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

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

All present enzymatic activity of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - 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 Dctp - Magnesium Form, PDB code: 2xcp 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) 49.55 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.757, 100.429, 105.873, 90.00, 96.08, 90.00
R / Rfree (%) 22.3 / 26.8

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 Dctp - Magnesium Form (pdb code 2xcp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - Magnesium Form, PDB code: 2xcp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2xcp

Go back to Magnesium Binding Sites List in 2xcp
Magnesium binding site 1 out of 6 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - 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 Dctp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:27.2
occ:1.00
 OD2 A:ASP105 2.1 33.6 1.0
O A:HOH2120 2.1 35.3 1.0
O A:PHE8 2.1 29.0 1.0
O2G A:DCP5000 2.1 36.4 1.0
O3A A:DCP5000 2.4 34.4 1.0
OD1 A:ASP7 2.5 32.0 1.0
O2B A:DCP5000 2.5 36.5 1.0
PB A:DCP5000 3.0 34.0 1.0
C A:PHE8 3.2 28.5 1.0
CG A:ASP105 3.3 32.7 1.0
PG A:DCP5000 3.5 32.2 1.0
CG A:ASP7 3.5 30.6 1.0
O3B A:DCP5000 3.6 35.6 1.0
MG A:MG1004 3.7 31.5 1.0
PA A:DCP5000 3.8 35.5 1.0
N A:PHE8 3.9 28.5 1.0
C5' A:DCP5000 3.9 31.0 1.0
OD2 A:ASP7 4.0 30.4 1.0
CA A:PHE8 4.0 28.6 1.0
OD1 A:ASP105 4.1 34.4 1.0
N A:ASP9 4.1 30.6 1.0
O1A A:DCP5000 4.1 39.8 1.0
O1G A:DCP5000 4.1 39.1 1.0
C A:ASP7 4.2 29.2 1.0
NZ A:LYS159 4.3 39.9 1.0
CA A:ASP9 4.3 30.5 1.0
O1B A:DCP5000 4.3 32.4 1.0
CB A:ASP105 4.3 29.8 1.0
N A:TYR10 4.3 29.9 1.0
O5' A:DCP5000 4.4 36.3 1.0
CB A:PHE8 4.5 27.0 1.0
C A:ASP9 4.5 28.6 1.0
CB A:PHE11 4.5 28.4 1.0
O A:ASP7 4.5 31.4 1.0
N A:PHE11 4.5 28.5 1.0
O3G A:DCP5000 4.6 39.7 1.0
CE A:LYS159 4.6 39.6 1.0
CB A:ASP7 4.7 29.9 1.0
O A:HOH2118 4.7 38.0 1.0
CA A:ASP7 4.9 29.9 1.0
O A:ASP105 4.9 29.4 1.0
O2A A:DCP5000 4.9 42.5 1.0

Magnesium binding site 2 out of 6 in 2xcp

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Magnesium binding site 2 out of 6 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - 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 Dctp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:30.4
occ:1.00
 O B:PHE8 1.9 33.7 1.0
O1G B:DCP5000 2.1 25.2 1.0
O A:HOH2130 2.2 41.6 1.0
O3A B:DCP5000 2.2 34.0 1.0
OD2 B:ASP7 2.4 32.4 1.0
OD2 B:ASP105 2.4 30.6 1.0
O2B B:DCP5000 2.6 33.6 1.0
PB B:DCP5000 2.9 29.0 1.0
C B:PHE8 3.1 31.6 1.0
PG B:DCP5000 3.3 26.5 1.0
CG B:ASP7 3.4 32.1 1.0
CG B:ASP105 3.6 30.8 1.0
O3B B:DCP5000 3.6 30.0 1.0
PA B:DCP5000 3.7 30.7 1.0
O2G B:DCP5000 3.7 28.6 1.0
O A:HOH2124 3.8 50.7 1.0
OD1 B:ASP7 3.8 32.9 1.0
N B:PHE8 3.8 27.8 1.0
O1A B:DCP5000 3.9 37.3 1.0
MG B:MG1005 3.9 48.5 1.0
CA B:PHE8 3.9 31.2 1.0
N B:ASP9 4.0 30.6 1.0
C5' B:DCP5000 4.1 27.8 1.0
NZ B:LYS159 4.2 41.1 1.0
OD1 B:ASP105 4.2 32.3 1.0
CA B:ASP9 4.2 29.9 1.0
C B:ASP7 4.3 28.4 1.0
O1B B:DCP5000 4.3 30.7 1.0
N B:TYR10 4.3 25.4 1.0
CE B:LYS159 4.3 43.9 1.0
C B:ASP9 4.4 28.8 1.0
O5' B:DCP5000 4.4 31.5 1.0
O3G B:DCP5000 4.6 30.2 1.0
CB B:PHE8 4.6 31.1 1.0
N B:PHE11 4.6 23.3 1.0
O B:ASP7 4.6 27.7 1.0
O2A B:DCP5000 4.6 33.9 1.0
CB B:ASP105 4.7 28.8 1.0
CB B:ASP7 4.7 30.4 1.0
O A:HOH2126 4.7 41.7 1.0
CB B:PHE11 4.8 26.1 1.0
O A:HOH2129 4.9 51.3 1.0
CA B:ASP7 4.9 29.6 1.0

Magnesium binding site 3 out of 6 in 2xcp

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Magnesium binding site 3 out of 6 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - 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 Dctp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:79.0
occ:1.00
 OP2 P:DG9 2.4 58.5 1.0
O P:HOH2014 2.5 87.5 1.0
O A:HOH2100 2.5 67.8 1.0
OD1 A:ASP294 2.6 48.1 0.5
CG A:ASP294 3.6 48.8 0.5
P P:DG9 3.7 59.5 1.0
OD2 A:ASP294 3.9 50.0 0.5
O A:ILE295 4.0 45.3 1.0
C3' P:DG8 4.1 54.2 1.0
O3' P:DG8 4.1 56.4 1.0
OP1 P:DG9 4.4 60.1 1.0
C2' P:DG8 4.6 52.2 1.0
N A:ILE295 4.7 47.2 1.0
O5' P:DG9 4.9 58.8 1.0
CB A:ASP294 4.9 49.0 0.5

Magnesium binding site 4 out of 6 in 2xcp

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Magnesium binding site 4 out of 6 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - 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 Dctp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:55.5
occ:1.00
 OP2 E:DG9 2.4 58.1 1.0
OD2 B:ASP294 2.5 66.1 1.0
O B:HOH2085 2.7 66.4 1.0
CG B:ASP294 3.2 63.1 1.0
OD1 B:ASP294 3.3 65.7 1.0
C3' E:DG8 3.4 56.6 1.0
P E:DG9 3.6 59.7 1.0
O B:ILE295 3.7 48.9 1.0
O3' E:DG8 3.8 57.3 1.0
C5' E:DG8 4.2 59.4 1.0
C2' E:DG8 4.3 55.5 1.0
C4' E:DG8 4.4 56.9 1.0
N B:ILE295 4.5 49.4 1.0
O5' E:DG9 4.6 57.0 1.0
CB B:ASP294 4.6 58.3 1.0
OP1 E:DG9 4.7 60.7 1.0
C B:ILE295 4.7 49.0 1.0

Magnesium binding site 5 out of 6 in 2xcp

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Magnesium binding site 5 out of 6 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - Magnesium Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:31.5
occ:1.00
 O A:HOH2120 2.0 35.3 1.0
O A:HOH2121 2.1 33.3 1.0
O1A A:DCP5000 2.1 39.8 1.0
OD2 A:ASP7 2.3 30.4 1.0
OE1 A:GLU106 2.3 46.9 1.0
OD1 A:ASP105 2.8 34.4 1.0
OD2 A:ASP105 3.2 33.6 1.0
CG A:ASP7 3.2 30.6 1.0
PA A:DCP5000 3.3 35.5 1.0
CG A:ASP105 3.4 32.7 1.0
OD1 A:ASP7 3.4 32.0 1.0
CD A:GLU106 3.4 43.5 1.0
O3A A:DCP5000 3.5 34.4 1.0
O A:HOH2118 3.7 38.0 1.0
MG A:MG1000 3.7 27.2 1.0
O5' A:DCP5000 4.0 36.3 1.0
C3' P:DOC13 4.1 47.9 1.0
O A:HOH2002 4.1 51.8 1.0
C5' P:DOC13 4.1 51.4 1.0
C5' A:DCP5000 4.1 31.0 1.0
CG A:GLU106 4.2 42.3 1.0
O5' P:DOC13 4.4 54.8 1.0
OE2 A:GLU106 4.4 46.3 1.0
C4' P:DOC13 4.4 50.9 1.0
CB A:GLU106 4.4 35.0 1.0
O2A A:DCP5000 4.5 42.5 1.0
CB A:ASP7 4.5 29.9 1.0
OP1 P:DOC13 4.7 55.2 1.0
OG A:SER103 4.7 30.1 1.0
O A:HOH2119 4.8 44.3 1.0
CB A:ASP105 4.9 29.8 1.0
O2G A:DCP5000 4.9 36.4 1.0
O A:ASP105 4.9 29.4 1.0

Magnesium binding site 6 out of 6 in 2xcp

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Magnesium binding site 6 out of 6 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - Magnesium Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna and Dctp - Magnesium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1005

b:48.5
occ:1.00
 OE1 B:GLU106 1.7 46.1 1.0
O A:HOH2126 2.0 41.7 1.0
O A:HOH2130 2.0 41.6 1.0
OD1 B:ASP7 2.1 32.9 1.0
O1A B:DCP5000 2.7 37.3 1.0
OD1 B:ASP105 2.7 32.3 1.0
CD B:GLU106 2.9 41.8 1.0
CG B:ASP7 3.0 32.1 1.0
OD2 B:ASP7 3.4 32.4 1.0
CG B:ASP105 3.5 30.8 1.0
OD2 B:ASP105 3.5 30.6 1.0
CG B:GLU106 3.8 37.6 1.0
OE2 B:GLU106 3.8 42.5 1.0
O A:HOH2124 3.8 50.7 1.0
PA B:DCP5000 3.9 30.7 1.0
MG B:MG1001 3.9 30.4 1.0
CB B:GLU106 4.0 33.3 1.0
O3A B:DCP5000 4.0 34.0 1.0
CB B:ASP7 4.1 30.4 1.0
C3' E:DOC13 4.3 49.5 1.0
OG B:SER103 4.4 31.8 1.0
O B:ASP105 4.4 27.3 1.0
O5' B:DCP5000 4.4 31.5 1.0
O5' E:DOC13 4.5 50.0 1.0
C5' B:DCP5000 4.5 27.8 1.0
C5' E:DOC13 4.5 48.6 1.0
O1G B:DCP5000 4.6 25.2 1.0
O A:HOH2132 4.7 45.4 1.0
NZ B:LYS152 4.7 36.4 1.0
C B:ASP105 4.7 27.2 1.0
CA B:ASP7 4.8 29.6 1.0
OP1 E:DOC13 4.8 47.1 1.0
C4' E:DOC13 4.9 49.8 1.0
CB B:ASP105 4.9 28.8 1.0
CZ B:PHE5 5.0 27.7 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 07:05:33 2024

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