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Magnesium in PDB 2ago: 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: 2ago 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 / 2.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.044, 101.939, 53.017, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.3

Other elements in 2ago:

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

Calcium (Ca) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 2ago

Go back to Magnesium Binding Sites List in 2ago
Magnesium binding site 1 out of 4 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
B:Mg405

b:63.2
occ:1.00
 O C:HOH93 2.4 45.3 1.0
O C:HOH70 2.6 51.8 1.0
O C:HOH15 4.3 43.8 1.0
O4' B:DG1808 4.3 54.1 1.0
C4' B:DG1808 4.5 57.4 1.0
C5' C:DC1914 4.7 75.9 1.0
O2 C:DT1913 4.8 65.7 1.0
C5' B:DG1808 4.8 59.8 1.0
N3 B:DA1807 4.8 48.7 1.0
C4' C:DC1914 4.9 74.4 1.0
O4' C:DC1914 4.9 73.1 1.0

Magnesium binding site 2 out of 4 in 2ago

Go back to Magnesium Binding Sites List in 2ago
Magnesium binding site 2 out of 4 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:Mg402

b:46.6
occ:1.00
 O A:HOH416 1.9 49.2 1.0
OP1 B:DG1814 2.6 76.5 1.0
O1 A:POP401 2.6 91.7 1.0
O2 A:POP401 2.7 91.5 1.0
OD1 A:ASP105 2.8 48.3 1.0
O5' B:DG1814 2.8 78.5 1.0
P1 A:POP401 3.0 93.7 1.0
OD2 A:ASP105 3.3 51.4 1.0
P B:DG1814 3.4 76.5 1.0
OE1 A:GLU106 3.4 62.8 1.0
CG A:ASP105 3.4 48.9 1.0
CD A:GLU106 3.8 60.6 1.0
OG A:SER103 3.9 37.6 1.0
O3 A:POP401 4.0 93.4 1.0
CG A:GLU106 4.0 57.1 1.0
C5' B:DG1814 4.1 79.6 1.0
O A:POP401 4.2 92.4 1.0
O3' B:DC1813 4.2 68.1 1.0
OP2 B:DG1814 4.5 77.1 1.0
C4' B:DG1814 4.6 79.2 1.0
CA A:CA403 4.6 58.1 1.0
CB A:SER103 4.6 37.2 1.0
OE2 A:GLU106 4.7 62.6 1.0
CB A:ASP105 4.9 47.0 1.0

Magnesium binding site 3 out of 4 in 2ago

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Magnesium binding site 3 out of 4 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
A:Mg404

b:64.6
occ:1.00
 O A:HOH431 2.0 51.7 1.0
O A:ALA181 2.4 58.4 1.0
O A:HOH475 2.4 60.0 1.0
O A:HOH446 2.6 60.5 1.0
O A:ILE186 2.7 49.8 1.0
C A:ALA181 3.5 57.2 1.0
C A:ILE186 3.9 47.4 1.0
CA A:ALA181 4.3 57.1 1.0
CA A:GLY187 4.4 44.4 1.0
CB A:ALA181 4.4 51.0 1.0
N A:ASP182 4.5 53.1 1.0
CA A:ASP182 4.6 52.2 1.0
N A:GLY187 4.7 43.1 1.0
C A:GLY187 4.7 45.8 1.0
OP2 B:DC1813 4.7 62.9 1.0
ND2 A:ASN188 4.9 62.9 1.0
O A:VAL183 4.9 45.7 1.0
CA A:ILE186 5.0 46.7 1.0

Magnesium binding site 4 out of 4 in 2ago

Go back to Magnesium Binding Sites List in 2ago
Magnesium binding site 4 out of 4 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
A:Mg406

b:47.1
occ:1.00
 OD2 A:ASP294 2.4 72.1 1.0
OD1 A:ASP294 2.9 71.4 1.0
CG A:ASP294 3.0 70.7 1.0
O B:HOH10 3.7 54.9 1.0
OP2 B:DA1810 4.1 59.7 1.0
CB A:ASP294 4.5 69.1 1.0
NH2 A:ARG328 4.6 63.5 1.0
O A:ILE295 4.7 56.0 1.0
C3' B:DG1809 4.9 58.0 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 21:29:52 2024

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