Aluminium 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
Magnesium	(Mg)	4 atoms

The binding sites of Aluminium atom in the Crystal Structure of PLEXINC1/RAP1B Complex (pdb code 4m8n). This binding sites where shown within 5.0 Angstroms radius around Aluminium atom.
In total 4 binding sites of Aluminium where determined in the Crystal Structure of PLEXINC1/RAP1B Complex, PDB code: 4m8n:
Jump to Aluminium binding site number: 1; 2; 3; 4;

Aluminium binding site 1 out of 4 in the Crystal Structure of PLEXINC1/RAP1B Complex


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 1 of Crystal Structure of PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Al202 b:89.2 occ:1.00 AL E:AF3202 0.0 89.2 1.0 F2 E:AF3202 1.6 0.1 1.0 F1 E:AF3202 1.6 0.6 1.0 F3 E:AF3202 1.6 0.8 1.0 O3B E:GDP201 2.1 91.3 1.0 MG E:MG200 3.3 88.3 1.0 PB E:GDP201 3.5 0.8 1.0 O2B E:GDP201 3.8 92.5 1.0 NE2 E:GLN63 3.8 86.3 1.0 N E:THR35 3.8 0.2 1.0 N E:GLY13 4.0 0.2 1.0 NE A:ARG711 4.0 0.1 1.0 NH1 A:ARG711 4.1 0.8 1.0 N E:GLY60 4.2 0.4 1.0 OE1 E:GLN63 4.2 82.9 1.0 O E:THR35 4.3 1.0 1.0 CA E:PRO34 4.3 0.5 1.0 CB E:THR35 4.4 94.3 1.0 NZ E:LYS16 4.4 89.3 1.0 O1B E:GDP201 4.4 94.2 1.0 CD E:GLN63 4.4 84.3 1.0 CZ A:ARG711 4.5 0.3 1.0 CA E:GLY12 4.5 0.1 1.0 O3A E:GDP201 4.5 0.0 1.0 OG1 E:THR35 4.5 0.4 1.0 C E:PRO34 4.5 99.3 1.0 CA E:THR35 4.6 98.0 1.0 CA E:ALA59 4.7 1.0 1.0 C E:ALA59 4.7 0.2 1.0 C E:GLY12 4.7 0.1 1.0 CA E:GLY13 4.8 0.3 1.0 O E:SER11 4.8 0.2 1.0 CA E:GLY60 4.8 0.9 1.0 CG A:ARG711 4.8 0.4 1.0 C E:THR35 4.9 0.2 1.0 CB E:PRO34 5.0 0.7 1.0 CD A:ARG711 5.0 0.5 1.0 O2A E:GDP201 5.0 0.2 1.0

Aluminium binding site 2 out of 4 in the Crystal Structure of PLEXINC1/RAP1B Complex


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 2 of Crystal Structure of PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Al202 b:91.3 occ:1.00 AL F:AF3202 0.0 91.3 1.0 F2 F:AF3202 1.6 0.3 1.0 F3 F:AF3202 1.6 0.5 1.0 F1 F:AF3202 1.6 0.4 1.0 O3B F:GDP201 1.9 0.6 1.0 PB F:GDP201 3.1 0.6 1.0 MG F:MG200 3.4 88.4 1.0 O2B F:GDP201 3.5 0.7 1.0 N F:THR35 3.6 0.8 1.0 O1B F:GDP201 3.7 0.6 1.0 NZ F:LYS16 3.9 93.5 1.0 NE2 F:GLN63 3.9 99.0 1.0 N F:GLY60 4.0 0.3 1.0 O F:THR35 4.2 0.3 1.0 CB F:THR35 4.2 0.2 1.0 OE1 F:GLN63 4.3 94.5 1.0 CA F:PRO34 4.3 0.9 1.0 OG1 F:THR35 4.4 0.5 1.0 N F:GLY13 4.4 0.3 1.0 CA F:THR35 4.4 0.7 1.0 NE C:ARG711 4.4 0.2 1.0 NH2 C:ARG711 4.4 0.4 1.0 O3A F:GDP201 4.4 0.4 1.0 CD F:GLN63 4.5 97.7 1.0 C F:PRO34 4.5 1.0 1.0 CA F:GLY60 4.5 0.2 1.0 C F:ALA59 4.6 0.8 1.0 C F:THR35 4.8 0.7 1.0 CA F:ALA59 4.8 0.1 1.0 CA F:GLY12 4.8 0.7 1.0 CZ C:ARG711 4.9 0.7 1.0 O F:THR58 5.0 0.3 1.0

Aluminium binding site 3 out of 4 in the Crystal Structure of PLEXINC1/RAP1B Complex


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 3 of Crystal Structure of PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Al202 b:97.5 occ:1.00 AL G:AF3202 0.0 97.5 1.0 F1 G:AF3202 1.6 0.2 1.0 F2 G:AF3202 1.6 87.5 1.0 F3 G:AF3202 1.6 91.9 1.0 O3B G:GDP201 2.0 0.1 1.0 PB G:GDP201 3.3 0.5 1.0 MG G:MG200 3.5 0.8 1.0 O2B G:GDP201 3.5 0.1 1.0 NE2 G:GLN63 3.7 98.9 1.0 N G:GLY60 3.9 0.9 1.0 N G:THR35 4.0 0.2 1.0 O1B G:GDP201 4.0 0.9 1.0 OE1 G:GLN63 4.1 93.8 1.0 NH2 B:ARG711 4.2 0.6 1.0 C G:ALA59 4.2 0.9 1.0 N G:GLY13 4.3 0.7 1.0 CB G:THR35 4.3 0.6 1.0 NE B:ARG711 4.3 0.7 1.0 O G:THR35 4.3 0.4 1.0 NZ G:LYS16 4.3 0.6 1.0 CD G:GLN63 4.3 95.5 1.0 CA G:ALA59 4.4 0.0 1.0 CA G:GLY12 4.4 0.9 1.0 OG1 G:THR35 4.4 0.1 1.0 O3A G:GDP201 4.5 0.0 1.0 CA G:GLY60 4.5 0.1 1.0 CE G:LYS16 4.6 0.5 1.0 CA G:THR35 4.6 0.3 1.0 CZ B:ARG711 4.7 0.7 1.0 O G:THR58 4.8 0.4 1.0 C G:GLY12 4.9 0.2 1.0 CA G:PRO34 4.9 0.3 1.0 C G:THR35 5.0 0.4 1.0 C G:PRO34 5.0 1.0 1.0 O G:ALA59 5.0 0.5 1.0

Aluminium binding site 4 out of 4 in the Crystal Structure of PLEXINC1/RAP1B Complex


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 4 of Crystal Structure of PLEXINC1/RAP1B Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Al202 b:0.1 occ:1.00 AL H:AF3202 0.0 0.1 1.0 F1 H:AF3202 1.6 0.6 1.0 F2 H:AF3202 1.6 0.9 1.0 F3 H:AF3202 1.6 0.4 1.0 O3B H:GDP201 1.9 0.9 1.0 PB H:GDP201 3.1 0.4 1.0 O2B H:GDP201 3.2 0.8 1.0 MG H:MG200 3.5 0.1 1.0 NZ H:LYS16 3.5 0.9 1.0 N H:THR35 3.6 0.2 1.0 NE2 H:GLN63 3.9 0.4 1.0 N H:GLY13 3.9 0.5 1.0 O1B H:GDP201 4.0 0.1 1.0 CB H:THR35 4.1 0.8 1.0 N H:GLY60 4.1 0.2 1.0 O3A H:GDP201 4.2 0.8 1.0 O H:THR35 4.2 0.5 1.0 OG1 H:THR35 4.3 1.0 1.0 CA H:PRO34 4.3 0.3 1.0 OE1 H:GLN63 4.3 0.7 1.0 CA H:THR35 4.3 0.1 1.0 NH2 D:ARG711 4.4 0.8 1.0 C H:PRO34 4.4 0.5 1.0 C H:ALA59 4.4 0.7 1.0 CD H:GLN63 4.5 0.9 1.0 CA H:ALA59 4.5 0.7 1.0 CE H:LYS16 4.6 0.3 1.0 CA H:GLY12 4.6 0.0 1.0 CA H:GLY13 4.7 0.5 1.0 O H:THR58 4.7 0.9 1.0 C H:THR35 4.8 1.0 1.0 CA H:GLY60 4.8 0.3 1.0 CD D:ARG711 4.8 0.8 1.0 C H:GLY12 4.8 0.4 1.0 CB H:PRO34 5.0 0.2 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