Magnesium in PDB 2zbd: Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium

All present enzymatic activity of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium:
3.6.3.8;

The structure of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium, PDB code: 2zbd was solved by C.Toyoshima, H.Nomura, T.Tsuda, 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 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.900, 75.100, 152.100, 90.00, 109.30, 90.00
R / Rfree (%)	24.6 / 27.1

The structure of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Aluminium	(Al)	1 atom
Calcium	(Ca)	2 atoms

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

Magnesium binding site 1 out of 2 in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg997 b:0.5 occ:1.00 O1B A:ADP1002 2.1 50.0 1.0 O A:HOH1041 2.8 55.8 1.0 O1A A:ADP1002 2.9 52.8 1.0 O A:HOH1046 2.9 73.3 1.0 O A:HOH1059 3.0 63.5 1.0 PB A:ADP1002 3.1 52.4 1.0 O3B A:ADP1002 3.2 48.9 1.0 F4 A:ALF998 3.2 55.3 1.0 F2 A:ALF998 3.3 55.3 1.0 MG A:MG1001 3.7 49.4 1.0 O3A A:ADP1002 3.8 53.1 1.0 AL A:ALF998 3.9 57.0 1.0 PA A:ADP1002 3.9 53.3 1.0 O A:HOH1038 4.2 65.2 1.0 CB A:THR353 4.3 61.4 1.0 NH2 A:ARG560 4.3 61.7 1.0 O2B A:ADP1002 4.5 51.5 1.0 OG1 A:THR353 4.5 61.2 1.0 OD1 A:ASN706 4.6 54.2 1.0 O5' A:ADP1002 4.8 52.5 1.0 O A:THR353 4.8 62.5 1.0 O A:HOH1055 4.8 64.7 1.0 CG2 A:THR353 4.8 60.7 1.0 ND2 A:ASN706 4.9 57.0 1.0 OE2 A:GLU439 5.0 75.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Sr Calcium Pump with Bound Aluminium Fluoride, Adp and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:49.4 occ:1.00 O A:HOH1038 2.0 65.2 1.0 F4 A:ALF998 2.0 55.3 1.0 O A:HOH1041 2.0 55.8 1.0 OD1 A:ASP703 2.1 62.7 1.0 O A:THR353 2.2 62.5 1.0 OD2 A:ASP351 2.4 59.4 1.0 CG A:ASP703 2.8 62.9 1.0 OD2 A:ASP703 2.8 63.5 1.0 CG A:ASP351 3.1 59.9 1.0 OD1 A:ASP351 3.2 58.7 1.0 F2 A:ALF998 3.2 55.3 1.0 C A:THR353 3.3 62.5 1.0 AL A:ALF998 3.4 57.0 1.0 MG A:MG997 3.7 0.5 1.0 CA A:THR353 4.0 61.7 1.0 CB A:THR353 4.0 61.4 1.0 N A:THR353 4.0 61.1 1.0 OD2 A:ASP707 4.1 53.0 1.0 OG1 A:THR355 4.2 64.9 1.0 N A:GLY704 4.2 60.8 1.0 CB A:ASP703 4.3 61.9 1.0 F1 A:ALF998 4.4 57.1 1.0 CB A:ASP351 4.4 60.8 1.0 N A:GLY354 4.4 63.4 1.0 O3B A:ADP1002 4.4 48.9 1.0 N A:ASP703 4.6 62.3 1.0 CA A:GLY704 4.7 60.3 1.0 OG1 A:THR353 4.7 61.2 1.0 CA A:GLY354 4.8 63.9 1.0 C A:LYS352 4.8 60.8 1.0 OD1 A:ASN706 4.9 54.2 1.0 CA A:ASP703 4.9 61.9 1.0 O A:HOH1046 4.9 73.3 1.0 C A:ASP703 4.9 61.5 1.0 N A:THR355 5.0 64.8 1.0

C.Toyoshima, H.Nomura, T.Tsuda. Lumenal Gating Mechanism Revealed in Calcium Pump Crystal Structures with Phosphate Analogues Nature V. 432 361 2004.
ISSN: ISSN 0028-0836
PubMed: 15448704
DOI: 10.1038/NATURE02981