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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

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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

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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

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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

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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: Sun Aug 10 16:22:53 2025

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