Magnesium in PDB 7kdc: The Complex Between Rhod and the Plexin B2 Rbd

The structure of The Complex Between Rhod and the Plexin B2 Rbd, PDB code: 7kdc was solved by Y.Kuo, Y.Wang, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.63 / 3.10
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	82.81, 82.81, 136.761, 90, 90, 120
R / Rfree (%)	21.5 / 26.6

The binding sites of Magnesium atom in the The Complex Between Rhod and the Plexin B2 Rbd (pdb code 7kdc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Complex Between Rhod and the Plexin B2 Rbd, PDB code: 7kdc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Complex Between Rhod and the Plexin B2 Rbd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Complex Between Rhod and the Plexin B2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:119.3 occ:1.00 OG1 A:THR31 2.1 122.3 1.0 O2G A:GNP201 2.1 98.0 1.0 O A:HOH301 2.1 106.4 1.0 OG1 A:THR49 2.1 131.1 1.0 O2B A:GNP201 2.1 110.9 1.0 CB A:THR49 2.9 125.1 1.0 PG A:GNP201 3.1 107.6 1.0 PB A:GNP201 3.2 111.5 1.0 CB A:THR31 3.2 123.6 1.0 N3B A:GNP201 3.2 113.8 1.0 N A:THR49 3.2 125.0 1.0 O2A A:GNP201 3.6 114.7 1.0 O A:THR47 3.6 129.3 1.0 CA A:THR49 3.7 129.1 1.0 O1G A:GNP201 4.0 100.7 1.0 CG2 A:THR31 4.1 122.6 1.0 N A:THR31 4.1 126.3 1.0 OD2 A:ASP71 4.2 123.3 1.0 CG2 A:THR49 4.2 132.3 1.0 O3A A:GNP201 4.2 114.0 1.0 CA A:THR31 4.3 125.9 1.0 PA A:GNP201 4.3 116.2 1.0 O1B A:GNP201 4.3 100.4 1.0 C A:PRO48 4.3 120.9 1.0 O3G A:GNP201 4.3 113.2 1.0 CA A:PRO48 4.5 123.5 1.0 O1A A:GNP201 4.6 122.0 1.0 OD1 A:ASP71 4.7 110.4 1.0 C A:THR47 4.7 128.3 1.0 CG A:ASP71 4.8 120.3 1.0 O A:THR72 4.8 116.0 1.0 C A:THR49 4.9 130.3 1.0 CE1 A:TYR46 5.0 120.8 1.0

Magnesium binding site 2 out of 4 in the The Complex Between Rhod and the Plexin B2 Rbd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Complex Between Rhod and the Plexin B2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:107.7 occ:1.00 OD1 A:ASP76 3.2 124.3 1.0 OD2 A:ASP77 3.2 120.8 1.0 OD1 A:ASP77 3.6 143.1 1.0 CG A:ASP77 3.8 132.8 1.0 CG A:ASP76 4.0 118.7 1.0 OD2 A:ASP76 4.1 99.5 1.0

Magnesium binding site 3 out of 4 in the The Complex Between Rhod and the Plexin B2 Rbd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Complex Between Rhod and the Plexin B2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:115.7 occ:1.00 O2G B:GNP201 2.0 101.2 1.0 OG1 B:THR31 2.0 117.2 1.0 O B:HOH301 2.1 103.1 1.0 OG1 B:THR49 2.1 131.6 1.0 O2B B:GNP201 2.2 110.8 1.0 CB B:THR49 2.8 123.4 1.0 PG B:GNP201 3.2 108.2 1.0 N B:THR49 3.2 125.4 1.0 PB B:GNP201 3.3 111.2 1.0 CB B:THR31 3.3 116.4 1.0 N3B B:GNP201 3.3 119.0 1.0 CA B:THR49 3.6 127.3 1.0 O2A B:GNP201 3.8 118.7 1.0 O B:THR47 3.8 131.4 1.0 OD2 B:ASP71 4.0 131.1 1.0 O1G B:GNP201 4.1 100.9 1.0 CG2 B:THR49 4.1 129.2 1.0 CG2 B:THR31 4.1 108.6 1.0 N B:THR31 4.2 118.9 1.0 C B:PRO48 4.2 121.9 1.0 O3G B:GNP201 4.3 115.6 1.0 O1B B:GNP201 4.3 102.5 1.0 O3A B:GNP201 4.3 116.4 1.0 CA B:THR31 4.3 118.6 1.0 PA B:GNP201 4.4 113.2 1.0 OD1 B:ASP71 4.5 120.7 1.0 CA B:PRO48 4.5 122.1 1.0 CG B:ASP71 4.7 127.9 1.0 O1A B:GNP201 4.7 119.3 1.0 C B:THR49 4.8 126.2 1.0 C B:THR47 4.9 130.2 1.0 CE1 B:TYR46 5.0 120.7 1.0

Magnesium binding site 4 out of 4 in the The Complex Between Rhod and the Plexin B2 Rbd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Complex Between Rhod and the Plexin B2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:106.0 occ:1.00 OD1 B:ASP76 3.1 116.7 1.0 OD2 B:ASP77 3.4 118.8 1.0 OD2 B:ASP76 3.7 102.2 1.0 OD1 B:ASP77 3.8 137.8 1.0 CG B:ASP76 3.8 115.7 1.0 CG B:ASP77 4.0 129.5 1.0

Y.Liu, P.Ke, Y.C.Kuo, Y.Wang, X.Zhang, C.Song, Y.Shan. A Putative Structural Mechanism Underlying the Antithetic Effect of Homologous RND1 and Rhod Gtpases in Mammalian Plexin Regulation. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 34114565
DOI: 10.7554/ELIFE.64304