Magnesium in PDB 2zbe: Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg

All present enzymatic activity of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg:
3.6.3.8;

The structure of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg, PDB code: 2zbe was solved by C.Toyoshima, H.Ogawa, Y.Norimatsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 3.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	133.869, 91.592, 248.464, 90.00, 90.00, 90.00
R / Rfree (%)	29.3 / 32.7

The structure of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg (pdb code 2zbe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg, PDB code: 2zbe:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg997 b:89.4 occ:1.00 F2 A:BEF998 1.9 0.0 1.0 OD1 A:ASP351 2.0 0.7 1.0 O A:THR353 2.4 95.1 1.0 OD1 A:ASP703 2.6 0.2 1.0 BE A:BEF998 2.9 0.8 1.0 CG A:ASP351 3.0 0.4 1.0 OD2 A:ASP351 3.4 0.6 1.0 C A:THR353 3.5 93.4 1.0 OD2 A:ASP707 3.7 0.2 1.0 CG A:ASP703 3.7 0.7 1.0 F3 A:BEF998 3.8 0.1 1.0 F1 A:BEF998 3.9 0.5 1.0 OD2 A:ASP703 4.1 0.9 1.0 OD1 A:ASN706 4.1 0.1 1.0 CA A:GLY182 4.1 0.2 1.0 CA A:THR353 4.2 91.5 1.0 N A:THR353 4.2 91.6 1.0 CB A:ASP351 4.3 0.3 1.0 CB A:THR353 4.3 0.4 1.0 N A:GLY704 4.3 0.7 1.0 O A:SER178 4.4 0.7 1.0 ND2 A:ASN706 4.5 0.5 1.0 OD1 A:ASP707 4.5 0.7 1.0 N A:GLY354 4.5 0.1 1.0 CG A:ASP707 4.5 0.2 1.0 OG1 A:THR355 4.7 98.9 1.0 NZ A:LYS684 4.8 90.3 1.0 CG A:ASN706 4.8 0.9 1.0 CA A:GLY704 4.8 0.1 1.0 C A:LYS352 4.8 0.4 1.0 CA A:GLY354 4.8 0.0 1.0 N A:GLY182 4.9 0.1 1.0 N A:LYS352 4.9 0.8 1.0 N A:ASP703 5.0 0.3 1.0

Magnesium binding site 2 out of 2 in the Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Calcium Pump Crystal Structure with Bound BEF3 in the Absence of Calcium and Tg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg997 b:68.0 occ:1.00 OD1 B:ASP703 1.9 92.8 1.0 O B:THR353 1.9 76.1 1.0 F2 B:BEF1098 1.9 0.1 1.0 OD1 B:ASP351 2.0 1.0 1.0 CG B:ASP703 2.9 95.3 1.0 BE B:BEF1098 2.9 0.9 1.0 CG B:ASP351 3.0 0.7 1.0 C B:THR353 3.1 74.4 1.0 OD2 B:ASP703 3.2 99.5 1.0 OD2 B:ASP351 3.4 0.8 1.0 F3 B:BEF1098 3.8 0.3 1.0 F1 B:BEF1098 3.9 0.6 1.0 OD2 B:ASP707 4.0 97.8 1.0 N B:GLY354 4.0 87.2 1.0 CA B:GLY354 4.0 88.1 1.0 CA B:THR353 4.0 72.5 1.0 OG1 B:THR355 4.1 90.2 1.0 N B:GLY704 4.1 0.4 1.0 CB B:THR353 4.2 0.5 1.0 N B:THR353 4.2 72.6 1.0 CB B:ASP703 4.3 92.0 1.0 O B:SER178 4.3 0.8 1.0 CB B:ASP351 4.3 0.6 1.0 N B:THR355 4.5 91.6 1.0 C B:GLY354 4.5 89.7 1.0 N B:ASP703 4.6 0.5 1.0 CA B:GLY182 4.7 1.0 1.0 C B:LYS352 4.7 0.4 1.0 CA B:GLY704 4.8 0.8 1.0 OD1 B:ASN706 4.8 96.8 1.0 CA B:ASP703 4.8 1.0 1.0 C B:ASP703 4.8 0.1 1.0 CG B:ASP707 5.0 98.8 1.0

C.Toyoshima, Y.Norimatsu, S.Iwasawa, T.Tsuda, H.Ogawa. How Processing of Aspartylphosphate Is Coupled to Lumenal Gating of the Ion Pathway in the Calcium Pump Proc.Natl.Acad.Sci.Usa V. 104 19831 2007.
ISSN: ISSN 0027-8424
PubMed: 18077416
DOI: 10.1073/PNAS.0709978104