Calcium in PDB 9b9j: Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab

The binding sites of Calcium atom in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab (pdb code 9b9j). 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-5 Beta-1 in Complex with BIIG2 Fab, PDB code: 9b9j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:102.8 occ:1.00 OD1 A:ASP247 2.1 95.6 1.0 OD1 A:ASP243 2.2 105.9 1.0 O A:THR245 2.3 101.6 1.0 OE2 A:GLU239 2.4 99.3 1.0 OD2 A:ASP247 2.6 95.8 1.0 CG A:ASP247 2.7 88.7 1.0 HB2 A:SER241 2.8 89.1 1.0 OE1 A:GLU239 2.8 99.6 1.0 CG A:ASP243 2.9 103.8 1.0 CD A:GLU239 3.0 94.6 1.0 OD2 A:ASP243 3.0 103.1 1.0 HG1 A:THR245 3.1 97.2 1.0 HG A:SER241 3.2 90.5 1.0 H A:SER241 3.3 91.7 1.0 C A:THR245 3.5 95.2 1.0 CB A:SER241 3.5 80.5 1.0 OG A:SER241 3.6 90.4 1.0 H A:PHE240 3.6 82.6 1.0 OG1 A:THR245 3.8 103.7 1.0 H A:THR245 3.8 97.0 1.0 HA A:GLU239 3.8 88.0 1.0 N A:SER241 3.9 95.1 1.0 H A:GLY267 3.9 91.6 1.0 CB A:ASP247 4.1 82.7 1.0 HA A:GLU246 4.1 94.6 1.0 H A:ASP243 4.1 101.0 1.0 H A:ASP247 4.2 89.9 1.0 N A:ASP247 4.2 91.0 1.0 CA A:SER241 4.2 86.0 1.0 HB3 A:SER241 4.3 89.2 1.0 N A:THR245 4.3 93.6 1.0 C A:GLU246 4.3 94.3 1.0 CB A:ASP243 4.4 100.4 1.0 N A:PHE240 4.4 81.3 1.0 CA A:THR245 4.4 91.7 1.0 CG A:GLU239 4.4 84.0 1.0 N A:GLU246 4.5 92.4 1.0 CA A:GLU246 4.5 90.0 1.0 HB2 A:ASP247 4.6 88.7 1.0 HA3 A:GLY267 4.6 90.6 1.0 CA A:ASP247 4.6 84.4 1.0 HB3 A:ASP247 4.6 89.1 1.0 C A:SER241 4.6 93.1 1.0 HA A:ASP247 4.7 88.9 1.0 CB A:THR245 4.7 93.5 1.0 HG3 A:GLU239 4.7 86.8 1.0 CA A:GLU239 4.7 81.5 1.0 O A:SER241 4.7 98.5 1.0 N A:GLY267 4.8 90.7 1.0 HB2 A:ASP243 4.8 101.0 1.0 C A:ASP243 4.8 100.7 1.0 N A:ASP243 4.8 101.8 1.0 O A:ASP243 4.8 99.1 1.0 O A:GLU246 4.8 91.5 1.0 C A:PHE240 4.9 80.0 1.0 OD1 A:ASN266 4.9 82.5 1.0 CA A:ASP243 4.9 102.7 1.0 HB3 A:ASP243 4.9 101.3 1.0 HG2 A:GLU239 5.0 87.8 1.0

Calcium binding site 2 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:93.5 occ:1.00 OD1 A:ASN295 2.2 91.3 1.0 OD1 A:ASP293 2.3 83.5 1.0 OD1 A:ASP301 2.3 82.8 1.0 OD2 A:ASP301 2.3 90.8 1.0 OD1 A:ASP297 2.4 100.1 1.0 O A:LEU299 2.4 97.2 1.0 OD2 A:ASP297 2.5 86.5 1.0 CG A:ASP301 2.6 78.6 1.0 CG A:ASP297 2.8 93.1 1.0 CG A:ASN295 3.3 84.7 1.0 CG A:ASP293 3.4 86.5 1.0 HA A:ASP293 3.5 85.5 1.0 H A:ASN295 3.5 81.5 1.0 HB2 A:LEU299 3.6 88.3 1.0 HD22 A:ASN295 3.6 82.2 1.0 C A:LEU299 3.6 87.4 1.0 H A:LEU299 3.6 89.1 1.0 H A:ASP297 3.8 89.9 1.0 H A:VAL294 3.8 82.8 1.0 HD21 A:LEU328 3.8 79.7 1.0 ND2 A:ASN295 3.9 87.6 1.0 H A:GLN329 3.9 86.5 1.0 CB A:ASP301 4.1 73.8 1.0 O A:GLN329 4.2 96.0 1.0 CA A:ASP293 4.2 83.9 1.0 CB A:ASP297 4.2 85.2 1.0 CB A:ASP293 4.2 83.0 1.0 N A:LEU299 4.3 88.2 1.0 OD2 A:ASP293 4.3 90.3 1.0 CA A:LEU299 4.3 86.6 1.0 N A:ASN295 4.3 75.9 1.0 HB3 A:GLN329 4.3 86.9 1.0 HB2 A:ASP293 4.3 85.0 1.0 N A:VAL294 4.4 79.0 1.0 CB A:LEU299 4.4 87.3 1.0 C A:ASP300 4.5 85.8 1.0 HB3 A:ASP297 4.5 88.2 1.0 HB2 A:ASP301 4.5 82.8 1.0 N A:ASP301 4.5 80.8 1.0 N A:ASP297 4.5 93.0 1.0 CB A:ASN295 4.5 74.2 1.0 HB3 A:ASP301 4.6 81.8 1.0 HG21 A:VAL294 4.6 82.9 1.0 N A:GLN329 4.6 84.5 1.0 HB3 A:LEU328 4.6 79.1 1.0 HA A:LEU328 4.6 79.8 1.0 O A:ASP300 4.7 97.2 1.0 N A:ASP300 4.7 82.1 1.0 HA A:ASP300 4.7 91.1 1.0 C A:ASP293 4.7 86.9 1.0 H A:ASP301 4.7 83.6 1.0 HD21 A:ASN295 4.7 82.0 1.0 CD2 A:LEU328 4.8 79.4 1.0 HB3 A:ASN295 4.8 81.1 1.0 HB2 A:ASP297 4.8 88.7 1.0 H A:GLY296 4.8 80.9 1.0 HB3 A:LEU299 4.8 88.1 1.0 CA A:ASP301 4.8 77.4 1.0 H A:GLY298 4.8 85.4 1.0 CA A:ASN295 4.8 73.0 1.0 CA A:ASP297 4.9 88.0 1.0 CA A:ASP300 4.9 83.8 1.0 HA A:ASP301 4.9 82.3 1.0 HD23 A:LEU328 5.0 79.9 1.0

Calcium binding site 3 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:88.5 occ:1.00 OD1 A:ASP368 2.3 87.8 1.0 OD1 A:ASP362 2.3 110.7 1.0 O A:TYR366 2.4 93.2 1.0 OD1 A:ASP364 2.4 104.4 1.0 OD1 A:ASP360 2.7 94.8 1.0 OD2 A:ASP368 2.9 90.1 1.0 CG A:ASP368 2.9 85.0 1.0 CG A:ASP364 3.2 99.1 1.0 CG A:ASP362 3.3 105.5 1.0 OD2 A:ASP364 3.5 95.9 1.0 H A:ASP362 3.5 102.1 1.0 C A:TYR366 3.5 82.0 1.0 H A:TYR366 3.6 86.2 1.0 HA A:ASP360 3.6 93.3 1.0 OD2 A:ASP362 3.7 107.1 1.0 HB2 A:TYR366 3.7 83.8 1.0 H A:ASP364 3.8 98.8 1.0 H A:GLY389 3.8 86.0 1.0 CG A:ASP360 3.9 95.4 1.0 H A:LEU361 3.9 93.9 1.0 N A:TYR366 4.3 88.3 1.0 CA A:TYR366 4.3 79.7 1.0 N A:ASP362 4.3 99.7 1.0 N A:LEU361 4.3 92.4 1.0 HA A:ASN367 4.4 83.3 1.0 CA A:ASP360 4.4 89.9 1.0 CB A:ASP368 4.4 78.7 1.0 C A:ASN367 4.4 80.1 1.0 CB A:ASP364 4.4 95.0 1.0 CB A:TYR366 4.5 77.0 1.0 N A:GLY389 4.5 87.2 1.0 HB3 A:ASP364 4.5 97.3 1.0 H A:GLN363 4.5 96.1 1.0 N A:ASP368 4.5 82.8 1.0 N A:ASN367 4.6 75.4 1.0 HA A:PRO388 4.6 83.7 1.0 C A:ASP360 4.6 91.8 1.0 N A:ASP364 4.6 102.0 1.0 OD2 A:ASP360 4.7 100.8 1.0 CB A:ASP362 4.7 99.3 1.0 CA A:ASN367 4.7 75.7 1.0 O A:ASN367 4.7 85.8 1.0 H A:ASP368 4.7 84.4 1.0 H A:GLY365 4.7 92.1 1.0 CB A:ASP360 4.7 93.6 1.0 HA3 A:GLY389 4.8 85.2 1.0 HB3 A:ASP368 4.8 83.0 1.0 HB3 A:LEU361 4.8 94.1 1.0 O A:GLY389 4.8 93.5 1.0 N A:GLN363 4.9 96.9 1.0 HB2 A:ASP368 4.9 83.2 1.0 HB2 A:PRO388 4.9 83.3 1.0 CA A:ASP362 4.9 100.3 1.0 HB3 A:TYR366 4.9 83.9 1.0 CA A:ASP368 5.0 81.5 1.0

Calcium binding site 4 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:92.1 occ:1.00 OD1 A:ASP424 2.1 101.5 1.0 OD2 A:ASP426 2.4 109.6 1.0 OD1 A:ASP432 2.5 95.3 1.0 O A:TYR430 2.6 94.1 1.0 HB2 A:ASN428 3.0 102.0 1.0 HB2 A:ASP426 3.1 106.5 1.0 OD2 A:ASP432 3.2 96.7 1.0 CG A:ASP432 3.2 90.1 1.0 H A:ASP426 3.2 106.8 1.0 CG A:ASP424 3.4 103.0 1.0 CG A:ASP426 3.4 109.6 1.0 CB A:ASP426 3.7 107.3 1.0 H A:LEU425 3.8 96.3 1.0 H A:GLY448 3.8 89.7 1.0 C A:TYR430 3.8 91.2 1.0 HB2 A:TYR430 3.8 94.1 1.0 HA A:ASP424 3.9 97.8 1.0 CB A:ASN428 4.0 97.7 1.0 N A:ASP426 4.0 107.4 1.0 H A:TYR430 4.0 94.8 1.0 H A:ASN428 4.0 102.1 1.0 OD2 A:ASP424 4.1 108.2 1.0 HB3 A:ARG447 4.2 93.6 1.0 CB A:ASP424 4.3 92.3 1.0 O A:GLY448 4.4 93.6 1.0 HD21 A:ASN428 4.4 101.5 1.0 N A:LEU425 4.4 94.4 1.0 HB2 A:ASP424 4.4 97.5 1.0 CG A:ASN428 4.5 105.4 1.0 CA A:ASP426 4.5 105.0 1.0 HB3 A:ASP426 4.5 106.8 1.0 HB3 A:ASN428 4.5 101.8 1.0 CA A:ASP424 4.5 92.7 1.0 OD1 A:ASP426 4.5 111.7 1.0 N A:GLY448 4.5 83.3 1.0 CB A:TYR430 4.5 90.1 1.0 C A:PRO431 4.5 90.3 1.0 HA A:PRO431 4.5 90.3 1.0 CA A:TYR430 4.6 94.0 1.0 ND2 A:ASN428 4.6 102.9 1.0 H A:GLY427 4.6 105.0 1.0 CB A:ASP432 4.6 85.3 1.0 HD2 A:ARG447 4.6 95.1 1.0 N A:ASN428 4.6 101.7 1.0 HA A:ARG447 4.6 93.3 1.0 O A:PRO431 4.6 91.6 1.0 N A:TYR430 4.7 96.2 1.0 HB3 A:TYR430 4.7 93.9 1.0 HG2 A:ARG447 4.7 93.7 1.0 N A:ASP432 4.8 85.6 1.0 N A:PRO431 4.8 80.3 1.0 CA A:ASN428 4.8 102.1 1.0 C A:ASP424 4.8 94.6 1.0 CA A:PRO431 4.8 89.1 1.0 CB A:ARG447 5.0 90.1 1.0

Calcium binding site 5 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:109.4 occ:1.00 HB2 B:SER132 2.6 91.4 1.0 HB3 B:SER132 2.6 92.1 1.0 OE1 B:GLU229 2.6 100.9 1.0 OG B:SER132 2.7 100.0 1.0 CB B:SER132 2.8 93.2 1.0 HG B:SER132 3.3 92.5 1.0 HG B:SER134 3.6 89.7 1.0 CD B:GLU229 3.7 102.2 1.0 OG B:SER134 3.8 91.0 1.0 HB1 B:ALA260 4.0 86.3 1.0 OD1 B:ASP259 4.0 100.0 1.0 HD22 B:ASN224 4.1 90.9 1.0 HG3 B:GLU229 4.1 94.7 1.0 OD2 B:ASP130 4.1 93.8 1.0 CA B:SER132 4.3 85.6 1.0 HG2 B:GLU229 4.3 94.3 1.0 CG B:GLU229 4.3 97.5 1.0 H B:SER134 4.4 89.6 1.0 O B:SER227 4.5 95.1 1.0 HB2 B:ALA260 4.5 85.7 1.0 CB B:ALA260 4.7 88.4 1.0 HA B:SER132 4.7 90.9 1.0 ND2 B:ASN224 4.7 96.1 1.0 HD21 B:ASN224 4.7 91.0 1.0 H B:SER132 4.7 91.9 1.0 OE2 B:GLU229 4.7 103.6 1.0 HB3 B:SER134 4.8 89.9 1.0 HA B:SER227 4.8 90.1 1.0 CB B:SER134 4.9 89.2 1.0 C B:SER132 4.9 88.7 1.0 H B:TYR133 5.0 92.3 1.0 HB3 B:ALA260 5.0 86.3 1.0 CG B:ASP130 5.0 93.5 1.0 CG B:ASP259 5.0 97.2 1.0

Calcium binding site 6 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:92.1 occ:1.00 O B:SER134 2.4 91.9 1.0 OD1 B:ASP137 2.4 106.6 1.0 OD1 B:ASP138 2.5 103.0 1.0 O B:ALA342 2.5 93.5 1.0 OD2 B:ASP137 2.7 102.9 1.0 CG B:ASP137 2.9 101.2 1.0 HA B:MET135 3.5 94.9 1.0 C B:SER134 3.6 90.2 1.0 CG B:ASP138 3.7 101.0 1.0 C B:ALA342 3.7 91.1 1.0 HA B:ASN343 3.8 102.1 1.0 H B:ASP138 3.8 99.5 1.0 HB2 B:SER134 4.2 89.9 1.0 CA B:MET135 4.3 88.5 1.0 OD2 B:ASP138 4.3 106.8 1.0 H B:ASP137 4.4 97.7 1.0 HB2 B:ALA342 4.4 91.4 1.0 N B:MET135 4.4 93.1 1.0 CB B:ASP137 4.4 95.5 1.0 N B:ASP138 4.5 99.9 1.0 HA B:ALA342 4.5 90.9 1.0 CA B:ASN343 4.5 97.4 1.0 HB3 B:ASN343 4.6 101.4 1.0 HA B:SER134 4.6 89.8 1.0 N B:ASN343 4.6 101.5 1.0 CA B:SER134 4.6 87.7 1.0 CA B:ALA342 4.7 88.0 1.0 HB2 B:ASP138 4.8 98.2 1.0 CB B:ASP138 4.8 93.3 1.0 HB2 B:ASP137 4.8 98.6 1.0 HB3 B:ASP137 4.9 98.4 1.0 OD2 B:ASP259 4.9 98.5 1.0 C B:MET135 4.9 93.1 1.0 CB B:SER134 4.9 89.2 1.0 N B:ASP137 4.9 94.6 1.0

Calcium binding site 7 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Integrin Alpha-5 Beta-1 in Complex with BIIG2 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:101.5 occ:1.00 OD1 B:ASN224 2.0 102.2 1.0 O B:PRO228 2.1 90.4 1.0 OD1 B:ASP226 2.1 95.7 1.0 OE2 B:GLU169 2.4 97.4 1.0 O B:ASP226 2.4 91.0 1.0 OE2 B:GLU229 2.7 103.6 1.0 CG B:ASN224 2.9 96.6 1.0 HA B:GLU229 3.0 93.8 1.0 HD22 B:ASN224 3.1 90.9 1.0 C B:PRO228 3.2 84.9 1.0 CG B:ASP226 3.3 90.7 1.0 HG2 B:GLU169 3.3 89.8 1.0 ND2 B:ASN224 3.3 96.1 1.0 CD B:GLU169 3.4 92.5 1.0 C B:ASP226 3.4 86.7 1.0 CD B:GLU229 3.5 102.2 1.0 HB2 B:GLU169 3.6 89.9 1.0 HE2 B:HIS263 3.6 86.6 1.0 CG B:GLU169 3.8 89.6 1.0 CA B:GLU229 3.8 90.0 1.0 H B:ASP226 3.8 88.0 1.0 OE1 B:GLU229 3.9 100.9 1.0 N B:GLU229 3.9 90.8 1.0 OD2 B:ASP226 4.0 91.8 1.0 O B:SER227 4.0 95.1 1.0 C B:SER227 4.1 91.0 1.0 HD21 B:ASN224 4.1 91.0 1.0 N B:ASP226 4.1 84.6 1.0 CA B:ASP226 4.2 85.9 1.0 CB B:ASN224 4.2 88.8 1.0 HB2 B:ASN224 4.2 89.5 1.0 N B:PRO228 4.2 86.3 1.0 CB B:GLU169 4.2 90.2 1.0 CB B:ASP226 4.3 84.7 1.0 NE2 B:HIS263 4.3 85.9 1.0 CA B:PRO228 4.3 79.8 1.0 HD2 B:HIS263 4.3 86.8 1.0 N B:SER227 4.4 85.4 1.0 HD2 B:PRO228 4.4 85.8 1.0 CG B:GLU229 4.6 97.5 1.0 OE1 B:GLU169 4.6 92.3 1.0 HB3 B:ASN224 4.6 90.7 1.0 H B:LEU225 4.6 87.6 1.0 H B:GLY230 4.7 85.4 1.0 HB2 B:ASP226 4.7 87.5 1.0 CD2 B:HIS263 4.7 85.5 1.0 HG3 B:GLU169 4.7 89.4 1.0 HB3 B:TYR175 4.7 79.9 1.0 CB B:GLU229 4.7 93.1 1.0 CA B:SER227 4.7 87.5 1.0 HB2 B:PRO228 4.7 84.2 1.0 HG2 B:GLU229 4.8 94.3 1.0 HA B:SER227 4.8 90.1 1.0 HB3 B:GLU169 4.8 89.6 1.0 O B:VAL168 4.8 93.2 1.0 H B:GLU229 4.8 93.8 1.0 C B:GLU229 4.9 90.0 1.0 CD B:PRO228 4.9 86.9 1.0 HB3 B:GLU229 4.9 94.0 1.0 N B:LEU225 5.0 87.8 1.0

A.Nguyen, J.B.Heim, G.Cordara, M.C.Chan, H.Johannesen, C.Charlesworth, M.Li, C.M.Azumaya, B.Madden, U.Krengel, A.Meves, M.G.Campbell. Structural and Functional Characterization of Integrin Alpha 5-Targeting Antibodies For Anti-Angiogenic Therapy. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 39829743
DOI: 10.1101/2025.01.08.631572