAL183 3.1 29.9 1.0
O A:ALA181 3.5 41.8 1.0
C A:VAL183 3.6 31.5 1.0
O A:ILE186 3.7 29.5 1.0
CA A:PRO184 3.9 28.7 1.0
N A:PRO184 4.0 29.0 1.0
O P:HOH2018 4.0 57.4 1.0
P P:DOC13 4.1 36.0 1.0
O A:HOH2096 4.1 54.2 1.0
OP2 P:DOC13 4.1 36.1 1.0
C A:ASP182 4.2 37.2 1.0
N A:VAL183 4.2 34.1 1.0
N A:ILE186 4.4 26.7 1.0
O A:ASP182 4.4 36.6 1.0
N A:GLY185 4.4 30.0 1.0
C A:ILE186 4.4 27.8 1.0
C A:ALA181 4.5 41.2 1.0
C A:PRO184 4.5 30.3 1.0
CA A:VAL183 4.5 33.0 1.0
CA A:ASP182 4.6 39.2 1.0
CA A:ILE186 4.9 28.3 1.0
O A:HOH2098 4.9 51.8 1.0
O5' P:DOC13 5.0 36.2 1.0

Reference:

A.Irimia, L.V.Loukachevitch, R.L.Eoff, F.P.Guengerich, M.Egli. Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion Dna Polymerase DPO4 From Sulfolobus Solfataricus Acta Crystallogr.,Sect.F V. 66 1013 2010.
ISSN: ISSN 1744-3091
PubMed: 20823515
DOI: 10.1107/S1744309110029374
Page generated: Wed Aug 14 07:04:49 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy