Calcium in PDB 9iuj: Integrin Alpha-V Beta-3 in Complex with Rhodostomin

The structure of Integrin Alpha-V Beta-3 in Complex with Rhodostomin also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin (pdb code 9iuj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin, PDB code: 9iuj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin Alpha-V Beta-3 in Complex with Rhodostomin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:250.5 occ:1.00 O A:VAL601 2.3 231.6 1.0 O A:CYS596 2.6 220.2 1.0 OD1 A:ASP599 2.6 228.8 1.0 OE1 A:GLU636 2.8 262.2 1.0 OE2 A:GLU636 2.9 262.8 1.0 CD A:GLU636 3.1 262.7 1.0 OD2 A:ASP599 3.3 227.4 1.0 CG A:ASP599 3.4 228.2 1.0 C A:CYS596 3.4 219.2 1.0 C A:VAL601 3.5 231.7 1.0 N A:LYS603 4.0 237.8 1.0 CA A:GLY597 4.1 220.9 1.0 CA A:CYS602 4.1 243.1 1.0 N A:GLY597 4.1 220.3 1.0 N A:CYS602 4.2 243.2 1.0 CE A:LYS603 4.2 238.2 1.0 CG A:LYS603 4.2 237.3 1.0 CA A:CYS596 4.3 219.1 1.0 C A:CYS602 4.4 242.3 1.0 N A:VAL601 4.5 231.9 1.0 CG A:GLU636 4.5 263.2 1.0 CB A:LYS603 4.5 237.7 1.0 CA A:VAL601 4.6 231.5 1.0 CB A:CYS596 4.6 219.9 1.0 CG2 A:VAL601 4.7 229.7 1.0 CD A:LYS603 4.7 237.6 1.0 C A:GLY597 4.8 221.6 1.0 CB A:ASP599 4.8 228.5 1.0 CA A:LYS603 4.9 237.9 1.0

Calcium binding site 2 out of 7 in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin Alpha-V Beta-3 in Complex with Rhodostomin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1202 b:37.6 occ:1.00 OD1 A:ASN232 2.1 31.7 1.0 OD2 A:ASP238 2.5 27.2 1.0 OD1 A:ASP234 2.8 31.8 1.0 O A:ILE236 2.9 32.4 1.0 OD1 A:ASP238 2.9 31.0 1.0 OD1 A:ASP230 3.0 29.4 1.0 CG A:ASP238 3.0 22.4 1.0 CG A:ASN232 3.1 24.0 1.0 ND2 A:ASN232 3.5 16.3 1.0 C A:ILE236 3.7 24.9 1.0 CG A:ASP234 3.9 32.0 1.0 CG A:ASP230 4.2 29.1 1.0 CB A:ILE236 4.2 21.5 1.0 CA A:ILE236 4.3 20.8 1.0 OD2 A:ASP234 4.3 34.6 1.0 N A:ILE236 4.3 29.7 1.0 N A:ASP238 4.3 20.2 1.0 N A:ASN232 4.3 27.9 1.0 CB A:ASP238 4.4 17.3 1.0 N A:PHE231 4.4 15.4 1.0 CB A:ASN232 4.5 20.9 1.0 OD1 A:ASP257 4.5 34.2 1.0 O A:ASP234 4.5 31.6 1.0 C A:ASP237 4.6 25.5 1.0 CA A:ASP230 4.7 11.8 1.0 N A:ASP237 4.7 22.9 1.0 CA A:ASP238 4.7 11.8 1.0 N A:GLY258 4.8 26.9 1.0 CA A:ASN232 4.8 21.0 1.0 CB A:ASP230 4.9 16.5 1.0 C A:ASP234 4.9 32.4 1.0 CG1 A:ILE236 4.9 25.1 1.0 CA A:ASP237 4.9 18.6 1.0 C A:ASN232 5.0 21.6 1.0

Calcium binding site 3 out of 7 in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin Alpha-V Beta-3 in Complex with Rhodostomin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1203 b:47.7 occ:1.00 OD1 A:ASP292 2.3 20.9 1.0 O A:TYR290 2.3 37.3 1.0 OD1 A:ASN286 2.5 40.9 1.0 OD1 A:ASP284 2.5 31.8 1.0 CG A:ASP292 3.0 23.6 1.0 OD2 A:ASP292 3.0 27.4 1.0 C A:TYR290 3.4 34.0 1.0 CG A:ASN286 3.5 34.7 1.0 OD1 A:ASP288 3.6 35.0 1.0 CG A:ASP284 3.7 34.5 1.0 OD2 A:ASP288 3.7 38.2 1.0 ND2 A:ASN286 3.7 28.1 1.0 CB A:TYR290 3.9 32.2 1.0 CG A:ASP288 4.0 34.2 1.0 CA A:TYR290 4.1 32.1 1.0 O A:GLN320 4.2 33.4 1.0 N A:TYR290 4.2 34.0 1.0 CA A:ASP284 4.3 26.7 1.0 N A:ILE285 4.4 25.5 1.0 N A:GLN320 4.4 23.7 1.0 CB A:ASP292 4.4 19.3 1.0 N A:ASP292 4.4 20.0 1.0 C A:ALA291 4.5 21.2 1.0 N A:ALA291 4.5 22.5 1.0 CB A:ASP284 4.5 26.9 1.0 OD2 A:ASP284 4.5 36.6 1.0 N A:ASN286 4.5 28.5 1.0 CA A:ALA291 4.8 19.2 1.0 C A:ASP284 4.8 30.2 1.0 O A:ALA291 4.8 32.0 1.0 CA A:ASP292 4.8 13.7 1.0 CB A:ASN286 4.9 29.2 1.0 CB A:GLN320 5.0 21.1 1.0

Calcium binding site 4 out of 7 in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin Alpha-V Beta-3 in Complex with Rhodostomin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1204 b:46.8 occ:1.00 OD1 A:ASP357 2.3 27.6 1.0 O A:PHE355 2.5 37.0 1.0 OD1 A:ASP351 2.6 40.2 1.0 OD1 A:ASP349 2.8 30.2 1.0 OD2 A:ASP357 2.9 32.4 1.0 CG A:ASP357 2.9 28.0 1.0 CG A:ASP351 3.5 34.8 1.0 OD2 A:ASP351 3.7 38.1 1.0 C A:PHE355 3.7 32.2 1.0 CG A:ASP349 4.0 30.9 1.0 ND2 A:ASN377 4.0 27.8 1.0 CB A:ASP353 4.1 28.5 1.0 OD2 A:ASP353 4.3 40.4 1.0 N A:LEU350 4.3 22.6 1.0 CB A:ASP357 4.4 23.8 1.0 N A:ASP351 4.4 29.8 1.0 CA A:ASP349 4.4 25.8 1.0 N A:PHE355 4.4 36.9 1.0 C A:ASN356 4.5 23.1 1.0 N A:ASP357 4.5 18.6 1.0 CA A:PHE355 4.6 33.4 1.0 N A:ASP353 4.6 41.3 1.0 O A:GLY378 4.6 41.0 1.0 N A:GLY378 4.6 26.2 1.0 C A:ASP349 4.7 32.6 1.0 CB A:ASN377 4.7 28.7 1.0 CG A:ASP353 4.7 41.2 1.0 N A:ASN356 4.7 25.5 1.0 CA A:ASN356 4.8 22.4 1.0 O A:ASN356 4.8 32.8 1.0 OD2 A:ASP349 4.8 31.1 1.0 CB A:ASP351 4.8 27.4 1.0 CB A:ASP349 4.8 27.3 1.0 CB A:PHE355 4.8 24.6 1.0 CG A:ASN377 4.9 31.8 1.0 N A:GLY354 4.9 32.1 1.0 CA A:ASP353 4.9 32.7 1.0 CA A:ASP357 4.9 22.1 1.0 CA A:ASN377 4.9 28.3 1.0 O A:GLY348 5.0 34.2 1.0

Calcium binding site 5 out of 7 in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin Alpha-V Beta-3 in Complex with Rhodostomin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1205 b:55.5 occ:1.00 OD1 A:ASP415 2.1 39.9 1.0 OD1 A:ASN417 2.3 40.9 1.0 OD1 A:ASP413 2.4 35.4 1.0 O A:TYR419 2.4 31.7 1.0 OD1 A:ASP421 2.7 26.5 1.0 CG A:ASP415 3.1 35.7 1.0 CG A:ASP421 3.4 25.9 1.0 OD2 A:ASP421 3.4 39.5 1.0 OD2 A:ASP415 3.4 31.6 1.0 CG A:ASN417 3.4 34.0 1.0 CG A:ASP413 3.6 38.1 1.0 C A:TYR419 3.6 30.0 1.0 ND2 A:ASN417 4.1 30.2 1.0 N A:ASP415 4.1 36.6 1.0 CA A:ASP413 4.1 26.9 1.0 N A:TYR419 4.2 25.4 1.0 N A:ILE414 4.2 28.5 1.0 CA A:TYR419 4.3 25.8 1.0 CB A:ASP413 4.4 30.8 1.0 C A:PRO420 4.4 28.6 1.0 CB A:ASP415 4.4 31.4 1.0 OD2 A:ASP413 4.4 38.6 1.0 CB A:ASN417 4.5 29.9 1.0 O A:ALA437 4.5 30.0 1.0 CB A:TYR419 4.5 25.4 1.0 C A:ASP413 4.5 29.7 1.0 N A:ASN417 4.5 32.7 1.0 N A:ASP421 4.6 23.1 1.0 N A:PRO420 4.6 25.9 1.0 O A:PRO420 4.6 33.6 1.0 N A:ALA437 4.7 24.4 1.0 CB A:ASP421 4.7 25.2 1.0 CA A:PRO420 4.7 19.9 1.0 CA A:ASP415 4.7 30.6 1.0 N A:LYS416 4.9 37.4 1.0 CA A:ASP421 4.9 17.3 1.0 CA A:ASN417 4.9 32.9 1.0 C A:ASP415 5.0 36.5 1.0

Calcium binding site 6 out of 7 in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin Alpha-V Beta-3 in Complex with Rhodostomin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:30.6 occ:1.00 O B:SER123 2.1 22.1 1.0 OD2 B:ASP251 2.4 27.6 1.0 OD2 B:ASP127 2.5 33.7 1.0 OD1 B:ASP126 2.9 40.4 1.0 C B:SER123 3.3 19.6 1.0 CG B:ASP251 3.5 22.9 1.0 OD2 B:ASP126 3.5 41.8 1.0 CG B:ASP126 3.5 39.5 1.0 CG B:ASP127 3.6 37.6 1.0 N B:MET124 4.1 28.7 1.0 OD1 B:ASP127 4.1 43.7 1.0 CB B:ASP251 4.2 20.7 1.0 CA B:MET124 4.2 20.3 1.0 CA B:SER123 4.2 16.1 1.0 CB B:SER123 4.3 18.3 1.0 OD1 B:ASP251 4.4 25.0 1.0 N C:ASP54 4.6 52.5 1.0 OD2 C:ASP54 4.6 59.4 1.0 CA C:PRO53 4.6 32.8 1.0 CB B:ASP127 4.8 29.9 1.0 NH2 C:ARG56 4.8 72.9 1.0 SD B:MET124 4.9 30.2 1.0 C B:MET124 4.9 19.8 1.0 CB B:ASP126 4.9 35.9 1.0 N B:ASP127 5.0 34.6 1.0 N B:ASP126 5.0 39.6 1.0

Calcium binding site 7 out of 7 in the Integrin Alpha-V Beta-3 in Complex with Rhodostomin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Integrin Alpha-V Beta-3 in Complex with Rhodostomin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:8.8 occ:1.00 O B:PRO219 2.1 14.4 1.0 OD2 B:ASP158 2.2 20.3 1.0 OD1 B:ASP217 2.3 24.0 1.0 ND2 B:ASN215 2.3 19.2 1.0 O B:ASP217 2.9 19.0 1.0 CG B:ASP217 3.2 18.3 1.0 CG B:ASP158 3.3 13.5 1.0 C B:PRO219 3.4 13.8 1.0 OE1 B:GLU220 3.6 4.0 1.0 CG B:ASN215 3.6 17.4 1.0 OD2 B:ASP217 3.6 21.9 1.0 C B:ASP217 3.7 17.3 1.0 CB B:ASP158 3.8 10.3 1.0 NE2 B:HIS255 3.8 10.2 1.0 CA B:GLU220 4.0 12.8 1.0 CD2 B:HIS255 4.1 7.6 1.0 CD B:GLU220 4.1 8.2 1.0 N B:GLU220 4.1 13.3 1.0 N B:ASP217 4.2 11.5 1.0 CB B:ASP217 4.2 15.3 1.0 CA B:ASP217 4.2 15.9 1.0 OD1 B:ASN215 4.3 32.6 1.0 N B:PRO219 4.4 16.8 1.0 OD1 B:ASP158 4.4 16.7 1.0 OE2 B:GLU220 4.4 14.7 1.0 CA B:PRO219 4.5 4.2 1.0 C B:ALA218 4.5 18.7 1.0 CB B:ASN215 4.5 9.7 1.0 O B:ALA218 4.6 24.6 1.0 CD1 B:TYR164 4.6 19.8 1.0 N B:ALA218 4.7 18.9 1.0 CB B:TYR164 4.8 17.6 1.0 CG B:GLU220 4.8 15.9 1.0 CB B:GLU220 4.8 12.5 1.0 CG B:TYR164 4.9 14.7 1.0

Y.T.Wang, W.J.Chuang. Integrin Alpha-V Beta-3 in Complex with Rhodostomin To Be Published.