Magnesium in PDB 3rfe: Crystal Structure of Glycoprotein Gpib Ectodomain

The structure of Crystal Structure of Glycoprotein Gpib Ectodomain, PDB code: 3rfe was solved by P.A.Mcewan, W.Yang, K.H.Carr, X.Mo, X.Zheng, R.Li, J.Emsley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.30 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.506, 34.764, 71.532, 90.00, 92.15, 90.00
R / Rfree (%)	20.1 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of Glycoprotein Gpib Ectodomain (pdb code 3rfe). 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 Glycoprotein Gpib Ectodomain, PDB code: 3rfe:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Glycoprotein Gpib Ectodomain


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 Glycoprotein Gpib Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg131 b:5.3 occ:1.00 O A:HOH244 3.1 16.0 1.0 N A:TRP21 3.3 6.7 1.0 OG1 A:THR43 3.3 6.5 1.0 N A:THR43 3.3 5.2 1.0 O A:HOH186 3.5 12.3 1.0 CB A:TRP21 3.8 7.8 1.0 O A:ASN41 3.9 7.4 1.0 CB A:THR43 4.0 6.4 1.0 CB A:THR20 4.0 9.1 1.0 CA A:LEU42 4.1 5.3 1.0 CA A:THR20 4.1 6.8 1.0 CA A:THR43 4.1 5.5 1.0 CA A:TRP21 4.1 6.9 1.0 CG2 A:THR43 4.1 7.7 1.0 C A:THR20 4.2 5.9 1.0 C A:LEU42 4.2 5.7 1.0 O A:HOH251 4.4 24.4 1.0 N A:ALA44 4.4 5.0 1.0 O A:ALA44 4.6 6.1 1.0 CG2 A:THR20 4.7 10.0 1.0 C A:THR43 4.8 4.0 1.0 C A:ASN41 4.8 5.7 1.0 CD2 A:LEU42 4.8 7.4 1.0 N A:LEU42 4.9 5.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Glycoprotein Gpib Ectodomain


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 Glycoprotein Gpib Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg131 b:5.6 occ:1.00 O B:HOH258 3.1 17.2 1.0 O B:HOH243 3.2 16.6 1.0 N B:TRP21 3.3 6.6 1.0 OG1 B:THR43 3.3 6.8 1.0 N B:THR43 3.3 5.0 1.0 O B:HOH227 3.5 13.8 1.0 CB B:TRP21 3.7 8.1 1.0 O B:ASN41 3.9 7.4 1.0 CB B:THR20 3.9 8.9 1.0 CB B:THR43 4.0 6.8 1.0 CA B:LEU42 4.0 5.3 1.0 CA B:THR20 4.1 7.1 1.0 CG2 B:THR43 4.1 7.1 1.0 CA B:THR43 4.1 5.3 1.0 CA B:TRP21 4.1 7.0 1.0 C B:THR20 4.2 6.2 1.0 C B:LEU42 4.2 4.5 1.0 N B:ALA44 4.4 5.5 1.0 O B:ALA44 4.6 5.5 1.0 C B:THR43 4.7 4.5 1.0 CG2 B:THR20 4.7 10.9 1.0 C B:ASN41 4.8 6.2 1.0 CD2 B:LEU42 4.8 7.3 1.0 OG1 B:THR20 4.9 12.8 1.0 N B:LEU42 4.9 5.2 1.0

P.A.Mcewan, W.Yang, K.H.Carr, X.Mo, X.Zheng, R.Li, J.Emsley. Quaternary Organization of Gpib-IX Complex and Insights Into Bernard-Soulier Syndrome Revealed By the Structures of Gpibbeta and A Gpibbeta/Gpix Chimer Blood V. 118 5292 2011.
ISSN: ISSN 0006-4971
PubMed: 21908432
DOI: 10.1182/BLOOD-2011-05-356253