Calcium in PDB 9ckv: Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin

The structure of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin (pdb code 9ckv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin, PDB code: 9ckv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin


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 ALPHA5BETA1 Integrin in Complex with Neonectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:111.9 occ:1.00 OD1 A:ASP301 2.3 109.6 1.0 OD1 A:ASN295 2.3 110.3 1.0 OD1 A:ASP297 2.3 113.9 1.0 O A:LEU299 2.4 112.7 1.0 OD2 A:ASP301 2.4 109.6 1.0 OD2 A:ASP297 2.4 113.9 1.0 CG A:ASP297 2.7 113.9 1.0 OD1 A:ASP293 2.7 110.8 1.0 CG A:ASP301 2.7 109.6 1.0 HD21 A:ASN295 3.2 110.3 1.0 CG A:ASN295 3.3 110.3 1.0 H A:LEU299 3.4 112.7 1.0 C A:LEU299 3.5 112.7 1.0 HA A:ASP293 3.5 110.8 1.0 HB2 A:LEU299 3.5 112.7 1.0 H A:ASP297 3.6 113.9 1.0 ND2 A:ASN295 3.6 110.3 1.0 CG A:ASP293 3.7 110.8 1.0 H A:ASN295 3.8 110.3 1.0 H A:GLN329 3.9 111.2 1.0 N A:LEU299 4.1 112.7 1.0 CB A:ASP297 4.1 113.9 1.0 CB A:ASP301 4.2 109.6 1.0 CA A:LEU299 4.2 112.7 1.0 HB3 A:GLN329 4.3 111.2 1.0 CB A:LEU299 4.3 112.7 1.0 CA A:ASP293 4.3 110.8 1.0 N A:ASP297 4.4 113.9 1.0 HB3 A:ASP297 4.4 113.9 1.0 H A:VAL294 4.4 110.8 1.0 OD2 A:ASP293 4.5 110.8 1.0 C A:ASP300 4.5 112.5 1.0 HD22 A:ASN295 4.5 110.3 1.0 HD22 A:LEU328 4.5 107.8 1.0 CB A:ASP293 4.5 110.8 1.0 O A:GLN329 4.5 111.2 1.0 H A:GLY298 4.6 113.9 1.0 H A:GLY296 4.6 111.5 1.0 HB2 A:ASP301 4.6 109.6 1.0 N A:ASP300 4.6 112.5 1.0 N A:ASN295 4.6 110.3 1.0 N A:ASP301 4.6 109.6 1.0 HA A:ASP300 4.6 112.5 1.0 HG22 A:VAL294 4.6 110.8 1.0 HB3 A:ASP301 4.6 109.6 1.0 O A:ASP300 4.7 112.5 1.0 HB2 A:ASP293 4.7 110.8 1.0 CB A:ASN295 4.7 110.3 1.0 N A:GLN329 4.7 111.2 1.0 HB2 A:ASP297 4.7 113.9 1.0 HB3 A:LEU328 4.7 107.8 1.0 N A:VAL294 4.7 110.8 1.0 CA A:ASP297 4.8 113.9 1.0 C A:ASP293 4.8 110.8 1.0 HA A:LEU328 4.8 107.8 1.0 CA A:ASP300 4.8 112.5 1.0 H A:ASP301 4.8 109.6 1.0 CA A:ASP301 4.9 109.6 1.0 N A:GLY296 4.9 111.5 1.0 N A:GLY298 4.9 113.9 1.0 HB3 A:LEU299 4.9 112.7 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin


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 ALPHA5BETA1 Integrin in Complex with Neonectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1202 b:119.6 occ:1.00 HB A:THR245 2.2 128.0 1.0 OG A:SER241 2.3 119.0 1.0 O A:THR245 2.4 128.0 1.0 OD1 A:ASP247 2.4 115.6 1.0 HG A:SER241 2.5 119.0 1.0 CB A:THR245 3.1 128.0 1.0 C A:THR245 3.1 128.0 1.0 H A:THR245 3.4 128.0 1.0 CA A:THR245 3.5 128.0 1.0 CG A:ASP247 3.5 115.6 1.0 CB A:SER241 3.6 119.0 1.0 N A:THR245 3.7 128.0 1.0 H A:GLY267 3.7 120.4 1.0 OD2 A:ASP247 3.8 115.6 1.0 HB3 A:SER241 3.8 119.0 1.0 HB2 A:SER241 3.9 119.0 1.0 HG21 A:THR245 3.9 128.0 1.0 OG1 A:THR245 4.0 128.0 1.0 O A:ASP243 4.0 130.1 1.0 CG2 A:THR245 4.0 128.0 1.0 CB A:ASP243 4.1 130.1 1.0 HG1 A:THR245 4.1 128.0 1.0 HA3 A:GLY267 4.2 120.4 1.0 OD1 A:ASN266 4.2 120.5 1.0 H A:SER241 4.3 119.0 1.0 N A:GLU246 4.3 122.6 1.0 HG22 A:THR245 4.3 128.0 1.0 C A:ASP243 4.4 130.1 1.0 H A:ASP243 4.4 130.1 1.0 HA A:THR245 4.4 128.0 1.0 O A:GLU246 4.4 122.6 1.0 C A:GLU246 4.5 122.6 1.0 N A:GLY267 4.5 120.4 1.0 CA A:ASP243 4.7 130.1 1.0 C A:ASP244 4.7 135.9 1.0 CA A:SER241 4.8 119.0 1.0 N A:ASP247 4.8 115.6 1.0 N A:ASP243 4.8 130.1 1.0 CA A:GLY267 4.8 120.4 1.0 HA A:ASP247 4.8 115.6 1.0 CB A:ASP247 4.8 115.6 1.0 CA A:GLU246 4.8 122.6 1.0 HA A:GLU246 4.9 122.6 1.0 HG23 A:THR245 4.9 128.0 1.0 N A:SER241 4.9 119.0 1.0 H1 F:NAG1 4.9 129.0 1.0 H A:GLU246 4.9 122.6 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin


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 ALPHA5BETA1 Integrin in Complex with Neonectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1203 b:128.5 occ:1.00 O A:TYR366 2.3 115.2 1.0 OD2 A:ASP362 2.3 120.5 1.0 OD1 A:ASP362 2.4 120.5 1.0 OD1 A:ASP364 2.4 122.0 1.0 OD1 A:ASP368 2.4 113.9 1.0 HB2 A:TYR366 2.7 115.2 1.0 CG A:ASP362 2.7 120.5 1.0 CG A:ASP364 3.2 122.0 1.0 OD2 A:ASP364 3.2 122.0 1.0 C A:TYR366 3.2 115.2 1.0 H A:GLY389 3.3 114.1 1.0 CG A:ASP368 3.4 113.9 1.0 H A:TYR366 3.5 115.2 1.0 CB A:TYR366 3.5 115.2 1.0 OD2 A:ASP368 3.7 113.9 1.0 CA A:TYR366 3.8 115.2 1.0 HB3 A:TYR366 3.8 115.2 1.0 OD1 A:ASP360 3.9 120.6 1.0 N A:GLY389 4.0 114.1 1.0 N A:TYR366 4.0 115.2 1.0 H A:ASP364 4.2 122.0 1.0 HA3 A:GLY389 4.2 114.1 1.0 O A:ASN367 4.2 113.5 1.0 O A:GLY389 4.2 114.1 1.0 CB A:ASP362 4.2 120.5 1.0 N A:ASN367 4.3 113.5 1.0 H A:ASP362 4.3 120.5 1.0 C A:ASN367 4.3 113.5 1.0 HD1 A:TYR366 4.4 115.2 1.0 HB2 A:PRO388 4.4 111.8 1.0 CA A:GLY389 4.4 114.1 1.0 C A:GLY389 4.5 114.1 1.0 HA A:ASP360 4.5 120.6 1.0 HA A:ASN367 4.5 113.5 1.0 HA A:PRO388 4.6 111.8 1.0 HB3 A:ASP362 4.6 120.5 1.0 HB2 A:ASP362 4.6 120.5 1.0 CA A:ASN367 4.6 113.5 1.0 CB A:ASP364 4.6 122.0 1.0 N A:ASP368 4.7 113.9 1.0 HA A:TYR366 4.7 115.2 1.0 CG A:TYR366 4.7 115.2 1.0 CB A:ASP368 4.8 113.9 1.0 N A:ASP364 4.8 122.0 1.0 HA A:ASP368 4.9 113.9 1.0 H A:GLN363 4.9 121.8 1.0 CG A:ASP360 4.9 120.6 1.0 N A:ASP362 4.9 120.5 1.0 CD1 A:TYR366 4.9 115.2 1.0 C A:PRO388 5.0 111.8 1.0 HB3 A:PRO388 5.0 111.8 1.0 CB A:PRO388 5.0 111.8 1.0 H A:ASN367 5.0 113.5 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin


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 ALPHA5BETA1 Integrin in Complex with Neonectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1204 b:126.6 occ:1.00 OD1 A:ASP426 2.4 121.2 1.0 O A:TYR430 2.4 119.3 1.0 OD1 A:ASP432 2.4 115.5 1.0 OD2 A:ASP426 2.4 121.2 1.0 OD1 A:ASN428 2.4 120.7 1.0 CG A:ASP426 2.7 121.2 1.0 HB2 A:TYR430 2.8 119.3 1.0 H A:TYR430 3.1 119.3 1.0 C A:TYR430 3.2 119.3 1.0 CG A:ASP432 3.3 115.5 1.0 H A:GLY448 3.3 113.5 1.0 OD2 A:ASP432 3.4 115.5 1.0 CG A:ASN428 3.5 120.7 1.0 OD1 A:ASP424 3.5 120.2 1.0 CB A:TYR430 3.5 119.3 1.0 CA A:TYR430 3.7 119.3 1.0 N A:TYR430 3.7 119.3 1.0 O A:PRO431 3.8 117.3 1.0 HB3 A:TYR430 3.8 119.3 1.0 O A:GLY448 3.8 113.5 1.0 HD22 A:ASN428 3.8 120.7 1.0 H A:ASN428 4.1 120.7 1.0 N A:GLY448 4.1 113.5 1.0 ND2 A:ASN428 4.1 120.7 1.0 H A:ASP426 4.1 121.2 1.0 C A:PRO431 4.1 117.3 1.0 N A:PRO431 4.2 117.3 1.0 HA3 A:GLY448 4.2 113.5 1.0 CB A:ASP426 4.2 121.2 1.0 HA A:ASP424 4.4 120.2 1.0 HB3 A:ASP426 4.5 121.2 1.0 CA A:GLY448 4.5 113.5 1.0 CA A:PRO431 4.5 117.3 1.0 HB3 A:ARG447 4.6 116.9 1.0 H A:GLY429 4.6 123.1 1.0 HA A:PRO431 4.6 117.3 1.0 C A:GLY448 4.6 113.5 1.0 HA A:TYR430 4.6 119.3 1.0 CB A:ASN428 4.7 120.7 1.0 HA A:ARG447 4.7 116.9 1.0 CB A:ASP432 4.7 115.5 1.0 CG A:ASP424 4.7 120.2 1.0 HB2 A:ASP426 4.7 121.2 1.0 H A:GLY427 4.7 123.3 1.0 HB3 A:ASN428 4.7 120.7 1.0 N A:ASP432 4.7 115.5 1.0 N A:ASN428 4.8 120.7 1.0 N A:ASP426 4.8 121.2 1.0 HD1 A:TYR430 4.8 119.3 1.0 CG A:TYR430 4.8 119.3 1.0 N A:GLY429 4.9 123.1 1.0 HD21 A:ASN428 4.9 120.7 1.0 HA A:ASP432 4.9 115.5 1.0 C A:GLY429 5.0 123.1 1.0

X.Wang, J.Guillem-Marti, S.Kumar, D.S.Lee, D.Cabrerizo-Aguado, R.Werther, K.A.Estrada Alamo, Y.T.Zhao, A.Nguyen, I.Kopyeva, B.Huang, J.Li, Y.Hao, X.Li, A.Brizuela-Velasco, A.N.Murray, S.Gerben, A.Roy, C.A.Deforest, T.Springer, H.Ruohola-Baker, J.A.Cooper, M.G.Campbell, J.Maria Manero, M.Ginebra, D.Baker. De Novo Design of Integrin ALPHA5BETA1 Modulating Proteins For Regenerative Medicine To Be Published.