Calcium in PDB 9b9k: Integrin Alpha-5 Beta-1 in Complex with MINT1526A Fab

The binding sites of Calcium atom in the Integrin Alpha-5 Beta-1 in Complex with MINT1526A Fab (pdb code 9b9k). 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 MINT1526A Fab, PDB code: 9b9k:
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 MINT1526A 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 MINT1526A Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:129.1 occ:1.00 HG A:SER241 2.1 118.0 1.0 OE1 A:GLU239 2.3 116.8 1.0 O A:THR245 2.3 116.2 1.0 OD1 A:ASP243 2.3 127.5 1.0 OD1 A:ASP247 2.3 113.0 1.0 OG A:SER241 2.4 118.0 1.0 OD2 A:ASP247 2.4 113.7 1.0 OE2 A:GLU239 2.5 117.1 1.0 CG A:ASP247 2.7 112.8 1.0 CD A:GLU239 2.7 116.9 1.0 H A:SER241 3.1 117.1 1.0 HG1 A:THR245 3.1 117.4 1.0 CG A:ASP243 3.1 127.5 1.0 HB3 A:SER241 3.2 117.2 1.0 H A:ASP243 3.3 127.8 1.0 C A:THR245 3.3 116.0 1.0 CB A:SER241 3.4 117.2 1.0 H A:THR245 3.5 118.0 1.0 OD2 A:ASP243 3.5 127.4 1.0 H A:PHE240 3.7 113.0 1.0 HA A:GLU239 3.7 115.3 1.0 HA A:GLU246 3.8 118.0 1.0 H A:GLY267 3.8 115.6 1.0 N A:SER241 4.0 117.1 1.0 OG1 A:THR245 4.0 117.4 1.0 H A:GLY242 4.0 129.4 1.0 OD1 A:ASN266 4.0 121.5 1.0 N A:THR245 4.1 118.0 1.0 CB A:ASP247 4.2 111.8 1.0 HB2 A:SER241 4.2 117.2 1.0 N A:ASP247 4.2 112.4 1.0 N A:ASP243 4.2 127.8 1.0 C A:GLU246 4.2 117.9 1.0 CA A:THR245 4.2 116.3 1.0 N A:GLU246 4.2 118.2 1.0 H A:ASP247 4.2 112.4 1.0 CG A:GLU239 4.3 116.0 1.0 CA A:SER241 4.3 117.3 1.0 CA A:GLU246 4.3 118.0 1.0 CB A:ASP243 4.3 127.3 1.0 O A:ASP243 4.4 128.0 1.0 C A:ASP243 4.4 127.8 1.0 CA A:ASP243 4.5 127.5 1.0 N A:PHE240 4.5 113.0 1.0 HB2 A:ASP247 4.6 111.8 1.0 CB A:THR245 4.6 116.1 1.0 CA A:ASP247 4.7 111.7 1.0 CA A:GLU239 4.7 115.3 1.0 N A:GLY242 4.7 129.4 1.0 HA3 A:GLY267 4.7 114.8 1.0 O A:GLU246 4.7 118.0 1.0 HA A:ASP247 4.7 111.7 1.0 HG3 A:GLU239 4.8 116.0 1.0 N A:GLY267 4.8 115.6 1.0 HG2 A:GLU239 4.8 116.0 1.0 HB3 A:ASP247 4.8 111.8 1.0 HB A:THR245 4.8 116.1 1.0 HB3 A:ASP243 4.8 127.3 1.0 C A:SER241 4.9 118.5 1.0 CB A:GLU239 4.9 115.0 1.0 HB2 A:GLU239 4.9 115.0 1.0

Calcium binding site 2 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with MINT1526A 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 MINT1526A Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:142.9 occ:1.00 OD1 A:ASP297 2.3 131.7 1.0 OD2 A:ASP301 2.3 113.8 1.0 OD1 A:ASN295 2.4 129.3 1.0 OD1 A:ASP293 2.4 125.6 1.0 OD1 A:ASP301 2.4 114.2 1.0 O A:LEU299 2.4 122.4 1.0 OD2 A:ASP297 2.7 131.5 1.0 CG A:ASP301 2.7 113.4 1.0 CG A:ASP297 2.7 131.4 1.0 H A:ASP297 3.2 130.7 1.0 HA A:ASP293 3.2 124.2 1.0 H A:ASN295 3.3 129.0 1.0 CG A:ASP293 3.3 125.4 1.0 H A:LEU299 3.3 122.7 1.0 CG A:ASN295 3.4 129.3 1.0 HD22 A:ASN295 3.5 129.9 1.0 HB2 A:LEU299 3.5 122.7 1.0 C A:LEU299 3.5 122.3 1.0 H A:GLY296 3.8 123.9 1.0 H A:VAL294 3.9 122.7 1.0 ND2 A:ASN295 3.9 129.9 1.0 HD22 A:LEU328 3.9 112.5 1.0 H A:GLN329 3.9 123.9 1.0 CA A:ASP293 4.0 124.2 1.0 CB A:ASP297 4.0 131.0 1.0 N A:ASP297 4.1 130.7 1.0 N A:LEU299 4.1 122.7 1.0 CB A:ASP293 4.1 124.5 1.0 OD2 A:ASP293 4.1 125.8 1.0 CB A:ASP301 4.2 112.2 1.0 CA A:LEU299 4.2 122.4 1.0 H A:GLY298 4.2 125.0 1.0 HB2 A:ASP293 4.2 124.5 1.0 N A:ASN295 4.3 129.0 1.0 N A:VAL294 4.3 122.7 1.0 C A:ASP293 4.3 124.2 1.0 H A:ASP301 4.3 112.8 1.0 HB3 A:ASP297 4.3 131.0 1.0 N A:ASP301 4.4 112.8 1.0 CB A:LEU299 4.4 122.7 1.0 N A:GLY296 4.5 123.9 1.0 CA A:ASP297 4.5 130.9 1.0 O A:GLN329 4.5 126.6 1.0 HB3 A:GLN329 4.6 125.5 1.0 CB A:ASN295 4.6 128.8 1.0 HB3 A:LEU328 4.6 112.6 1.0 C A:ASP300 4.6 118.4 1.0 N A:ASP300 4.6 119.6 1.0 HB2 A:ASP301 4.6 112.2 1.0 HA A:ASP300 4.7 118.9 1.0 N A:GLY298 4.7 125.0 1.0 CA A:ASN295 4.8 128.6 1.0 HA A:LEU328 4.8 112.2 1.0 CA A:ASP301 4.8 112.0 1.0 HB2 A:ASP297 4.9 131.0 1.0 HB3 A:ASP301 4.9 112.2 1.0 HD21 A:ASN295 4.9 129.9 1.0 N A:GLN329 4.9 123.9 1.0 C A:ASN295 4.9 128.2 1.0 C A:ASP297 4.9 131.1 1.0 CA A:ASP300 4.9 118.9 1.0 HA A:ASP301 4.9 112.0 1.0 HB3 A:ASN295 4.9 128.8 1.0 CD2 A:LEU328 4.9 112.5 1.0 HG22 A:VAL294 5.0 122.8 1.0 HB3 A:LEU299 5.0 122.7 1.0

Calcium binding site 3 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with MINT1526A 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 MINT1526A Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:117.1 occ:1.00 OD1 A:ASP362 2.3 117.2 1.0 OD1 A:ASP360 2.3 122.2 1.0 OD1 A:ASP364 2.3 121.1 1.0 OD2 A:ASP368 2.4 110.8 1.0 O A:TYR366 2.4 115.5 1.0 OD1 A:ASP368 2.5 111.2 1.0 OD2 A:ASP364 2.6 121.7 1.0 CG A:ASP364 2.6 121.3 1.0 CG A:ASP368 2.9 110.5 1.0 H A:ASP364 3.0 120.3 1.0 H A:ASP362 3.1 116.2 1.0 HA A:ASP360 3.2 121.8 1.0 CG A:ASP360 3.4 122.6 1.0 H A:TYR366 3.4 114.8 1.0 H A:LEU361 3.4 106.2 1.0 CG A:ASP362 3.5 117.1 1.0 C A:TYR366 3.6 115.3 1.0 H A:GLY389 3.8 118.9 1.0 HB2 A:TYR366 3.8 115.1 1.0 CB A:ASP364 3.9 120.7 1.0 CA A:ASP360 4.0 121.8 1.0 N A:LEU361 4.0 106.2 1.0 N A:ASP364 4.0 120.3 1.0 OD2 A:ASP362 4.0 117.9 1.0 HB3 A:ASP364 4.0 120.7 1.0 N A:ASP362 4.1 116.2 1.0 H A:ASP368 4.1 109.3 1.0 C A:ASP360 4.1 121.2 1.0 N A:TYR366 4.2 114.8 1.0 OD2 A:ASP360 4.2 123.2 1.0 H A:GLN363 4.2 114.4 1.0 CB A:ASP360 4.2 122.4 1.0 H A:GLY365 4.2 114.6 1.0 N A:ASP368 4.3 109.3 1.0 CA A:TYR366 4.3 115.0 1.0 CB A:ASP368 4.3 108.9 1.0 HA A:ASN367 4.4 113.0 1.0 CA A:ASP364 4.4 120.4 1.0 HB3 A:LEU361 4.4 105.4 1.0 N A:GLN363 4.5 114.4 1.0 CB A:TYR366 4.6 115.1 1.0 HB2 A:ASP360 4.6 122.4 1.0 N A:ASN367 4.6 113.5 1.0 C A:ASN367 4.6 112.7 1.0 CB A:ASP362 4.6 116.2 1.0 HA3 A:GLY389 4.6 119.7 1.0 N A:GLY389 4.7 118.9 1.0 CA A:ASP362 4.7 116.3 1.0 HB2 A:ASP364 4.7 120.7 1.0 HD2 A:TYR366 4.8 115.6 1.0 C A:ASP362 4.8 116.7 1.0 HB2 A:ASP368 4.8 108.9 1.0 CA A:ASN367 4.8 113.0 1.0 N A:GLY365 4.8 114.6 1.0 CA A:ASP368 4.8 108.6 1.0 HA A:PRO388 4.9 99.0 1.0 O A:ASP360 4.9 121.7 1.0 CA A:LEU361 4.9 106.0 1.0 C A:ASP364 5.0 120.5 1.0 HB3 A:ASP368 5.0 108.9 1.0 HA A:ASP368 5.0 108.6 1.0

Calcium binding site 4 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with MINT1526A 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 MINT1526A Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:112.9 occ:1.00 OD1 A:ASP432 2.3 91.4 1.0 OD1 A:ASN428 2.3 107.6 1.0 OD1 A:ASP426 2.3 112.5 1.0 O A:TYR430 2.4 96.8 1.0 OD1 A:ASP424 2.5 109.5 1.0 OD2 A:ASP432 2.5 91.4 1.0 CG A:ASP432 2.8 90.2 1.0 CG A:ASN428 3.3 107.8 1.0 H A:ASN428 3.4 109.2 1.0 CG A:ASP426 3.4 111.9 1.0 H A:TYR430 3.4 99.0 1.0 H A:ASP426 3.4 110.5 1.0 CG A:ASP424 3.5 110.1 1.0 C A:TYR430 3.6 96.2 1.0 H A:GLY448 3.6 89.3 1.0 H A:LEU425 3.7 103.6 1.0 HD22 A:ASN428 3.7 106.7 1.0 HA A:ASP424 3.8 109.2 1.0 HB2 A:TYR430 3.8 97.0 1.0 H A:GLY427 3.8 118.9 1.0 OD2 A:ASP426 3.8 111.3 1.0 ND2 A:ASN428 3.9 106.7 1.0 OD2 A:ASP424 4.1 110.2 1.0 HB3 A:ARG447 4.2 91.1 1.0 N A:TYR430 4.2 99.0 1.0 N A:ASN428 4.2 109.2 1.0 CB A:ASP432 4.3 88.1 1.0 CB A:ASN428 4.3 108.6 1.0 N A:ASP426 4.3 110.5 1.0 CA A:TYR430 4.3 97.4 1.0 O A:GLY448 4.3 90.4 1.0 C A:PRO431 4.4 89.7 1.0 HB3 A:ASN428 4.4 108.6 1.0 CB A:ASP424 4.4 109.9 1.0 N A:GLY448 4.4 89.3 1.0 O A:PRO431 4.5 90.8 1.0 N A:LEU425 4.5 103.6 1.0 CA A:ASP424 4.5 109.2 1.0 H A:GLY429 4.5 107.0 1.0 N A:GLY427 4.5 118.9 1.0 CB A:TYR430 4.5 97.0 1.0 HA A:ARG447 4.5 90.8 1.0 HG2 A:ARG447 4.6 91.7 1.0 N A:ASP432 4.6 89.1 1.0 N A:PRO431 4.6 89.1 1.0 CB A:ASP426 4.6 112.2 1.0 HA A:PRO431 4.6 89.3 1.0 HB2 A:ASP424 4.7 109.9 1.0 CA A:ASN428 4.7 108.5 1.0 HB2 A:ASP432 4.7 88.1 1.0 HA3 A:GLY448 4.8 89.1 1.0 CA A:PRO431 4.8 89.3 1.0 C A:ASP424 4.8 109.5 1.0 HE A:ARG447 4.8 92.7 1.0 CA A:ASP426 4.8 111.8 1.0 HD21 A:ASN428 4.8 106.7 1.0 HB3 A:TYR430 4.9 97.0 1.0 N A:GLY429 4.9 107.0 1.0 HB3 A:ASP432 4.9 88.1 1.0 CA A:ASP432 4.9 87.9 1.0 H A:ASP432 5.0 89.1 1.0 HA A:ASP432 5.0 87.9 1.0 C A:ASN428 5.0 108.0 1.0

Calcium binding site 5 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with MINT1526A 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 MINT1526A Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:127.4 occ:1.00 OD1 B:ASP137 2.3 133.6 1.0 OD1 B:ASP138 2.4 133.1 1.0 O B:SER134 2.5 123.2 1.0 O B:ALA342 2.7 128.0 1.0 CG B:ASP137 3.3 127.5 1.0 HA B:MET135 3.4 111.7 1.0 OD2 B:ASP137 3.5 122.7 1.0 H B:ASP138 3.5 124.3 1.0 CG B:ASP138 3.5 126.2 1.0 C B:SER134 3.7 121.3 1.0 C B:ALA342 3.8 123.1 1.0 HA B:ASN343 3.9 115.5 1.0 H B:ASP137 4.1 121.7 1.0 OD2 B:ASP138 4.2 126.8 1.0 CA B:MET135 4.2 111.7 1.0 HB2 B:ALA342 4.3 119.3 1.0 N B:ASP138 4.4 124.3 1.0 N B:MET135 4.4 112.2 1.0 HA B:ALA342 4.5 121.9 1.0 HB2 B:SER134 4.5 119.0 1.0 OD2 B:ASP259 4.6 124.7 1.0 CA B:ALA342 4.7 121.9 1.0 CB B:ASP137 4.7 121.1 1.0 CB B:ASP138 4.7 120.8 1.0 N B:ASN343 4.7 120.0 1.0 C B:MET135 4.7 115.7 1.0 CA B:ASN343 4.7 115.5 1.0 HA B:SER134 4.8 122.1 1.0 HB2 B:ASP138 4.8 120.8 1.0 CA B:SER134 4.8 122.1 1.0 N B:ASP137 4.8 121.7 1.0 H B:LYS136 4.8 112.8 1.0 CB B:ALA342 5.0 119.3 1.0 HB3 B:ASN343 5.0 117.3 1.0 N B:LYS136 5.0 112.8 1.0

Calcium binding site 6 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with MINT1526A 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 MINT1526A Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:125.2 occ:1.00 OD1 B:ASN224 2.3 116.7 1.0 OE1 B:GLU229 2.3 125.7 1.0 OE2 B:GLU169 2.3 102.8 1.0 O B:PRO228 2.3 107.6 1.0 OD1 B:ASP226 2.3 124.6 1.0 O B:ASP226 2.4 109.3 1.0 HA B:GLU229 2.7 114.2 1.0 HE2 B:HIS263 3.0 103.6 1.0 C B:PRO228 3.3 103.1 1.0 C B:ASP226 3.4 110.1 1.0 CD B:GLU169 3.4 103.2 1.0 CD B:GLU229 3.4 123.1 1.0 HG2 B:GLU169 3.5 99.5 1.0 CG B:ASN224 3.5 113.4 1.0 CG B:ASP226 3.5 116.3 1.0 CA B:GLU229 3.7 114.2 1.0 HB2 B:GLU169 3.8 97.6 1.0 NE2 B:HIS263 3.8 103.6 1.0 H B:ASP226 3.8 108.6 1.0 HD2 B:HIS263 3.9 95.5 1.0 CG B:GLU169 3.9 99.5 1.0 N B:GLU229 3.9 111.0 1.0 CA B:ASP226 4.0 109.7 1.0 N B:ASP226 4.1 108.6 1.0 HD22 B:ASN224 4.1 106.1 1.0 O B:SER227 4.1 119.5 1.0 HB3 B:ASN224 4.1 106.7 1.0 C B:SER227 4.2 113.8 1.0 OE2 B:GLU229 4.2 122.0 1.0 CD2 B:HIS263 4.2 95.5 1.0 ND2 B:ASN224 4.3 106.1 1.0 HB3 B:TYR175 4.3 94.0 1.0 CB B:ASP226 4.3 110.8 1.0 N B:PRO228 4.3 103.9 1.0 N B:SER227 4.3 106.8 1.0 CB B:GLU229 4.4 109.5 1.0 CG B:GLU229 4.4 117.4 1.0 CB B:ASN224 4.4 106.7 1.0 OD2 B:ASP226 4.4 110.0 1.0 H B:GLY230 4.4 110.5 1.0 CA B:PRO228 4.5 100.9 1.0 HB3 B:GLU229 4.5 109.5 1.0 CB B:GLU169 4.5 97.6 1.0 OE1 B:GLU169 4.5 103.6 1.0 HG2 B:PRO228 4.6 103.0 1.0 C B:GLU229 4.7 117.6 1.0 HG2 B:GLU229 4.7 117.4 1.0 CA B:SER227 4.7 108.9 1.0 HD2 B:PRO228 4.7 105.6 1.0 HA B:SER227 4.8 108.9 1.0 O B:TYR175 4.8 107.0 1.0 H B:LEU225 4.8 102.6 1.0 HB2 B:ASP226 4.8 110.8 1.0 N B:GLY230 4.9 110.5 1.0 HG3 B:GLU169 4.9 99.5 1.0 H B:GLU229 4.9 111.0 1.0 C B:LEU225 4.9 107.8 1.0 HB2 B:ASN224 5.0 106.7 1.0 CD B:PRO228 5.0 105.6 1.0

Calcium binding site 7 out of 7 in the Integrin Alpha-5 Beta-1 in Complex with MINT1526A 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 MINT1526A Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:50.0 occ:1.00 OG B:SER134 3.1 119.2 1.0 OD1 B:ASP259 3.2 124.9 1.0 OE2 B:GLU229 3.2 122.0 1.0 HB1 B:ALA260 3.3 108.3 1.0 HG B:SER134 3.4 119.2 1.0 HB2 B:SER132 3.5 101.6 1.0 HB3 B:SER132 3.8 101.6 1.0 CB B:SER132 4.1 101.6 1.0 CG B:ASP259 4.2 126.0 1.0 HB3 B:SER134 4.2 119.0 1.0 CB B:SER134 4.3 119.0 1.0 CD B:GLU229 4.3 123.1 1.0 CB B:ALA260 4.3 108.3 1.0 H B:SER134 4.3 119.3 1.0 HG3 B:GLU229 4.4 117.4 1.0 HB2 B:ALA260 4.5 108.3 1.0 OD2 B:ASP259 4.5 124.7 1.0 OG B:SER132 4.6 110.2 1.0 O B:SER227 4.6 119.5 1.0 HG2 B:GLU229 4.7 117.4 1.0 CG B:GLU229 4.8 117.4 1.0 OD2 B:ASP130 4.8 117.1 1.0 HB3 B:ALA260 4.8 108.3 1.0 HG B:SER132 4.8 110.2 1.0 HB2 B:SER134 4.9 119.0 1.0 O B:ASP259 4.9 125.6 1.0 HA B:SER227 4.9 108.9 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