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Magnesium in PDB 2agq: 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: 2agq 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) 26.79 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 98.101, 103.009, 52.399, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25.4

Other elements in 2agq:

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 2agq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis, PDB code: 2agq:

Magnesium binding site 1 out of 1 in 2agq

Go back to Magnesium Binding Sites List in 2agq
Magnesium binding site 1 out of 1 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:Mg4002

b:32.7
occ:1.00
 O A:HOH4032 2.1 56.4 1.0
OE2 A:GLU106 2.1 42.2 1.0
O A:HOH4100 2.2 39.5 1.0
O A:HOH4004 2.3 33.6 1.0
OD2 A:ASP7 2.4 34.3 1.0
OP1 B:DOC13 2.6 47.6 1.0
CD A:GLU106 3.0 39.4 1.0
CG A:ASP7 3.5 32.8 1.0
CG A:GLU106 3.7 39.5 1.0
O5' B:DOC13 3.7 43.8 1.0
P B:DOC13 3.7 45.0 1.0
OE1 A:GLU106 3.8 41.3 1.0
OD1 A:ASP7 4.0 35.2 1.0
O1A A:DTP1814 4.0 35.5 1.0
C5' B:DOC13 4.0 42.3 1.0
NZ A:LYS152 4.3 45.9 1.0
NZ A:LYS159 4.3 42.0 1.0
CE A:LYS152 4.4 39.4 1.0
CZ A:PHE5 4.5 30.2 1.0
OP2 B:DOC13 4.6 42.5 1.0
O2A A:DTP1814 4.6 35.3 1.0
CB A:ASP7 4.6 30.6 1.0
C3' B:DOC13 4.7 44.4 1.0
OD1 A:ASP105 4.7 32.4 1.0
CA A:CA4001 4.8 34.3 1.0
PA A:DTP1814 4.9 36.1 1.0
C4' B:DOC13 4.9 45.4 1.0
O3' B:DT12 4.9 45.1 1.0
OD1 A:ASP156 5.0 40.6 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 21:30:47 2024

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