Calcium in PDB 7nxd: Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation

The structure of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation (pdb code 7nxd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation, PDB code: 7nxd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:112.0 occ:1.00 OD2 A:ASP243 1.9 118.0 1.0 OG A:SER241 1.9 110.8 1.0 O A:THR245 2.4 123.1 1.0 OE2 A:GLU239 2.5 114.5 1.0 OD1 A:ASP247 2.6 130.2 1.0 OE1 A:GLU239 2.8 114.5 1.0 CD A:GLU239 3.0 114.5 1.0 CG A:ASP243 3.0 118.0 1.0 CB A:SER241 3.2 110.8 1.0 OG1 A:THR245 3.4 123.1 1.0 C A:THR245 3.4 123.1 1.0 CG A:ASP247 3.6 130.2 1.0 OD1 A:ASP243 3.6 118.0 1.0 O A:ASP243 3.8 118.0 1.0 OD2 A:ASP247 4.0 130.2 1.0 N A:ASP243 4.0 118.0 1.0 N A:ASP247 4.2 130.2 1.0 CB A:ASP243 4.2 118.0 1.0 CA A:SER241 4.3 110.8 1.0 N A:GLU246 4.3 125.3 1.0 C A:ASP243 4.3 118.0 1.0 CA A:THR245 4.3 123.1 1.0 CA A:GLU246 4.4 125.3 1.0 CA A:ASP243 4.4 118.0 1.0 N A:GLY242 4.4 113.8 1.0 CB A:THR245 4.4 123.1 1.0 N A:SER241 4.4 110.8 1.0 C A:GLU246 4.5 125.3 1.0 CG A:GLU239 4.5 114.5 1.0 N A:THR245 4.5 123.1 1.0 C A:SER241 4.7 110.8 1.0 CB A:ASP247 4.8 130.2 1.0 CA A:ASP247 4.9 130.2 1.0

Calcium binding site 2 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:121.5 occ:1.00 OD1 A:ASN295 2.3 124.3 1.0 OD1 A:ASP301 2.3 107.2 1.0 O A:LEU299 2.3 116.0 1.0 OD1 A:ASP297 2.4 117.2 1.0 OD1 A:ASP293 2.5 112.1 1.0 CG A:ASP301 2.9 107.2 1.0 OD2 A:ASP301 2.9 107.2 1.0 CG A:ASP297 3.1 117.2 1.0 OD2 A:ASP297 3.2 117.2 1.0 CG A:ASP293 3.3 112.1 1.0 CG A:ASN295 3.4 124.3 1.0 C A:LEU299 3.4 116.0 1.0 ND2 A:ASN295 4.0 124.3 1.0 OD2 A:ASP293 4.0 112.1 1.0 N A:LEU299 4.0 116.0 1.0 CB A:LEU299 4.0 116.0 1.0 CA A:LEU299 4.1 116.0 1.0 CB A:ASP293 4.1 112.1 1.0 CA A:ASP293 4.1 112.1 1.0 CB A:ASP301 4.3 107.2 1.0 N A:ASN295 4.3 124.3 1.0 N A:GLN329 4.3 99.3 1.0 N A:VAL294 4.4 120.7 1.0 N A:ASP301 4.5 107.2 1.0 CB A:ASP297 4.5 117.2 1.0 C A:ASP300 4.5 119.1 1.0 O A:GLN329 4.5 99.3 1.0 N A:ASP300 4.5 119.1 1.0 CA A:LEU328 4.6 108.8 1.0 N A:ASP297 4.6 117.2 1.0 C A:ASP293 4.7 112.1 1.0 CB A:ASN295 4.7 124.3 1.0 O A:ASP300 4.8 119.1 1.0 CB A:LEU328 4.8 108.8 1.0 CA A:ASP301 4.8 107.2 1.0 CA A:ASP300 4.9 119.1 1.0 CA A:ASN295 4.9 124.3 1.0 N A:GLY296 4.9 115.1 1.0 C A:LEU328 4.9 108.8 1.0 N A:GLY298 5.0 120.4 1.0 CG A:LEU328 5.0 108.8 1.0 CB A:GLN329 5.0 99.3 1.0

Calcium binding site 3 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:91.4 occ:1.00 OD1 A:ASP362 2.0 103.8 1.0 O A:TYR366 2.2 98.3 1.0 OD1 A:ASP364 2.3 103.0 1.0 OD1 A:ASP368 2.4 105.7 1.0 OD1 A:ASP360 2.5 106.3 1.0 CG A:ASP364 2.7 103.0 1.0 OD2 A:ASP364 2.7 103.0 1.0 CG A:ASP362 2.9 103.8 1.0 CG A:ASP368 3.2 105.7 1.0 OD2 A:ASP362 3.2 103.8 1.0 OD2 A:ASP368 3.3 105.7 1.0 C A:TYR366 3.4 98.3 1.0 CG A:ASP360 3.6 106.3 1.0 CB A:ASP364 4.0 103.0 1.0 N A:ASP362 4.0 103.8 1.0 CA A:TYR366 4.1 98.3 1.0 N A:GLY389 4.1 98.7 1.0 CB A:ASP362 4.2 103.8 1.0 N A:TYR366 4.2 98.3 1.0 N A:ASP364 4.2 103.0 1.0 OD2 A:ASP360 4.3 106.3 1.0 CB A:TYR366 4.3 98.3 1.0 CA A:ASP360 4.4 106.3 1.0 N A:LEU361 4.4 104.0 1.0 N A:ASN367 4.4 106.2 1.0 CA A:GLY389 4.5 98.7 1.0 N A:ASP368 4.5 105.7 1.0 C A:ASN367 4.5 106.2 1.0 CA A:ASP362 4.5 103.8 1.0 CB A:ASP360 4.5 106.3 1.0 CB A:ASP368 4.5 105.7 1.0 N A:GLN363 4.6 90.2 1.0 C A:ASP360 4.6 106.3 1.0 CA A:ASN367 4.6 106.2 1.0 CA A:ASP364 4.6 103.0 1.0 O A:GLY389 4.7 98.7 1.0 C A:ASP362 4.8 103.8 1.0 O A:ASN367 4.9 106.2 1.0 CA A:ASP368 5.0 105.7 1.0

Calcium binding site 4 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:106.8 occ:1.00 OD1 A:ASN428 1.9 100.2 1.0 OD1 A:ASP426 2.5 106.9 1.0 OD1 A:ASP424 2.6 109.2 1.0 OD1 A:ASP432 2.6 120.9 1.0 O A:TYR430 2.7 100.9 1.0 CG A:ASN428 2.9 100.2 1.0 CG A:ASP432 3.2 120.9 1.0 OD2 A:ASP432 3.2 120.9 1.0 ND2 A:ASN428 3.3 100.2 1.0 CG A:ASP426 3.5 106.9 1.0 CG A:ASP424 3.5 109.2 1.0 OD2 A:ASP426 3.8 106.9 1.0 C A:TYR430 3.9 100.9 1.0 OD2 A:ASP424 3.9 109.2 1.0 CB A:ASN428 4.2 100.2 1.0 N A:ASP426 4.4 106.9 1.0 N A:ASN428 4.5 100.2 1.0 CB A:ASP432 4.5 120.9 1.0 CA A:TYR430 4.5 100.9 1.0 N A:GLY448 4.5 121.6 1.0 N A:TYR430 4.6 100.9 1.0 CB A:TYR430 4.6 100.9 1.0 N A:ASP432 4.6 120.9 1.0 N A:LEU425 4.7 109.6 1.0 CB A:ASP424 4.7 109.2 1.0 C A:PRO431 4.7 100.4 1.0 CA A:ASP424 4.7 109.2 1.0 CB A:ASP426 4.8 106.9 1.0 CA A:ASN428 4.9 100.2 1.0 N A:PRO431 4.9 100.4 1.0 CA A:ASP432 4.9 120.9 1.0 O A:PRO431 4.9 100.4 1.0

Calcium binding site 5 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:627.0 occ:1.00 OD1 A:ASP607 2.7 538.5 1.0 O A:ILE609 2.7 641.6 1.0 OE2 A:GLU644 2.7 1000.0 1.0 CA A:GLY605 2.8 542.8 1.0 OE1 A:GLU644 2.9 1000.0 1.0 CD A:GLU644 3.0 1000.0 1.0 N A:ILE609 3.3 641.6 1.0 O A:CYS604 3.3 568.2 1.0 N A:GLY605 3.4 542.8 1.0 C A:CYS604 3.5 568.2 1.0 C A:ILE609 3.6 641.6 1.0 C A:GLY605 3.6 542.8 1.0 CA A:ILE609 3.7 641.6 1.0 CG A:ASP607 3.8 538.5 1.0 CB A:ILE609 3.8 641.6 1.0 N A:GLU606 3.9 521.5 1.0 N A:ASN608 4.2 494.7 1.0 CG A:GLU644 4.3 1000.0 1.0 N A:ASP607 4.3 538.5 1.0 OD2 A:ASP607 4.3 538.5 1.0 C A:ASN608 4.4 494.7 1.0 O A:GLY605 4.5 542.8 1.0 CA A:ASN608 4.6 494.7 1.0 C A:ASP607 4.7 538.5 1.0 CA A:CYS604 4.8 568.2 1.0 CG1 A:ILE609 4.8 641.6 1.0 CG2 A:ILE609 4.8 641.6 1.0 CB A:CYS604 4.8 568.2 1.0 N A:CYS610 4.9 864.9 1.0 CA A:ASP607 4.9 538.5 1.0 CB A:ASP607 5.0 538.5 1.0

Calcium binding site 6 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:106.1 occ:1.00 O B:SER134 1.8 118.5 1.0 OD1 B:ASP137 2.7 105.4 1.0 O B:ALA342 2.9 93.2 1.0 C B:SER134 2.9 118.5 1.0 OD1 B:ASP138 3.1 104.3 1.0 OD2 B:ASP137 3.1 105.4 1.0 CG B:ASP137 3.2 105.4 1.0 CA B:MET135 3.4 115.3 1.0 N B:MET135 3.5 115.3 1.0 C B:ALA342 4.0 93.2 1.0 CA B:SER134 4.1 118.5 1.0 C B:MET135 4.1 115.3 1.0 CG B:ASP138 4.2 104.3 1.0 SD B:MET135 4.4 115.3 1.0 CB B:SER134 4.4 118.5 1.0 N B:LYS136 4.6 107.0 1.0 CB B:MET135 4.7 115.3 1.0 CA B:ALA342 4.7 93.2 1.0 OD2 B:ASP138 4.7 104.3 1.0 CB B:ASP137 4.7 105.4 1.0 O B:MET135 4.7 115.3 1.0 CG B:MET135 4.8 115.3 1.0 OG B:SER134 4.9 118.5 1.0 OD2 B:ASP259 5.0 95.8 1.0 N B:ASP138 5.0 104.3 1.0

Calcium binding site 7 out of 7 in the Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of Human Integrin ALPHA5BETA1 in the Half-Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:97.4 occ:1.00 OD1 B:ASP226 2.0 89.1 1.0 O B:PRO228 2.1 89.5 1.0 OE2 B:GLU229 2.1 90.0 1.0 CG B:ASP226 2.3 89.1 1.0 OD1 B:ASN224 2.3 99.0 1.0 OD2 B:ASP226 2.6 89.1 1.0 O B:ASP226 3.1 89.1 1.0 CG B:ASN224 3.1 99.0 1.0 CD B:GLU229 3.2 90.0 1.0 C B:PRO228 3.2 89.5 1.0 CB B:ASP226 3.3 89.1 1.0 OE1 B:GLU169 3.3 95.2 1.0 C B:ASP226 3.5 89.1 1.0 CA B:GLU229 3.6 90.0 1.0 NE2 B:HIS263 3.7 94.7 1.0 CB B:ASN224 3.7 99.0 1.0 CA B:ASP226 3.7 89.1 1.0 OE1 B:GLU229 3.8 90.0 1.0 N B:GLU229 3.8 90.0 1.0 ND2 B:ASN224 4.0 99.0 1.0 N B:ASP226 4.0 89.1 1.0 CG B:GLU169 4.1 95.2 1.0 CD B:GLU169 4.1 95.2 1.0 N B:PRO228 4.2 89.5 1.0 CG B:GLU229 4.3 90.0 1.0 CA B:PRO228 4.3 89.5 1.0 CD2 B:HIS263 4.3 94.7 1.0 CB B:GLU169 4.4 95.2 1.0 CB B:GLU229 4.4 90.0 1.0 C B:SER227 4.4 73.9 1.0 N B:SER227 4.4 73.9 1.0 C B:GLU229 4.6 90.0 1.0 O B:SER227 4.6 73.9 1.0 CD2 B:TYR175 4.8 93.5 1.0 CD B:PRO228 4.8 89.5 1.0 CE1 B:HIS263 4.9 94.7 1.0 N B:GLY230 4.9 94.0 1.0 CA B:SER227 5.0 73.9 1.0 CA B:ASN224 5.0 99.0 1.0

S.Schumacher, D.Dedden, R.V.Nunez, K.Matoba, J.Takagi, C.Biertumpfel, N.Mizuno. Structural Insights Into Integrin Alpha 5 Beta 1 Opening By Fibronectin Ligand. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33962943
DOI: 10.1126/SCIADV.ABE9716