Magnesium in PDB 2rex: Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase

The structure of Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase, PDB code: 2rex was solved by Y.Tong, W.Tempel, L.Shen, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.136, 71.653, 101.885, 90.00, 128.36, 90.00
R / Rfree (%)	21.5 / 24.8

The structure of Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase (pdb code 2rex). 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 Effector Domain of PLXNB1 Bound with RND1 Gtpase, PDB code: 2rex:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase


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 Effector Domain of PLXNB1 Bound with RND1 Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg550 b:36.6 occ:1.00 O2G B:GNP500 2.1 35.4 1.0 OG1 B:THR27 2.2 35.9 1.0 O1B B:GNP500 2.2 32.8 1.0 OG1 B:THR45 2.2 35.7 1.0 O B:HOH567 2.2 20.3 1.0 O B:HOH581 2.3 21.3 1.0 PG B:GNP500 3.1 34.0 1.0 CB B:THR45 3.2 33.8 1.0 PB B:GNP500 3.2 32.4 1.0 CB B:THR27 3.3 34.0 1.0 N3B B:GNP500 3.4 31.4 1.0 O3G B:GNP500 3.8 32.4 1.0 OD2 B:ASP67 3.8 36.1 1.0 N B:THR45 3.9 32.8 1.0 N B:THR27 4.0 33.5 1.0 OD1 B:ASP67 4.1 33.6 1.0 CA B:THR45 4.2 33.2 1.0 O3A B:GNP500 4.2 31.7 1.0 CG2 B:THR45 4.2 32.0 1.0 CA B:THR27 4.2 33.1 1.0 O2B B:GNP500 4.3 34.3 1.0 CG B:ASP67 4.3 34.5 1.0 CG2 B:THR27 4.4 29.6 1.0 O B:HOH579 4.4 29.3 1.0 O1G B:GNP500 4.4 31.0 1.0 O1A B:GNP500 4.5 29.3 1.0 O B:THR68 4.5 33.3 1.0 O B:VAL43 4.6 32.9 1.0 PA B:GNP500 4.6 33.6 1.0 O2A B:GNP500 4.8 30.1 1.0 C B:PRO44 4.9 32.6 1.0 CE B:LYS26 4.9 31.4 1.0 CB B:LYS26 5.0 32.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase


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 Effector Domain of PLXNB1 Bound with RND1 Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg550 b:36.0 occ:1.00 O D:HOH590 2.1 24.9 1.0 OG1 D:THR27 2.1 35.8 1.0 OG1 D:THR45 2.1 31.9 1.0 O1B D:GNP500 2.1 33.1 1.0 O3G D:GNP500 2.1 32.5 1.0 O D:HOH568 2.3 18.6 1.0 CB D:THR45 3.1 32.3 1.0 CB D:THR27 3.3 34.9 1.0 PB D:GNP500 3.3 33.0 1.0 PG D:GNP500 3.3 34.2 1.0 N3B D:GNP500 3.6 32.2 1.0 N D:THR45 3.8 32.4 1.0 O1G D:GNP500 3.9 31.1 1.0 OD2 D:ASP67 4.0 37.5 1.0 CA D:THR45 4.1 31.8 1.0 N D:THR27 4.1 34.7 1.0 OD1 D:ASP67 4.1 31.2 1.0 CG2 D:THR45 4.1 29.9 1.0 O3A D:GNP500 4.2 32.0 1.0 CG2 D:THR27 4.2 30.9 1.0 CA D:THR27 4.3 34.2 1.0 O D:HOH574 4.3 27.0 1.0 CG D:ASP67 4.4 34.6 1.0 O2B D:GNP500 4.4 29.2 1.0 O1A D:GNP500 4.4 30.7 1.0 O2G D:GNP500 4.5 31.0 1.0 O D:VAL43 4.5 34.5 1.0 O D:THR68 4.5 33.0 1.0 PA D:GNP500 4.6 31.8 1.0 C D:PRO44 4.8 33.3 1.0 O2A D:GNP500 4.9 32.7 1.0 CB D:LYS26 5.0 33.4 1.0

Y.Tong, W.Tempel, L.Shen, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park. Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase. To Be Published.