Manganese in PDB 4o02: ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment.

The structure of ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment., PDB code: 4o02 was solved by B.Mahalingam, J.Van Agthoven, J.Xiong, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.86 / 3.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.464, 266.988, 102.163, 90.00, 90.00, 90.00
R / Rfree (%)	24.6 / 31.2

The binding sites of Manganese atom in the ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment. (pdb code 4o02). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment., PDB code: 4o02:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1025 b:0.9 occ:1.00 OD2 A:ASP230 2.1 0.2 1.0 OD1 A:ASN232 2.2 0.7 1.0 O A:ASN232 2.3 0.3 1.0 OD2 A:ASP238 2.3 0.0 1.0 OD1 A:ASP238 2.3 0.8 1.0 O A:ASP234 2.4 0.7 1.0 CG A:ASP238 2.7 0.9 1.0 O A:ILE236 3.3 96.8 1.0 CG A:ASP230 3.3 0.8 1.0 CG A:ASN232 3.4 0.5 1.0 C A:ASN232 3.4 0.3 1.0 C A:ASP234 3.6 0.7 1.0 N A:ASN232 3.9 0.2 1.0 OD1 A:ASP230 4.0 0.8 1.0 CA A:ASN232 4.1 0.2 1.0 N A:ASP234 4.1 0.3 1.0 N A:PHE231 4.2 0.2 1.0 CB A:ASN232 4.2 0.3 1.0 CB A:ASP238 4.3 89.3 1.0 ND2 A:ASN232 4.3 0.4 1.0 CA A:ASP234 4.4 0.2 1.0 OD1 A:ASP257 4.4 0.9 1.0 C A:GLY233 4.4 0.3 1.0 CB A:ASP230 4.4 0.7 1.0 C A:ILE236 4.4 0.1 1.0 N A:ILE236 4.5 0.2 1.0 C A:GLY235 4.5 0.4 1.0 N A:GLY235 4.5 0.1 1.0 C A:PHE231 4.5 0.8 1.0 N A:GLY233 4.6 0.8 1.0 CA A:ASP230 4.6 0.8 1.0 C A:ASP230 4.8 0.2 1.0 O A:GLY233 4.8 0.6 1.0 O A:GLY235 4.8 0.1 1.0 CA A:GLY235 4.8 0.6 1.0 CA A:GLY233 4.9 0.3 1.0 N A:ASP238 4.9 98.1 1.0 CA A:ILE236 5.0 0.6 1.0

Manganese binding site 2 out of 5 in the ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1026 b:0.1 occ:1.00 OD1 A:ASP284 2.2 1.0 1.0 OD1 A:ASP292 2.2 0.9 1.0 OD1 A:ASP288 2.2 0.0 1.0 OD2 A:ASP292 2.2 0.9 1.0 O A:TYR290 2.2 0.5 1.0 OD1 A:ASN286 2.2 0.5 1.0 CG A:ASP292 2.4 0.9 1.0 CG A:ASP288 3.1 0.9 1.0 CG A:ASP284 3.3 0.6 1.0 CG A:ASN286 3.3 0.2 1.0 C A:TYR290 3.4 0.3 1.0 OD2 A:ASP288 3.4 0.4 1.0 ND2 A:ASN286 3.8 0.8 1.0 CB A:ASP292 4.0 0.0 1.0 OD2 A:ASP284 4.0 0.6 1.0 CA A:TYR290 4.1 0.7 1.0 CB A:TYR290 4.1 0.7 1.0 CA A:ASP284 4.2 0.0 1.0 N A:TYR290 4.2 0.8 1.0 CB A:ASP284 4.3 0.3 1.0 N A:ILE285 4.3 1.0 1.0 N A:ASP292 4.3 0.5 1.0 N A:ASN286 4.3 0.6 1.0 N A:GLN320 4.3 0.7 1.0 C A:ALA291 4.4 0.6 1.0 CB A:ASP288 4.4 0.4 1.0 O A:GLN320 4.4 0.5 1.0 N A:ALA291 4.4 0.3 1.0 N A:ASP288 4.5 0.4 1.0 CD2 A:LEU319 4.6 0.2 1.0 C A:ASP284 4.6 0.3 1.0 CB A:ASN286 4.6 0.5 1.0 CA A:ASP292 4.6 0.2 1.0 CA A:ALA291 4.7 1.0 1.0 O A:ALA291 4.7 0.0 1.0 CB A:GLN320 4.8 0.9 1.0 CA A:ASN286 4.9 0.9 1.0 N A:GLY287 4.9 0.6 1.0 CA A:ASP288 4.9 0.6 1.0

Manganese binding site 3 out of 5 in the ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1027 b:1.0 occ:1.00 OD2 A:ASP349 2.2 1.0 1.0 OD2 A:ASP351 2.2 0.4 1.0 OD1 A:ASP357 2.2 0.9 1.0 OD2 A:ASP357 2.2 0.9 1.0 OD2 A:ASP353 2.3 0.4 1.0 O A:PHE355 2.3 0.8 1.0 CG A:ASP357 2.5 0.8 1.0 CG A:ASP349 3.1 0.3 1.0 CG A:ASP351 3.3 0.8 1.0 CG A:ASP353 3.3 0.7 1.0 C A:PHE355 3.5 0.4 1.0 OD1 A:ASP353 3.7 0.3 1.0 OD1 A:ASP349 3.8 0.0 1.0 OD1 A:ASP351 3.8 0.7 1.0 CA A:ASP349 4.0 0.2 1.0 CB A:ASP357 4.0 0.2 1.0 CB A:ASP349 4.1 0.6 1.0 N A:LEU350 4.2 0.6 1.0 C A:ASN356 4.3 0.8 1.0 N A:GLY378 4.3 0.2 1.0 N A:ASP351 4.3 0.9 1.0 ND2 A:ASN377 4.3 0.7 1.0 N A:PHE355 4.4 0.6 1.0 CA A:PHE355 4.4 0.3 1.0 N A:ASN356 4.5 0.8 1.0 N A:ASP357 4.5 0.2 1.0 C A:ASP349 4.5 0.0 1.0 CB A:ASP351 4.5 0.4 1.0 O A:ASN356 4.5 0.9 1.0 CB A:ASP353 4.5 0.4 1.0 CA A:ASN356 4.6 0.5 1.0 N A:ASP353 4.6 1.0 1.0 O A:GLY378 4.6 0.1 1.0 CB A:PHE355 4.7 0.5 1.0 CB A:ASN377 4.7 0.6 1.0 CA A:ASP357 4.8 0.7 1.0 N A:GLN352 4.8 0.4 1.0 CA A:ASN377 4.9 0.2 1.0 CA A:ASP351 4.9 0.8 1.0 CG A:ASN377 4.9 0.8 1.0 O A:GLY348 4.9 0.7 1.0

Manganese binding site 4 out of 5 in the ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1028 b:0.3 occ:1.00 O A:TYR419 2.1 0.0 1.0 OD1 A:ASP415 2.2 0.1 1.0 OD1 A:ASP413 2.2 0.9 1.0 OD2 A:ASP421 2.2 0.1 1.0 OD1 A:ASP421 2.2 99.3 1.0 OD1 A:ASN417 2.2 0.9 1.0 CG A:ASP421 2.5 0.7 1.0 CG A:ASN417 3.2 0.0 1.0 C A:TYR419 3.3 0.9 1.0 CG A:ASP413 3.3 0.6 1.0 CG A:ASP415 3.4 0.5 1.0 ND2 A:ASN417 3.5 0.5 1.0 OD2 A:ASP415 3.9 0.8 1.0 CB A:ASP421 4.0 99.8 1.0 CB A:ASP413 4.1 0.7 1.0 C A:PRO420 4.1 0.3 1.0 O A:ASN417 4.1 0.5 1.0 O A:PRO420 4.2 0.4 1.0 N A:PRO420 4.2 1.0 1.0 CA A:TYR419 4.2 0.3 1.0 OD2 A:ASP413 4.3 1.0 1.0 N A:ASP415 4.3 0.1 1.0 N A:TYR419 4.3 0.8 1.0 N A:ASP421 4.3 99.3 1.0 CA A:ASP413 4.4 0.2 1.0 CA A:PRO420 4.4 0.2 1.0 N A:ALA437 4.4 0.1 1.0 N A:ILE414 4.4 0.1 1.0 O A:ALA437 4.5 0.3 1.0 CB A:ASP415 4.5 0.5 1.0 CB A:TYR419 4.6 0.4 1.0 CB A:ASN417 4.6 0.1 1.0 O A:ASP415 4.6 0.7 1.0 C A:ASN417 4.7 0.4 1.0 C A:ASP413 4.7 0.5 1.0 CA A:ASP421 4.7 98.0 1.0 CA A:ASP415 4.8 0.6 1.0 CB A:ALA437 4.8 0.3 1.0 C A:ASP415 4.8 0.3 1.0 N A:ASN417 4.9 0.4 1.0 CA A:ASN417 4.9 0.7 1.0

Manganese binding site 5 out of 5 in the ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of ALPHAVBETA3 Integrin in Complex with Monoclonal Antibody Fab Fragment. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn707 b:0.5 occ:1.00 OD2 B:ASP126 2.1 0.6 1.0 OD1 B:ASP126 2.2 0.7 1.0 OD1 B:ASP127 2.2 0.8 1.0 O B:SER123 2.2 0.3 1.0 O B:MET335 2.3 0.3 1.0 CG B:ASP126 2.5 0.1 1.0 C B:SER123 3.4 1.0 1.0 CG B:ASP127 3.4 0.0 1.0 C B:MET335 3.6 94.9 1.0 CA B:MET124 3.9 86.6 1.0 CB B:ASP126 4.0 0.4 1.0 N B:MET124 4.1 87.4 1.0 OD2 B:ASP127 4.1 0.6 1.0 N B:ASP127 4.1 95.7 1.0 CA B:ASP336 4.5 97.7 1.0 C B:MET124 4.5 89.9 1.0 SD B:MET124 4.5 0.2 1.0 CB B:ASP127 4.5 0.6 1.0 N B:ASP126 4.5 0.0 1.0 N B:ASP336 4.5 92.8 1.0 CA B:SER123 4.6 0.0 1.0 CA B:MET335 4.7 0.3 1.0 CA B:ASP126 4.7 0.4 1.0 N B:LYS125 4.7 93.9 1.0 C B:ASP126 4.8 0.1 1.0 CA B:ASP127 4.8 92.2 1.0 CB B:MET335 4.9 0.8 1.0 CB B:SER123 4.9 0.3 1.0

B.Mahalingam, J.Van Agthoven, J.Xiong, M.A.Arnaout. Atomic Basis For the Species-Specific Inhibition of Alphav Integrins By Mab 17E6 Is Revealed By the Crystal Structure of the Integrin ALPHAVBETA3 Ectodomain-17E6 Complex To Be Published.