Calcium in PDB 7ceb: Crystal Structure of ALPHA6BETA1 Integrin Headpiece

The structure of Crystal Structure of ALPHA6BETA1 Integrin Headpiece, PDB code: 7ceb was solved by T.Arimori, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.57 / 2.89
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.52, 251.31, 63.25, 90, 90, 90
R / Rfree (%)	20.7 / 24.9

The structure of Crystal Structure of ALPHA6BETA1 Integrin Headpiece also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of ALPHA6BETA1 Integrin Headpiece (pdb code 7ceb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of ALPHA6BETA1 Integrin Headpiece, PDB code: 7ceb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of ALPHA6BETA1 Integrin Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of ALPHA6BETA1 Integrin Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:78.2 occ:1.00 OD2 A:ASP309 2.3 57.8 1.0 OD1 A:ASP301 2.4 56.0 1.0 O A:TRP307 2.4 63.0 1.0 OD1 A:ASN303 2.4 73.7 1.0 OD1 A:ASP305 2.5 71.6 1.0 O A:HOH1101 2.6 50.5 1.0 OD1 A:ASP309 2.7 67.3 1.0 CG A:ASP309 2.8 59.3 1.0 CG A:ASP305 3.3 59.7 1.0 CG A:ASN303 3.4 68.1 1.0 OD2 A:ASP305 3.6 64.3 1.0 C A:TRP307 3.6 67.2 1.0 CG A:ASP301 3.6 62.0 1.0 ND2 A:ASN303 3.7 75.8 1.0 N A:ASP309 4.1 53.2 1.0 CB A:ASP309 4.2 61.2 1.0 CA A:ASP301 4.3 55.9 1.0 N A:ASN303 4.4 65.5 1.0 N A:LEU302 4.4 54.8 1.0 OD2 A:ASP301 4.4 62.9 1.0 CA A:TRP307 4.5 63.9 1.0 N A:TRP307 4.5 56.1 1.0 C A:GLN308 4.5 56.3 1.0 N A:ASP305 4.5 63.5 1.0 CB A:ASN333 4.5 50.6 1.0 CB A:ASP305 4.5 49.4 1.0 C A:ASP301 4.5 56.3 1.0 CB A:ASP301 4.5 51.2 1.0 CB A:TRP307 4.6 65.8 1.0 N A:GLN308 4.6 69.7 1.0 CA A:ASP309 4.6 60.7 1.0 N A:ASN333 4.7 64.0 1.0 CB A:ASN303 4.7 58.0 1.0 CA A:GLN308 4.7 62.9 1.0 SD A:MET332 4.7 66.3 1.0 N A:LYS304 4.7 60.6 1.0 CA A:ASN303 4.9 57.5 1.0 CA A:ASP305 5.0 54.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of ALPHA6BETA1 Integrin Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of ALPHA6BETA1 Integrin Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:78.4 occ:1.00 OD1 A:ASP371 2.4 88.2 1.0 OD1 A:ASP367 2.4 82.1 1.0 OD1 A:ASP363 2.5 70.7 1.0 OD1 A:ASN365 2.6 85.0 1.0 O A:TYR369 2.6 63.2 1.0 OD2 A:ASP371 2.7 81.9 1.0 CG A:ASP371 2.9 77.0 1.0 CG A:ASP367 3.1 76.7 1.0 OD2 A:ASP367 3.1 78.6 1.0 CG A:ASP363 3.6 72.2 1.0 CG A:ASN365 3.6 79.0 1.0 C A:TYR369 3.7 60.1 1.0 ND2 A:ASN365 4.1 79.1 1.0 CD2 A:HIS388 4.1 76.9 1.0 N A:TYR369 4.3 61.3 1.0 OD2 A:ASP363 4.3 72.0 1.0 CA A:ASP363 4.4 65.5 1.0 CA A:TYR369 4.4 59.4 1.0 CB A:ASP371 4.4 63.8 1.0 N A:GLY389 4.4 61.0 1.0 CB A:TYR369 4.4 58.9 1.0 CB A:ASP363 4.5 64.6 1.0 O A:GLY389 4.5 84.8 1.0 CB A:ASP367 4.5 70.0 1.0 N A:ASP367 4.6 61.7 1.0 NE2 A:HIS388 4.6 77.8 1.0 C A:PRO370 4.6 54.8 1.0 N A:ASN365 4.7 66.0 1.0 N A:ILE364 4.7 74.0 1.0 CG A:HIS388 4.7 73.4 1.0 N A:ASP371 4.7 54.4 1.0 O A:PRO370 4.7 56.7 1.0 C A:ASP363 4.8 73.0 1.0 N A:PRO370 4.8 57.0 1.0 CB A:ASN365 4.9 70.9 1.0 CA A:PRO370 5.0 50.1 1.0 N A:GLN366 5.0 77.2 1.0 CA A:GLY389 5.0 62.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of ALPHA6BETA1 Integrin Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of ALPHA6BETA1 Integrin Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:71.5 occ:1.00 OD1 A:ASP420 2.4 86.9 1.0 O A:TYR424 2.4 63.7 1.0 OD1 A:ASN422 2.4 95.7 1.0 OD1 A:ASP426 2.5 71.7 1.0 OD1 A:ASP418 2.5 92.9 1.0 O A:HOH1102 2.6 95.9 1.0 OD2 A:ASP426 2.7 64.5 1.0 CG A:ASP426 2.9 64.8 1.0 CG A:ASN422 3.3 91.3 1.0 CG A:ASP420 3.5 91.0 1.0 CG A:ASP418 3.5 88.8 1.0 C A:TYR424 3.6 62.4 1.0 ND2 A:ASN422 3.7 91.3 1.0 N A:ASP420 4.1 86.2 1.0 OD2 A:ASP420 4.1 94.7 1.0 N A:LEU419 4.1 75.2 1.0 OD2 A:ASP418 4.2 95.6 1.0 O A:PRO425 4.3 76.8 1.0 N A:ASN422 4.3 91.0 1.0 CA A:ASP418 4.3 81.1 1.0 CA A:TYR424 4.3 67.6 1.0 C A:PRO425 4.3 67.2 1.0 N A:TYR424 4.4 73.1 1.0 CB A:TYR424 4.4 72.7 1.0 CB A:ASP426 4.4 56.5 1.0 CB A:ASP418 4.5 82.0 1.0 N A:SER441 4.5 71.8 1.0 CB A:ASN422 4.5 87.1 1.0 N A:ARG421 4.5 95.9 1.0 CB A:ASP420 4.6 90.7 1.0 N A:PRO425 4.6 62.2 1.0 C A:ASP418 4.6 82.4 1.0 CA A:ASP420 4.6 86.1 1.0 O A:SER441 4.7 71.2 1.0 N A:ASP426 4.7 63.0 1.0 CA A:PRO425 4.7 68.3 1.0 C A:ASP420 4.7 89.7 1.0 CA A:ASN422 4.8 86.0 1.0 CB A:SER441 4.9 62.8 1.0 CA A:ASP426 5.0 56.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of ALPHA6BETA1 Integrin Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of ALPHA6BETA1 Integrin Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:104.7 occ:0.60 O B:PRO228 2.3 74.6 1.0 OD1 B:ASN224 2.3 77.9 1.0 OE1 B:GLU169 2.4 78.6 1.0 OD1 B:ASP226 2.4 75.7 1.0 O B:ASP226 2.4 72.5 1.0 C B:PRO228 3.3 62.1 1.0 CD B:GLU169 3.4 78.5 1.0 C B:ASP226 3.4 70.4 1.0 CG B:ASN224 3.4 79.2 1.0 CG B:ASP226 3.5 82.2 1.0 CA B:GLU229 3.7 58.0 1.0 CG B:GLU169 3.8 73.8 1.0 N B:GLU229 3.9 60.8 1.0 CG B:GLU229 3.9 59.4 1.0 O B:SER227 4.0 79.1 1.0 C B:SER227 4.0 68.4 1.0 CB B:GLU169 4.2 61.8 1.0 OD2 B:ASP226 4.2 81.7 1.0 CA B:ASP226 4.2 74.0 1.0 N B:PRO228 4.3 60.5 1.0 NE2 B:HIS263 4.3 57.5 1.0 N B:ASP226 4.3 70.0 1.0 ND2 B:ASN224 4.3 88.3 1.0 CB B:ASN224 4.3 67.3 1.0 CB B:GLU229 4.3 51.3 1.0 N B:SER227 4.3 67.3 1.0 CA B:PRO228 4.4 52.5 1.0 CB B:ASP226 4.4 78.3 1.0 O B:TYR175 4.4 64.7 1.0 OE2 B:GLU169 4.5 78.1 1.0 CD2 B:HIS263 4.5 53.4 1.0 CA B:SER227 4.5 65.7 1.0 C B:GLU229 4.9 63.7 1.0

T.Arimori, N.Miyazaki, M.Takizawa, Y.Taniguchi, C.Cabanas, K.Sekiguchi, J.Takagi. Structural Mechanism of Laminin-511 Recognition By ALPHA6BETA1 Integrin To Be Published.