Magnesium in PDB 7y4a: Crystal Structure of Human ELMO1 Rbd-Rhog Complex

The structure of Crystal Structure of Human ELMO1 Rbd-Rhog Complex, PDB code: 7y4a was solved by K.Tsuda, M.Kukimoto-Niino, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.37 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.72, 63.75, 115.33, 90, 100.5, 90
R / Rfree (%)	19.8 / 23.6

The binding sites of Magnesium atom in the Crystal Structure of Human ELMO1 Rbd-Rhog Complex (pdb code 7y4a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human ELMO1 Rbd-Rhog Complex, PDB code: 7y4a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human ELMO1 Rbd-Rhog Complex


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 Human ELMO1 Rbd-Rhog Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:16.1 occ:1.00 O1 A:PO4202 1.9 21.1 1.0 O1B A:GDP203 2.0 13.8 1.0 O A:HOH423 2.1 17.6 1.0 OG1 A:THR17 2.1 17.1 1.0 O A:HOH326 2.1 16.8 1.0 OG1 A:THR35 2.2 17.8 1.0 CB A:THR17 3.2 15.5 1.0 CB A:THR35 3.2 18.7 1.0 PB A:GDP203 3.3 17.0 1.0 P A:PO4202 3.3 18.2 1.0 O3B A:GDP203 3.6 19.0 1.0 N A:THR17 3.9 14.2 1.0 N A:THR35 4.0 16.4 1.0 O4 A:PO4202 4.0 21.7 1.0 OD2 A:ASP57 4.0 18.1 1.0 O2A A:GDP203 4.1 17.1 1.0 CA A:THR17 4.1 16.4 1.0 O3 A:PO4202 4.1 18.4 1.0 OD1 A:ASP57 4.2 19.1 1.0 CG2 A:THR17 4.2 17.9 1.0 CA A:THR35 4.2 16.1 1.0 O A:HOH369 4.2 22.6 1.0 CG2 A:THR35 4.2 17.3 1.0 O2B A:GDP203 4.3 16.6 1.0 O2 A:PO4202 4.3 17.9 1.0 O A:ILE33 4.4 22.1 1.0 O A:THR58 4.4 17.9 1.0 O3A A:GDP203 4.4 16.1 1.0 CG A:ASP57 4.5 17.5 1.0 PA A:GDP203 4.7 17.9 1.0 NZ A:LYS16 4.7 14.6 1.0 CE A:LYS16 4.8 15.1 1.0 CB A:LYS16 4.9 13.6 1.0 C A:PRO34 5.0 18.2 1.0 C A:LYS16 5.0 16.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human ELMO1 Rbd-Rhog Complex


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 Human ELMO1 Rbd-Rhog Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:19.6 occ:1.00 O3 C:PO4202 2.0 23.8 1.0 O3B C:GDP203 2.0 18.5 1.0 OG1 C:THR17 2.0 19.2 1.0 O C:HOH370 2.1 21.2 1.0 OG1 C:THR35 2.1 24.6 1.0 O C:HOH321 2.2 20.5 1.0 CB C:THR35 3.2 20.1 1.0 CB C:THR17 3.2 18.9 1.0 PB C:GDP203 3.3 18.3 1.0 P C:PO4202 3.4 21.4 1.0 O1B C:GDP203 3.6 20.5 1.0 N C:THR35 3.9 24.2 1.0 N C:THR17 4.0 16.4 1.0 O4 C:PO4202 4.0 23.4 1.0 O1 C:PO4202 4.1 21.1 1.0 OD2 C:ASP57 4.1 23.6 1.0 CA C:THR17 4.1 16.4 1.0 O C:HOH353 4.1 25.9 1.0 O1A C:GDP203 4.1 20.3 1.0 CA C:THR35 4.2 21.9 1.0 CG2 C:THR35 4.2 21.7 1.0 OD1 C:ASP57 4.2 25.4 1.0 CG2 C:THR17 4.2 24.0 1.0 O2B C:GDP203 4.3 18.4 1.0 O C:THR58 4.4 25.8 1.0 O C:ILE33 4.4 23.2 1.0 O2 C:PO4202 4.4 23.4 1.0 O3A C:GDP203 4.4 20.1 1.0 CG C:ASP57 4.5 29.8 1.0 PA C:GDP203 4.7 20.3 1.0 NZ C:LYS16 4.7 21.4 1.0 CE C:LYS16 4.8 21.7 1.0 CB C:LYS16 4.9 19.1 1.0 C C:PRO34 5.0 29.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human ELMO1 Rbd-Rhog Complex


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 Human ELMO1 Rbd-Rhog Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:17.1 occ:1.00 O3B E:GDP203 2.0 16.0 1.0 O E:HOH349 2.0 17.9 1.0 O4 E:PO4202 2.1 23.6 1.0 OG1 E:THR35 2.1 17.9 1.0 O E:HOH336 2.1 19.6 1.0 OG1 E:THR17 2.1 18.2 1.0 CB E:THR17 3.2 17.5 1.0 PB E:GDP203 3.2 16.8 1.0 CB E:THR35 3.2 20.1 1.0 O1B E:GDP203 3.4 16.4 1.0 P E:PO4202 3.5 19.1 1.0 N E:THR17 3.9 17.1 1.0 O3 E:PO4202 4.0 18.9 1.0 O1A E:GDP203 4.0 18.9 1.0 OD2 E:ASP57 4.1 18.8 1.0 N E:THR35 4.1 16.3 1.0 O2 E:PO4202 4.1 20.9 1.0 CA E:THR17 4.1 18.2 1.0 CG2 E:THR35 4.1 19.2 1.0 OD1 E:ASP57 4.2 19.7 1.0 CG2 E:THR17 4.2 16.9 1.0 CA E:THR35 4.3 14.8 1.0 O E:HOH341 4.3 23.4 1.0 O2B E:GDP203 4.3 18.9 1.0 O E:ILE33 4.3 18.4 1.0 O3A E:GDP203 4.3 15.0 1.0 O1 E:PO4202 4.5 20.2 1.0 CG E:ASP57 4.5 21.4 1.0 O E:THR58 4.6 19.4 1.0 PA E:GDP203 4.6 18.9 1.0 C E:PRO34 4.8 19.7 1.0 NZ E:LYS16 4.8 17.7 1.0 O2A E:GDP203 4.8 20.2 1.0 CE E:LYS16 4.8 14.6 1.0 CB E:LYS16 4.9 16.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human ELMO1 Rbd-Rhog Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human ELMO1 Rbd-Rhog Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg201 b:21.1 occ:1.00 O2 G:PO4202 2.0 26.4 1.0 O2B G:GDP203 2.0 18.1 1.0 OG1 G:THR17 2.1 22.4 1.0 O G:HOH322 2.1 22.4 1.0 OG1 G:THR35 2.1 23.6 1.0 O G:HOH341 2.2 19.8 1.0 CB G:THR35 3.2 21.2 1.0 CB G:THR17 3.2 19.7 1.0 PB G:GDP203 3.2 19.9 1.0 O3B G:GDP203 3.4 21.6 1.0 P G:PO4202 3.5 22.4 1.0 N G:THR17 3.9 20.5 1.0 OD2 G:ASP57 4.0 22.6 1.0 CG2 G:THR35 4.1 23.5 1.0 O1 G:PO4202 4.1 21.9 1.0 CA G:THR17 4.1 20.5 1.0 N G:THR35 4.2 23.8 1.0 O4 G:PO4202 4.2 24.1 1.0 OD1 G:ASP57 4.2 23.2 1.0 O2A G:GDP203 4.2 24.0 1.0 CG2 G:THR17 4.2 22.0 1.0 O1B G:GDP203 4.2 26.7 1.0 CA G:THR35 4.2 21.2 1.0 O G:HOH352 4.4 21.8 1.0 O3 G:PO4202 4.4 26.9 1.0 O3A G:GDP203 4.4 20.6 1.0 O G:ILE33 4.4 22.9 1.0 O G:THR58 4.5 23.9 1.0 CG G:ASP57 4.5 19.1 1.0 PA G:GDP203 4.7 23.6 1.0 NZ G:LYS16 4.7 22.9 1.0 CE G:LYS16 4.8 21.9 1.0 O1A G:GDP203 4.9 20.8 1.0 C G:PRO34 4.9 21.0 1.0 CB G:LYS16 4.9 20.4 1.0

C.Tam, M.Kukimoto-Niino, Y.Miyata-Yabuki, K.Tsuda, C.Mishima-Tsumagari, K.Ihara, M.Inoue, M.Yonemochi, K.Hanada, T.Matsumoto, M.Shirouzu, K.Y.J.Zhang. Targeting Ras-Binding Domain of ELMO1 By Computational Nanobody Design Commun Biol 2023.
ISSN: ESSN 2399-3642