Magnesium in PDB 5fbh: Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+

The structure of Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+, PDB code: 5fbh was solved by T.Zhang, C.Zhang, C.L.Miller, J.Zou, K.W.Moremen, E.M.Brown, J.J.Yang, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.08 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.107, 83.106, 94.470, 90.00, 105.15, 90.00
R / Rfree (%)	18.2 / 23.6

The structure of Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+ also contains other interesting chemical elements:

Gadolinium	(Gd)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+ (pdb code 5fbh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+, PDB code: 5fbh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+


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 Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:62.8 occ:1.00 OG B:SER240 2.4 52.4 1.0 O B:HOH706 2.5 48.2 1.0 O B:SER240 2.6 55.1 1.0 C B:SER240 3.5 49.8 1.0 CB B:SER240 3.7 50.6 1.0 CA B:SER240 4.1 53.4 1.0 CG A:GLU228 4.4 56.5 1.0 CB A:GLU228 4.5 53.3 1.0 N B:GLU241 4.5 51.9 1.0 N B:SER240 4.6 55.7 1.0 OE1 A:GLU228 4.7 75.8 1.0 OE1 B:GLU241 4.8 67.4 1.0 CA B:GLU241 4.8 50.1 1.0 CD A:GLU228 4.9 69.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+


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 Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:77.4 occ:1.00 O B:LEU88 2.6 94.8 1.0 O B:ILE81 2.8 65.9 1.0 O B:LEU87 2.9 78.7 1.0 CA B:ASN82 3.5 65.7 1.0 C B:LEU88 3.6 84.9 1.0 C B:ILE81 3.6 67.1 1.0 OD1 B:ASN82 3.7 68.1 1.0 CB B:LEU88 3.7 79.5 1.0 O B:LEU91 3.7 76.5 1.0 O B:SER84 3.7 86.7 1.0 O B:ASN82 3.9 69.8 1.0 N B:ASN82 4.0 63.3 1.0 C B:LEU87 4.0 76.3 1.0 C B:ASN82 4.0 69.6 1.0 CG2 B:ILE81 4.1 61.5 1.0 CA B:LEU88 4.1 80.6 1.0 CB B:ASN82 4.5 62.8 1.0 CG B:ASN82 4.5 63.5 1.0 N B:LEU88 4.5 79.5 1.0 N B:PRO89 4.7 98.5 1.0 C B:LEU91 4.8 87.1 1.0 CA B:ILE81 4.9 67.6 1.0 C B:SER84 4.9 91.6 1.0 CG B:LEU88 5.0 77.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Extracellular Domain of Human Calcium Sensing Receptor with Bound GD3+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:95.1 occ:1.00 O A:ILE81 2.5 87.9 1.0 O A:LEU87 2.5 91.4 1.0 O A:LEU88 2.7 0.1 1.0 O A:SER84 2.8 0.9 1.0 O A:ASN82 3.3 87.8 1.0 CA A:ASN82 3.6 87.3 1.0 C A:ILE81 3.6 88.7 1.0 C A:LEU88 3.6 0.6 1.0 C A:ASN82 3.7 92.7 1.0 C A:LEU87 3.7 0.9 1.0 C A:SER84 4.0 0.1 1.0 N A:ASN82 4.0 84.7 1.0 O A:LEU91 4.2 72.7 1.0 CB A:LEU88 4.2 0.3 1.0 CA A:LEU88 4.3 0.4 1.0 OD1 A:ASN82 4.4 78.7 1.0 N A:LEU88 4.5 0.1 1.0 N A:PRO89 4.6 0.6 1.0 N A:SER84 4.6 98.0 1.0 CG2 A:ILE81 4.7 79.7 1.0 CA A:SER84 4.7 0.6 1.0 CA A:PRO89 4.8 0.7 1.0 O A:PRO85 4.8 95.8 1.0 CB A:ASN82 4.8 79.2 1.0 N A:SER83 4.8 86.2 1.0 CA A:LEU87 4.9 0.6 1.0 CA A:ILE81 4.9 88.9 1.0 CB A:SER84 4.9 0.1 1.0 N A:PRO85 5.0 0.4 1.0 CA A:PRO85 5.0 0.1 1.0

C.Zhang, T.Zhang, J.Zou, C.L.Miller, R.Gorkhali, J.Y.Yang, A.Schilmiller, S.Wang, K.Huang, E.M.Brown, K.W.Moremen, J.Hu, J.J.Yang. Structural Basis For Regulation of Human Calcium-Sensing Receptor By Magnesium Ions and An Unexpected Tryptophan Derivative Co-Agonist. Sci Adv V. 2 00241 2016.
ISSN: ESSN 2375-2548
PubMed: 27386547
DOI: 10.1126/SCIADV.1600241