Magnesium in PDB 5mpm: SERCA2A From Pig Heart

All present enzymatic activity of SERCA2A From Pig Heart:
3.6.3.8;

The structure of SERCA2A From Pig Heart, PDB code: 5mpm was solved by N.D.Drachmann, A.Sitsel, J.L.Andersen, P.Nissen, C.Olesen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.32 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.349, 253.287, 64.981, 90.00, 100.86, 90.00
R / Rfree (%)	20.4 / 25.8

The structure of SERCA2A From Pig Heart also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Potassium	(K)	1 atom

The binding sites of Magnesium atom in the SERCA2A From Pig Heart (pdb code 5mpm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the SERCA2A From Pig Heart, PDB code: 5mpm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the SERCA2A From Pig Heart


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SERCA2A From Pig Heart within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:81.9 occ:1.00 MG A:MGF1001 0.0 81.9 1.0 F1 A:MGF1001 1.8 0.5 1.0 F3 A:MGF1001 1.8 68.6 1.0 F2 A:MGF1001 1.8 45.7 1.0 OD1 A:ASP351 2.0 95.4 1.0 O A:HOH1101 2.1 81.2 1.0 CG A:ASP351 2.7 82.2 1.0 OD2 A:ASP351 2.9 80.2 1.0 MG A:MG1004 3.4 0.6 1.0 O A:HOH1104 3.4 31.8 1.0 NZ A:LYS683 3.8 0.5 1.0 OG1 A:THR624 3.8 1.0 1.0 ND2 A:ASN705 3.9 43.4 1.0 N A:GLY625 3.9 79.2 1.0 CB A:THR353 3.9 0.3 1.0 CA A:GLY182 3.9 72.6 1.0 O A:GLY182 4.0 79.0 1.0 N A:THR353 4.0 0.2 1.0 CB A:ASP351 4.1 54.6 1.0 C A:GLY182 4.2 81.4 1.0 O A:THR353 4.2 63.0 1.0 O A:THR181 4.2 0.3 1.0 CA A:THR624 4.2 73.7 1.0 CA A:THR353 4.5 0.7 1.0 CB A:THR624 4.5 83.9 1.0 C A:THR624 4.5 62.6 1.0 N A:LYS352 4.6 86.9 1.0 OG1 A:THR353 4.6 94.8 1.0 C A:THR353 4.8 81.0 1.0 CG2 A:THR353 4.8 92.4 1.0 CA A:GLY625 4.8 93.0 1.0 OD2 A:ASP706 4.8 0.8 1.0 CA A:ASP351 4.8 63.8 1.0 O A:HOH1105 4.9 68.4 1.0 N A:GLY182 4.9 69.5 1.0 CE A:LYS683 4.9 0.4 1.0 CG A:ASN705 4.9 69.0 1.0 C A:THR181 4.9 92.9 1.0 O A:ILE623 5.0 0.8 1.0

Magnesium binding site 2 out of 3 in the SERCA2A From Pig Heart


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of SERCA2A From Pig Heart within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:0.1 occ:1.00 O2 A:CZA1002 2.0 0.7 1.0 OE1 A:GLN56 2.1 0.0 1.0 O A:HOH1103 2.2 80.7 1.0 O A:HOH1102 2.3 48.5 1.0 O1 A:CZA1002 2.3 0.7 1.0 C6 A:CZA1002 2.9 0.4 1.0 C2 A:CZA1002 3.2 0.0 1.0 CD A:GLN56 3.3 0.6 1.0 C3 A:CZA1002 3.4 0.4 1.0 NE2 A:GLN56 4.1 0.2 1.0 C5 A:CZA1002 4.2 0.1 1.0 CB A:GLN56 4.3 0.0 1.0 CG A:GLN56 4.3 0.6 1.0 O A:ASN101 4.5 0.4 1.0 O A:GLN56 4.5 0.3 1.0 C1 A:CZA1002 4.5 0.8 1.0 CA A:GLN56 4.6 0.1 1.0 C4 A:CZA1002 4.7 0.0 1.0 CA A:GLY105 4.8 0.3 1.0

Magnesium binding site 3 out of 3 in the SERCA2A From Pig Heart


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of SERCA2A From Pig Heart within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:0.6 occ:1.00 F1 A:MGF1001 1.7 0.5 1.0 O A:THR353 2.1 63.0 1.0 O A:HOH1104 2.1 31.8 1.0 OD2 A:ASP351 2.1 80.2 1.0 OD1 A:ASP702 2.1 0.1 1.0 O A:HOH1105 2.3 68.4 1.0 CG A:ASP702 3.0 0.7 1.0 C A:THR353 3.1 81.0 1.0 CG A:ASP351 3.3 82.2 1.0 OD2 A:ASP702 3.3 0.7 1.0 MG A:MGF1001 3.4 81.9 1.0 O A:GLY182 3.6 79.0 1.0 CB A:THR353 3.7 0.3 1.0 CG2 A:THR353 3.8 92.4 1.0 OD1 A:ASP351 3.8 95.4 1.0 CA A:THR353 3.9 0.7 1.0 N A:GLY354 4.0 88.5 1.0 OD2 A:ASP706 4.2 0.8 1.0 N A:THR353 4.3 0.2 1.0 CA A:GLY354 4.3 95.5 1.0 F3 A:MGF1001 4.4 68.6 1.0 CB A:ASP702 4.4 86.3 1.0 N A:GLY703 4.4 77.8 1.0 CB A:ASP351 4.5 54.6 1.0 C A:GLY182 4.5 81.4 1.0 F2 A:MGF1001 4.5 45.7 1.0 CA A:GLY182 4.5 72.6 1.0 N A:ASP702 4.6 79.6 1.0 CA A:GLY703 4.7 81.0 1.0 O A:HOH1101 4.7 81.2 1.0 C A:ASP702 4.8 68.5 1.0 CA A:ASP702 4.8 79.5 1.0 C A:GLY354 5.0 86.3 1.0

A.Sitsel, J.De Raeymaecker, N.D.Drachmann, R.Derua, S.Smaardijk, J.L.Andersen, I.Vandecaetsbeek, J.Chen, M.De Maeyer, E.Waelkens, C.Olesen, P.Vangheluwe, P.Nissen. Structures of the Heart Specific SERCA2A CA2+-Atpase. Embo J. V. 38 2019.
ISSN: ESSN 1460-2075
PubMed: 30777856
DOI: 10.15252/EMBJ.2018100020