Magnesium in PDB 2g4k: Anomalous Substructure of Human Adp-Ribosylhydrolase 3

The structure of Anomalous Substructure of Human Adp-Ribosylhydrolase 3, PDB code: 2g4k was solved by C.Mueller-Dieckmann, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.030, 59.340, 98.710, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.7

The structure of Anomalous Substructure of Human Adp-Ribosylhydrolase 3 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Anomalous Substructure of Human Adp-Ribosylhydrolase 3 (pdb code 2g4k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Anomalous Substructure of Human Adp-Ribosylhydrolase 3, PDB code: 2g4k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Anomalous Substructure of Human Adp-Ribosylhydrolase 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Anomalous Substructure of Human Adp-Ribosylhydrolase 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg351 b:24.8 occ:1.00 OD2 A:ASP300 1.9 31.0 1.0 O A:HOH357 2.0 18.2 1.0 OD1 A:ASP61 2.0 31.4 1.0 OD2 A:ASP62 2.1 30.8 1.0 O A:HOH355 2.2 20.0 1.0 OG1 A:THR60 2.2 30.1 1.0 CG A:ASP300 3.1 29.3 1.0 CG A:ASP61 3.1 36.8 1.0 CB A:THR60 3.2 30.2 1.0 CG A:ASP62 3.3 33.0 1.0 OD2 A:ASP61 3.6 34.0 1.0 OD1 A:ASP300 3.7 30.0 1.0 MG A:MG352 3.7 19.6 1.0 O A:HOH377 4.0 27.6 1.0 N A:ASP62 4.0 28.2 1.0 OD1 A:ASP18 4.0 31.1 1.0 CG2 A:THR60 4.0 35.0 1.0 OE1 A:GLU25 4.0 30.3 1.0 OD1 A:ASP62 4.0 33.1 1.0 N A:ASP61 4.0 26.1 1.0 O A:GLY99 4.1 29.3 1.0 OE2 A:GLU25 4.1 31.2 1.0 OG1 A:THR301 4.2 29.1 1.0 CB A:ASP300 4.3 29.1 1.0 CB A:ASP62 4.4 32.2 1.0 CB A:ASP61 4.4 29.0 1.0 CD A:GLU25 4.4 32.9 1.0 CA A:THR60 4.4 28.6 1.0 C A:THR60 4.5 28.9 1.0 CA A:ASP61 4.6 28.3 1.0 CA A:ASP62 4.8 29.8 1.0 C A:ASP61 4.8 29.6 1.0 O A:HOH356 4.9 19.5 1.0 C A:GLY99 4.9 32.5 1.0 CG A:ASP18 5.0 33.6 1.0

Magnesium binding site 2 out of 2 in the Anomalous Substructure of Human Adp-Ribosylhydrolase 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Anomalous Substructure of Human Adp-Ribosylhydrolase 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg352 b:19.6 occ:1.00 O A:HOH356 2.1 19.5 1.0 OE2 A:GLU25 2.1 31.2 1.0 OD1 A:ASP300 2.1 30.0 1.0 OD1 A:ASP298 2.1 29.4 1.0 OG1 A:THR301 2.1 29.1 1.0 O A:HOH355 2.2 20.0 1.0 CG A:ASP300 3.0 29.3 1.0 CD A:GLU25 3.0 32.9 1.0 CG A:ASP298 3.1 28.9 1.0 OD2 A:ASP300 3.3 31.0 1.0 CB A:THR301 3.3 28.7 1.0 OD2 A:ASP298 3.4 29.8 1.0 MG A:MG351 3.7 24.8 1.0 OE1 A:GLU25 3.8 30.3 1.0 N A:THR301 3.8 32.1 1.0 O A:HOH377 3.8 27.6 1.0 CG A:GLU25 3.9 30.2 1.0 CA A:THR301 4.2 30.6 1.0 O A:HOH418 4.3 38.2 1.0 OD2 A:ASP62 4.3 30.8 1.0 O A:HOH357 4.4 18.2 1.0 OD1 A:ASP62 4.4 33.1 1.0 CB A:ASP300 4.4 29.1 1.0 CG2 A:THR301 4.4 31.6 1.0 CB A:ASP298 4.5 25.7 1.0 C A:ASP300 4.7 31.8 1.0 CA A:ASP298 4.7 25.9 1.0 C A:ASP298 4.7 28.6 1.0 O A:ASP298 4.8 29.5 1.0 CG A:ASP62 4.8 33.0 1.0 CA A:ASP300 4.8 28.6 1.0 N A:ASP300 4.8 27.8 1.0

C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, M.S.Weiss. On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part IV. Efficient Determination of Anomalous Substructures in Biomacromolecules Using Longer X-Ray Wavelengths. Acta Crystallogr.,Sect.D V. 63 366 2007.
ISSN: ISSN 0907-4449
PubMed: 17327674
DOI: 10.1107/S0907444906055624