Magnesium in PDB 4m8n: Crystal Structure of PLEXINC1/RAP1B Complex

The structure of Crystal Structure of PLEXINC1/RAP1B Complex, PDB code: 4m8n was solved by H.G.Pascoe, Y.Wang, C.A.Brautigam, H.He, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.05 / 3.29
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.276, 84.734, 138.752, 91.09, 95.15, 90.32
R / Rfree (%)	24.3 / 29.9

The structure of Crystal Structure of PLEXINC1/RAP1B Complex also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Aluminium	(Al)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of PLEXINC1/RAP1B Complex (pdb code 4m8n). 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 PLEXINC1/RAP1B Complex, PDB code: 4m8n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of PLEXINC1/RAP1B 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 PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg200 b:88.3 occ:1.00 F2 E:AF3202 1.8 0.1 1.0 O2B E:GDP201 2.0 92.5 1.0 OG E:SER17 2.1 0.9 1.0 OG1 E:THR35 2.2 0.4 1.0 CB E:THR35 2.6 94.3 1.0 PB E:GDP201 3.0 0.8 1.0 O3B E:GDP201 3.1 91.3 1.0 AL E:AF3202 3.3 89.2 1.0 CB E:SER17 3.5 0.2 1.0 CG2 E:THR35 3.6 88.2 1.0 O1B E:GDP201 3.7 94.2 1.0 OD2 E:ASP57 3.7 0.6 1.0 O E:THR58 3.8 0.7 1.0 OD1 E:ASP57 3.8 0.5 1.0 CA E:THR35 3.8 98.0 1.0 N E:THR35 3.8 0.2 1.0 N E:SER17 4.0 0.4 1.0 F1 E:AF3202 4.0 0.6 1.0 CG E:ASP57 4.1 0.4 1.0 CA E:SER17 4.3 0.7 1.0 O3A E:GDP201 4.4 0.0 1.0 CE E:LYS16 4.4 88.6 1.0 F3 E:AF3202 4.5 0.8 1.0 CB E:LYS16 4.6 1.0 1.0 NZ E:LYS16 4.7 89.3 1.0 O2A E:GDP201 4.7 0.2 1.0 C E:THR35 4.7 0.2 1.0 O E:THR35 4.7 1.0 1.0 O1A E:GDP201 4.8 0.8 1.0 PA E:GDP201 4.9 0.2 1.0 C E:THR58 4.9 0.0 1.0 C E:LYS16 5.0 0.2 1.0 O E:ASP33 5.0 0.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of PLEXINC1/RAP1B 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 PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg200 b:88.4 occ:1.00 O2B F:GDP201 2.0 0.7 1.0 F2 F:AF3202 2.0 0.3 1.0 OG F:SER17 2.1 0.3 1.0 OG1 F:THR35 2.3 0.5 1.0 CB F:THR35 2.7 0.2 1.0 PB F:GDP201 2.8 0.6 1.0 O1B F:GDP201 3.0 0.6 1.0 O3B F:GDP201 3.3 0.6 1.0 AL F:AF3202 3.4 91.3 1.0 OD1 F:ASP57 3.4 0.2 1.0 CB F:SER17 3.5 0.3 1.0 NZ F:LYS16 3.6 93.5 1.0 CG2 F:THR35 3.6 99.2 1.0 OD2 F:ASP57 3.6 0.6 1.0 O F:THR58 3.7 0.3 1.0 N F:SER17 3.8 0.2 1.0 CG F:ASP57 3.9 0.7 1.0 CA F:THR35 4.0 0.7 1.0 N F:THR35 4.0 0.8 1.0 CA F:SER17 4.1 0.7 1.0 F1 F:AF3202 4.2 0.4 1.0 O3A F:GDP201 4.3 0.4 1.0 F3 F:AF3202 4.4 0.5 1.0 CB F:LYS16 4.4 0.5 1.0 C F:LYS16 4.8 0.6 1.0 C F:THR35 4.8 0.7 1.0 O1A F:GDP201 4.9 97.7 1.0 CE F:LYS16 4.9 96.8 1.0 C F:THR58 4.9 0.8 1.0 O F:THR35 4.9 0.3 1.0 PA F:GDP201 5.0 98.8 1.0 O2A F:GDP201 5.0 0.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of PLEXINC1/RAP1B 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 PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg200 b:0.8 occ:1.00 OG G:SER17 1.9 0.4 1.0 O2B G:GDP201 1.9 0.1 1.0 F2 G:AF3202 1.9 87.5 1.0 OG1 G:THR35 2.2 0.1 1.0 CB G:THR35 2.8 0.6 1.0 PB G:GDP201 3.1 0.5 1.0 CB G:SER17 3.2 0.7 1.0 AL G:AF3202 3.5 97.5 1.0 OD2 G:ASP57 3.5 0.6 1.0 O3B G:GDP201 3.5 0.1 1.0 CG2 G:THR35 3.6 0.9 1.0 OD1 G:ASP57 3.7 0.2 1.0 O1B G:GDP201 3.7 0.9 1.0 N G:SER17 3.7 0.3 1.0 O G:THR58 3.8 0.4 1.0 CG G:ASP57 4.0 0.6 1.0 CA G:SER17 4.0 0.7 1.0 CA G:THR35 4.1 0.3 1.0 N G:THR35 4.2 0.2 1.0 F3 G:AF3202 4.3 91.9 1.0 O2A G:GDP201 4.4 0.0 1.0 O3A G:GDP201 4.4 0.0 1.0 CB G:LYS16 4.4 0.7 1.0 CE G:LYS16 4.5 0.5 1.0 F1 G:AF3202 4.6 0.2 1.0 PA G:GDP201 4.8 0.5 1.0 O1A G:GDP201 4.8 0.4 1.0 C G:LYS16 4.8 0.2 1.0 C G:THR35 5.0 0.4 1.0 C G:THR58 5.0 0.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of PLEXINC1/RAP1B 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 PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg200 b:0.1 occ:1.00 F2 H:AF3202 1.9 0.9 1.0 OG1 H:THR35 2.1 1.0 1.0 O2B H:GDP201 2.1 0.8 1.0 OG H:SER17 2.2 0.9 1.0 CB H:THR35 2.5 0.8 1.0 OD2 H:ASP57 2.9 0.9 1.0 PB H:GDP201 3.0 0.4 1.0 O1B H:GDP201 3.1 0.1 1.0 OD1 H:ASP57 3.2 0.7 1.0 CG2 H:THR35 3.3 0.8 1.0 NZ H:LYS16 3.3 0.9 1.0 O H:THR58 3.4 0.9 1.0 O3B H:GDP201 3.4 0.9 1.0 CG H:ASP57 3.4 0.2 1.0 AL H:AF3202 3.5 0.1 1.0 CB H:SER17 3.5 0.2 1.0 N H:SER17 3.7 0.0 1.0 CE H:LYS16 3.8 0.3 1.0 CA H:THR35 3.8 0.1 1.0 N H:THR35 4.0 0.2 1.0 CA H:SER17 4.1 0.5 1.0 CB H:LYS16 4.2 0.2 1.0 F3 H:AF3202 4.5 0.4 1.0 O3A H:GDP201 4.5 0.8 1.0 F1 H:AF3202 4.5 0.6 1.0 C H:THR58 4.6 0.5 1.0 C H:LYS16 4.7 0.0 1.0 C H:THR35 4.7 1.0 1.0 CA H:LYS16 4.9 0.7 1.0 CB H:ASP57 4.9 1.0 1.0 O H:THR35 4.9 0.5 1.0 O1A H:GDP201 5.0 0.9 1.0

Y.Wang, H.G.Pascoe, C.A.Brautigam, H.He, X.Zhang. Structural Basis For Activation and Non-Canonical Catalysis of the Rap Gtpase Activating Protein Domain of Plexin. Elife V. 2 01279 2013.
ISSN: ESSN 2050-084X
PubMed: 24137545
DOI: 10.7554/ELIFE.01279