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Magnesium in PDB 2agp: Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis

Enzymatic activity of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis

All present enzymatic activity of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis:
2.7.7.7;

Protein crystallography data

The structure of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis, PDB code: 2agp was solved by H.Ling, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.867, 101.463, 105.642, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26.4

Other elements in 2agp:

The structure of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis (pdb code 2agp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis, PDB code: 2agp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2agp

Go back to Magnesium Binding Sites List in 2agp
Magnesium binding site 1 out of 5 in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:49.1
occ:1.00
 OD1 A:ASP105 2.2 60.0 1.0
OD2 A:ASP105 2.5 59.6 1.0
O5' A:DGT401 2.5 1.0 1.0
OE1 A:GLU106 2.6 53.8 1.0
CG A:ASP105 2.7 56.5 1.0
O2A A:DGT401 3.2 0.6 1.0
C5' A:DGT401 3.4 0.4 1.0
O2B A:DGT401 3.4 0.1 1.0
C3' C:DOC1813 3.4 0.5 1.0
PA A:DGT401 3.4 0.8 1.0
CD A:GLU106 3.5 50.0 1.0
CG A:GLU106 3.5 47.5 1.0
CA A:CA402 3.7 59.2 1.0
O5' C:DOC1813 3.7 0.1 1.0
C4' A:DGT401 3.7 0.2 1.0
O A:HOH1048 3.8 65.7 1.0
OD2 A:ASP7 4.0 42.7 1.0
OG A:SER103 4.1 34.2 1.0
OD1 A:ASP7 4.1 42.5 1.0
C5' C:DOC1813 4.2 0.0 1.0
CB A:ASP105 4.2 53.5 1.0
C2' C:DOC1813 4.2 0.8 1.0
O3B A:DGT401 4.3 0.6 1.0
C4' C:DOC1813 4.3 0.3 1.0
PB A:DGT401 4.3 0.7 1.0
O A:ASP105 4.3 33.4 1.0
O3A A:DGT401 4.3 1.0 1.0
CG A:ASP7 4.4 40.6 1.0
C A:ASP105 4.6 32.6 1.0
OE2 A:GLU106 4.6 52.6 1.0
C3' A:DGT401 4.7 0.3 1.0
O1A A:DGT401 4.8 0.7 1.0
O4' A:DGT401 4.8 0.4 1.0
CA A:ASP105 4.8 33.4 1.0
O3' A:DGT401 4.9 0.2 1.0
CB A:GLU106 4.9 44.9 1.0
P C:DOC1813 5.0 0.2 1.0

Magnesium binding site 2 out of 5 in 2agp

Go back to Magnesium Binding Sites List in 2agp
Magnesium binding site 2 out of 5 in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:33.3
occ:1.00
 O A:HOH562 2.1 70.6 1.0
O A:HOH851 2.3 54.8 1.0
O A:HOH1229 2.3 60.3 1.0
O A:HOH503 2.5 67.0 1.0
O A:ILE186 2.5 65.4 1.0
O A:ALA181 2.5 47.6 1.0
O A:HOH1044 2.6 80.1 1.0
O A:HOH1245 3.2 54.5 1.0
C A:ILE186 3.7 64.5 1.0
C A:ALA181 3.7 48.0 1.0
OP1 C:DT1812 3.9 79.9 1.0
O C:HOH1244 4.0 55.0 1.0
CA A:GLY187 4.2 51.6 1.0
N A:GLY187 4.4 49.9 1.0
CA A:ALA181 4.6 49.7 1.0
C A:GLY187 4.6 52.8 1.0
CA A:ASP182 4.7 43.4 1.0
N A:ASP182 4.7 43.0 1.0
CB A:ALA181 4.7 56.5 1.0
CA A:ILE186 4.7 62.3 1.0
OP2 C:DT1812 4.8 79.7 1.0
O A:VAL183 4.8 42.5 1.0
CB A:ILE186 4.9 52.6 1.0
P C:DT1812 4.9 63.0 1.0
O A:GLY187 4.9 52.2 1.0
N A:ILE186 4.9 59.1 1.0
OD1 A:ASP182 5.0 79.2 1.0

Magnesium binding site 3 out of 5 in 2agp

Go back to Magnesium Binding Sites List in 2agp
Magnesium binding site 3 out of 5 in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:38.1
occ:1.00
 O B:ALA181 2.2 54.8 1.0
O B:HOH704 2.2 46.2 1.0
O B:HOH845 2.5 73.0 1.0
O B:HOH1146 2.5 62.1 1.0
O B:ILE186 2.7 57.3 1.0
C B:ALA181 3.3 55.1 1.0
C B:ILE186 3.9 55.9 1.0
CA B:ALA181 4.2 56.3 1.0
N B:ASP182 4.3 46.8 1.0
CA B:ASP182 4.3 45.3 1.0
CB B:ALA181 4.4 48.7 1.0
CA B:GLY187 4.6 52.9 1.0
OD1 B:ASP182 4.8 58.6 1.0
N B:GLY187 4.8 50.3 1.0
C B:ASP182 4.9 43.6 1.0
O B:VAL183 4.9 34.0 1.0
C B:GLY187 4.9 55.4 1.0
CB B:ILE186 4.9 40.4 1.0
OP2 E:DOC1813 4.9 93.6 1.0
CA B:ILE186 4.9 53.4 1.0

Magnesium binding site 4 out of 5 in 2agp

Go back to Magnesium Binding Sites List in 2agp
Magnesium binding site 4 out of 5 in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:43.9
occ:1.00
 OD2 B:ASP294 2.3 85.6 1.0
O B:HOH587 2.4 46.7 1.0
O B:HOH619 2.7 55.0 1.0
O E:HOH593 2.9 41.8 1.0
O3' E:DG1809 3.0 83.0 1.0
CG B:ASP294 3.2 86.2 1.0
OD1 B:ASP294 3.4 88.9 1.0
OP2 E:DA1810 3.5 65.6 1.0
P E:DA1810 4.0 63.9 1.0
C3' E:DG1809 4.0 86.3 1.0
O B:ILE295 4.6 50.1 1.0
CB B:ASP294 4.6 84.9 1.0
C2' E:DG1809 4.7 87.1 1.0
OP1 E:DA1810 5.0 68.9 1.0

Magnesium binding site 5 out of 5 in 2agp

Go back to Magnesium Binding Sites List in 2agp
Magnesium binding site 5 out of 5 in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:32.4
occ:1.00
 OD1 B:ASP105 2.5 39.2 1.0
O5' B:DGT501 2.5 0.4 1.0
O2A B:DGT501 2.5 0.8 1.0
OE1 B:GLU106 2.7 52.8 1.0
CD B:GLU106 2.9 49.1 1.0
C5' B:DGT501 2.9 0.9 1.0
OD2 B:ASP105 2.9 37.6 1.0
O B:HOH580 2.9 38.6 1.0
CG B:ASP105 3.0 37.7 1.0
PA B:DGT501 3.1 1.0 1.0
CG B:GLU106 3.2 45.4 1.0
O2B B:DGT501 3.4 0.3 1.0
OE2 B:GLU106 3.6 49.3 1.0
C4' B:DGT501 3.7 0.8 1.0
OG B:SER103 3.8 46.3 1.0
OD2 B:ASP7 3.8 43.3 1.0
CA B:CA402 4.0 47.4 1.0
O4' B:DGT501 4.0 0.5 1.0
O B:HOH788 4.1 59.8 1.0
O3A B:DGT501 4.1 0.8 1.0
PB B:DGT501 4.3 0.1 1.0
O1A B:DGT501 4.4 0.1 1.0
O B:ASP105 4.4 41.4 1.0
CG B:ASP7 4.5 40.4 1.0
CB B:ASP105 4.5 37.5 1.0
CB B:GLU106 4.5 42.8 1.0
OD1 B:ASP7 4.5 43.5 1.0
C B:ASP105 4.6 41.4 1.0
CB B:SER103 4.9 44.7 1.0
O3B B:DGT501 5.0 0.0 1.0
O B:HOH1067 5.0 69.6 1.0

Reference:

A.Vaisman, H.Ling, R.Woodgate, W.Yang. Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis. Embo J. V. 24 2957 2005.
ISSN: ISSN 0261-4189
PubMed: 16107880
DOI: 10.1038/SJ.EMBOJ.7600786
Page generated: Tue Aug 13 21:30:09 2024

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