Calcium in PDB 3vi3: Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)

The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form), PDB code: 3vi3 was solved by M.Nagae, T.Nogi, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	92.956, 102.805, 125.079, 76.10, 70.19, 71.28
R / Rfree (%)	20.7 / 26.7

The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) (pdb code 3vi3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form), PDB code: 3vi3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


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 ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:70.0 occ:1.00 OG A:SER241 2.3 69.4 1.0 O A:THR245 2.3 71.3 1.0 OD1 A:ASP243 2.3 79.9 1.0 OD2 A:ASP247 2.3 71.2 1.0 OE2 A:GLU239 2.3 61.0 1.0 OD1 A:ASP247 2.8 69.9 1.0 CG A:ASP247 2.9 68.7 1.0 CD A:GLU239 3.1 61.6 1.0 OE1 A:GLU239 3.1 66.2 1.0 CG A:ASP243 3.2 81.4 1.0 OD2 A:ASP243 3.5 86.4 1.0 C A:THR245 3.5 71.9 1.0 CB A:SER241 3.7 70.2 1.0 OG1 A:THR245 3.8 83.8 1.0 N A:THR245 4.2 71.7 1.0 N A:SER241 4.2 65.4 1.0 OD1 A:ASN266 4.3 59.9 1.0 CB A:ASP247 4.3 64.6 1.0 CA A:THR245 4.3 72.6 1.0 O A:SER241 4.4 79.4 1.0 CA A:SER241 4.4 69.0 1.0 C A:GLU246 4.4 66.6 1.0 N A:ASP247 4.5 66.0 1.0 C A:SER241 4.5 73.1 1.0 N A:GLU246 4.5 71.6 1.0 CB A:ASP243 4.5 76.0 1.0 CG A:GLU239 4.5 58.2 1.0 C A:ASP243 4.6 71.7 1.0 N A:ASP243 4.6 76.2 1.0 CA A:GLU246 4.6 69.6 1.0 CB A:THR245 4.7 73.2 1.0 N A:GLY267 4.7 56.7 1.0 O A:GLU246 4.7 65.2 1.0 CA A:ASP243 4.8 72.9 1.0 N A:ASP244 4.8 73.5 1.0 O A:ASP243 4.8 72.4 1.0 CA A:ASP247 4.8 64.4 1.0 N A:PHE240 4.9 61.5 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


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 ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:84.6 occ:1.00 OD1 A:ASP297 2.3 85.8 1.0 OD1 A:ASN295 2.3 81.3 1.0 OD2 A:ASP293 2.3 78.8 1.0 O A:LEU299 2.3 84.0 1.0 OD1 A:ASP301 2.3 77.4 1.0 OD2 A:ASP301 3.0 69.3 1.0 CG A:ASP301 3.0 73.1 1.0 CG A:ASP297 3.4 80.6 1.0 C A:LEU299 3.4 82.9 1.0 CG A:ASN295 3.4 79.5 1.0 CG A:ASP293 3.6 78.6 1.0 OD2 A:ASP297 3.7 81.0 1.0 ND2 A:ASN295 3.9 82.5 1.0 CB A:LEU299 3.9 76.0 1.0 CA A:LEU299 3.9 81.8 1.0 N A:LEU299 4.0 84.3 1.0 O A:GLN329 4.1 81.1 1.0 OD1 A:ASP293 4.4 82.3 1.0 CB A:ASP301 4.5 69.1 1.0 N A:ASN295 4.5 75.7 1.0 CB A:ASP293 4.5 75.8 1.0 N A:ASP300 4.5 81.5 1.0 N A:ASP301 4.5 71.6 1.0 CA A:ASP293 4.5 71.9 1.0 N A:VAL294 4.6 74.1 1.0 C A:ASP300 4.7 76.6 1.0 CB A:ASP297 4.7 78.2 1.0 CB A:ASN295 4.7 77.0 1.0 N A:ASP297 4.8 78.5 1.0 N A:GLN329 4.9 69.4 1.0 C A:ASP297 4.9 78.9 1.0 CA A:ASP301 4.9 67.3 1.0 CA A:ASP300 4.9 79.2 1.0 C A:ASP293 5.0 74.4 1.0 CA A:ASN295 5.0 78.3 1.0 C A:GLY298 5.0 82.8 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


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 ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:78.1 occ:1.00 O A:TYR366 2.3 73.0 1.0 OD2 A:ASP364 2.3 75.0 1.0 OD1 A:ASP362 2.3 82.0 1.0 OD2 A:ASP368 2.3 74.7 1.0 OD2 A:ASP360 2.3 83.9 1.0 OD1 A:ASP368 2.9 69.2 1.0 CG A:ASP368 3.0 70.2 1.0 CG A:ASP364 3.3 78.3 1.0 C A:TYR366 3.4 75.6 1.0 CG A:ASP362 3.4 82.7 1.0 CG A:ASP360 3.5 82.6 1.0 OD1 A:ASP364 3.7 79.7 1.0 OD2 A:ASP362 3.9 81.9 1.0 N A:TYR366 4.0 82.4 1.0 CA A:TYR366 4.1 77.2 1.0 CB A:TYR366 4.1 78.1 1.0 CA A:ASP360 4.1 74.6 1.0 N A:LEU361 4.2 71.9 1.0 N A:ASP362 4.3 82.5 1.0 OD1 A:ASP360 4.3 85.6 1.0 CB A:ASP360 4.4 77.5 1.0 N A:ASP364 4.4 75.9 1.0 CB A:ASP368 4.4 68.0 1.0 C A:ASP360 4.5 72.5 1.0 N A:ASN367 4.5 74.2 1.0 CB A:ASP364 4.5 79.0 1.0 N A:ASP368 4.5 69.3 1.0 C A:ASN367 4.6 69.7 1.0 O A:GLY389 4.6 60.4 1.0 CB A:ASP362 4.7 81.9 1.0 CA A:ASN367 4.7 71.2 1.0 N A:GLN363 4.8 82.2 1.0 N A:GLY389 4.8 62.4 1.0 CA A:ASP362 4.9 81.3 1.0 N A:GLY365 4.9 73.0 1.0 CA A:ASP364 4.9 77.0 1.0 CA A:ASP368 5.0 68.7 1.0 C A:ASP362 5.0 84.3 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


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 ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:88.6 occ:1.00 O A:TYR430 2.2 73.3 1.0 OD1 A:ASP426 2.3 91.4 1.0 OD1 A:ASP424 2.3 80.1 1.0 OD2 A:ASP432 2.3 79.2 1.0 OD1 A:ASN428 2.3 0.1 1.0 OD1 A:ASP432 2.9 77.0 1.0 CG A:ASP432 3.0 76.2 1.0 CG A:ASN428 3.3 0.7 1.0 CG A:ASP424 3.4 81.5 1.0 C A:TYR430 3.4 74.3 1.0 CG A:ASP426 3.4 99.1 1.0 ND2 A:ASN428 3.7 98.6 1.0 OD2 A:ASP426 3.9 0.6 1.0 OD2 A:ASP424 3.9 81.3 1.0 CA A:TYR430 4.2 78.5 1.0 N A:TYR430 4.2 81.9 1.0 CB A:TYR430 4.2 82.5 1.0 O A:ASN428 4.2 0.1 1.0 O A:GLY448 4.3 96.2 1.0 N A:ASP426 4.4 98.2 1.0 N A:GLY448 4.4 81.2 1.0 C A:PRO431 4.4 67.7 1.0 N A:PRO431 4.5 68.3 1.0 CB A:ASP432 4.5 71.7 1.0 O A:PRO431 4.5 71.1 1.0 CB A:ARG447 4.5 79.3 1.0 O A:ASP426 4.5 0.6 1.0 N A:LEU425 4.6 81.4 1.0 CB A:ASP424 4.6 79.6 1.0 CA A:PRO431 4.6 66.4 1.0 CA A:ASP424 4.7 80.5 1.0 CB A:ASP426 4.7 99.2 1.0 C A:ASN428 4.7 0.0 1.0 CB A:ASN428 4.7 0.6 1.0 N A:ASP432 4.8 66.0 1.0 C A:ASP426 4.8 0.4 1.0 CA A:ASP426 4.8 0.2 1.0 C A:ASP424 5.0 79.0 1.0 CA A:GLY448 5.0 84.3 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:69.1 occ:1.00 OD1 B:ASP138 2.3 65.5 1.0 OD2 B:ASP137 2.3 73.7 1.0 O B:SER134 2.3 66.5 1.0 O B:ALA342 2.3 69.4 1.0 OD1 B:ASP137 2.3 74.3 1.0 CG B:ASP137 2.7 72.7 1.0 C B:ALA342 3.5 67.7 1.0 CG B:ASP138 3.5 61.9 1.0 C B:SER134 3.6 62.5 1.0 OD2 B:ASP259 3.9 65.9 1.0 OD2 B:ASP138 4.1 59.1 1.0 CA B:ALA342 4.1 66.7 1.0 CB B:ASP137 4.2 67.6 1.0 CA B:MET135 4.2 62.7 1.0 N B:MET135 4.3 62.1 1.0 CB B:ALA342 4.4 65.5 1.0 N B:ASP138 4.4 63.3 1.0 N B:ASN343 4.5 70.1 1.0 CA B:SER134 4.7 61.1 1.0 CB B:ASP138 4.7 60.8 1.0 SD B:MET135 4.8 60.2 1.0 CB B:SER134 4.9 57.2 1.0 CA B:ASN343 4.9 70.0 1.0 C B:MET135 5.0 67.2 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:62.0 occ:1.00 OD1 B:ASN224 2.3 59.0 1.0 OE1 B:GLU169 2.3 57.0 1.0 O B:PRO228 2.3 52.7 1.0 O B:ASP226 2.3 54.2 1.0 OE2 B:GLU229 2.3 66.2 1.0 OD1 B:ASP226 2.3 62.9 1.0 C B:PRO228 3.2 50.8 1.0 CG B:ASN224 3.2 63.6 1.0 C B:ASP226 3.3 56.3 1.0 CD B:GLU229 3.4 63.3 1.0 CD B:GLU169 3.5 55.5 1.0 ND2 B:ASN224 3.5 68.1 1.0 CG B:ASP226 3.5 60.7 1.0 O B:SER227 3.6 56.4 1.0 CA B:GLU229 3.7 53.0 1.0 C B:SER227 3.8 54.6 1.0 N B:GLU229 3.8 50.2 1.0 CE1 B:HIS263 4.0 53.3 1.0 CG B:GLU169 4.1 52.3 1.0 CA B:ASP226 4.1 55.5 1.0 N B:PRO228 4.1 51.2 1.0 N B:ASP226 4.1 57.4 1.0 N B:SER227 4.2 57.9 1.0 OE1 B:GLU229 4.2 64.2 1.0 CA B:PRO228 4.3 52.3 1.0 CB B:GLU229 4.4 53.4 1.0 CG B:GLU229 4.4 59.9 1.0 OD2 B:ASP226 4.4 61.4 1.0 CB B:ASP226 4.4 58.8 1.0 CA B:SER227 4.4 56.8 1.0 CB B:GLU169 4.5 51.5 1.0 OE2 B:GLU169 4.5 56.4 1.0 ND1 B:HIS263 4.6 53.8 1.0 CD B:PRO228 4.6 51.0 1.0 CB B:ASN224 4.6 65.1 1.0 C B:GLU229 4.7 53.2 1.0 O B:TYR175 4.9 51.4 1.0 C B:LEU225 4.9 58.8 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2001 b:63.6 occ:1.00 OG C:SER241 2.3 62.9 1.0 O C:THR245 2.3 69.7 1.0 OD1 C:ASP243 2.3 78.2 1.0 OE2 C:GLU239 2.3 58.8 1.0 OD2 C:ASP247 2.3 60.3 1.0 OE1 C:GLU239 2.7 56.5 1.0 CD C:GLU239 2.9 55.9 1.0 CG C:ASP247 2.9 58.4 1.0 OD1 C:ASP247 2.9 61.8 1.0 CG C:ASP243 3.1 76.8 1.0 OD2 C:ASP243 3.3 76.6 1.0 C C:THR245 3.5 68.1 1.0 CB C:SER241 3.7 66.4 1.0 C C:GLU246 4.1 58.1 1.0 N C:SER241 4.2 63.3 1.0 CA C:GLU246 4.2 58.9 1.0 N C:ASP247 4.3 57.4 1.0 OG1 C:THR245 4.3 69.6 1.0 N C:GLU246 4.3 62.0 1.0 CB C:ASP247 4.3 57.1 1.0 CB C:ASP243 4.3 71.9 1.0 CG C:GLU239 4.4 53.9 1.0 O C:GLU246 4.4 59.0 1.0 N C:THR245 4.4 66.9 1.0 CA C:SER241 4.4 67.6 1.0 N C:ASP243 4.5 71.7 1.0 C C:ASP243 4.5 65.2 1.0 CA C:THR245 4.5 68.1 1.0 CA C:ASP243 4.6 69.2 1.0 CA C:ASP247 4.7 57.2 1.0 N C:ASP244 4.7 65.8 1.0 OD1 C:ASN266 4.7 59.1 1.0 O C:ASP243 4.8 62.5 1.0 C C:SER241 4.8 71.0 1.0 N C:PHE240 4.8 58.7 1.0 N C:GLY267 4.9 54.6 1.0 C C:ASP244 4.9 66.9 1.0 CA C:GLU239 4.9 57.8 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2002 b:75.5 occ:1.00 OD1 C:ASN295 2.3 67.6 1.0 O C:LEU299 2.3 75.5 1.0 OD2 C:ASP293 2.3 71.7 1.0 OD1 C:ASP301 2.3 70.7 1.0 OD1 C:ASP297 2.3 79.2 1.0 OD2 C:ASP301 2.7 66.0 1.0 CG C:ASP301 2.9 69.1 1.0 CG C:ASP297 3.2 76.9 1.0 CG C:ASN295 3.3 64.9 1.0 OD2 C:ASP297 3.4 73.9 1.0 CG C:ASP293 3.4 70.2 1.0 C C:LEU299 3.5 73.0 1.0 ND2 C:ASN295 3.6 62.2 1.0 O C:GLN329 4.1 65.2 1.0 CB C:LEU299 4.1 69.8 1.0 CA C:LEU299 4.1 71.3 1.0 N C:LEU299 4.1 75.6 1.0 CA C:ASP293 4.3 70.0 1.0 CB C:ASP293 4.3 69.8 1.0 N C:VAL294 4.3 71.3 1.0 OD1 C:ASP293 4.3 70.3 1.0 CB C:ASP301 4.4 67.1 1.0 N C:ASN295 4.4 72.6 1.0 N C:ASP297 4.5 74.9 1.0 CB C:ASP297 4.5 73.3 1.0 C C:ASP300 4.5 70.0 1.0 N C:ASP300 4.6 73.1 1.0 N C:ASP301 4.6 68.0 1.0 CB C:ASN295 4.7 67.9 1.0 N C:GLN329 4.7 66.4 1.0 C C:ASP293 4.7 70.6 1.0 O C:ASP300 4.8 70.8 1.0 CA C:ASP300 4.9 69.5 1.0 CA C:ASP297 4.9 71.5 1.0 CA C:ASN295 4.9 72.0 1.0 CD2 C:LEU328 5.0 63.0 1.0 CA C:ASP301 5.0 65.3 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2003 b:84.9 occ:1.00 O C:TYR366 2.3 75.1 1.0 OD1 C:ASP362 2.3 77.3 1.0 OD2 C:ASP364 2.3 81.3 1.0 OD2 C:ASP368 2.3 76.1 1.0 OD2 C:ASP360 2.3 85.8 1.0 OD1 C:ASP368 2.6 75.4 1.0 CG C:ASP368 2.8 73.2 1.0 CG C:ASP364 3.3 81.3 1.0 CG C:ASP362 3.5 78.6 1.0 C C:TYR366 3.5 72.1 1.0 CG C:ASP360 3.5 81.1 1.0 N C:LEU361 3.9 73.1 1.0 OD1 C:ASP364 4.0 83.4 1.0 N C:ASP362 4.0 76.7 1.0 OD2 C:ASP362 4.1 84.8 1.0 CA C:ASP360 4.1 77.6 1.0 N C:ASP364 4.2 77.1 1.0 C C:ASP360 4.2 76.1 1.0 CB C:ASP364 4.3 78.9 1.0 N C:TYR366 4.3 75.8 1.0 CA C:TYR366 4.3 73.1 1.0 CB C:ASP368 4.3 70.3 1.0 OD1 C:ASP360 4.4 77.3 1.0 CB C:ASP360 4.4 79.7 1.0 N C:GLN363 4.5 77.1 1.0 N C:ASN367 4.5 70.0 1.0 N C:ASP368 4.5 67.9 1.0 CB C:TYR366 4.5 72.7 1.0 C C:ASN367 4.5 67.5 1.0 CA C:ASN367 4.6 68.0 1.0 CB C:ASP362 4.7 79.4 1.0 CA C:ASP362 4.7 78.5 1.0 CA C:ASP364 4.7 76.9 1.0 C C:ASP362 4.8 78.6 1.0 CA C:LEU361 4.8 71.3 1.0 N C:GLY389 4.9 67.9 1.0 C C:LEU361 5.0 72.5 1.0 CA C:ASP368 5.0 67.4 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2004 b:81.8 occ:1.00 O C:TYR430 2.3 72.7 1.0 OD1 C:ASP426 2.3 88.1 1.0 OD1 C:ASN428 2.3 85.0 1.0 OD2 C:ASP432 2.3 82.1 1.0 OD1 C:ASP424 2.3 85.8 1.0 OD1 C:ASP432 3.0 84.0 1.0 CG C:ASP432 3.0 79.2 1.0 CG C:ASN428 3.2 86.4 1.0 CG C:ASP426 3.4 91.1 1.0 C C:TYR430 3.5 74.5 1.0 CG C:ASP424 3.6 84.4 1.0 O C:ASN428 3.6 81.9 1.0 ND2 C:ASN428 3.7 87.6 1.0 OD2 C:ASP426 4.0 90.9 1.0 O C:ASP426 4.1 91.9 1.0 N C:ASP426 4.1 88.4 1.0 N C:TYR430 4.2 78.1 1.0 CA C:TYR430 4.2 77.6 1.0 OD2 C:ASP424 4.2 78.1 1.0 C C:ASP426 4.4 94.5 1.0 O C:GLY448 4.4 99.1 1.0 C C:ASN428 4.4 81.2 1.0 CB C:TYR430 4.4 82.0 1.0 CB C:ASN428 4.5 84.7 1.0 CA C:ASP424 4.5 81.4 1.0 CB C:ASP432 4.5 73.5 1.0 C C:PRO431 4.5 65.8 1.0 CA C:ASP426 4.5 91.7 1.0 N C:PRO431 4.5 71.0 1.0 CB C:ASP426 4.6 92.2 1.0 N C:ASN428 4.6 88.0 1.0 N C:LEU425 4.6 79.0 1.0 CB C:ASP424 4.6 81.4 1.0 CA C:ASN428 4.7 83.7 1.0 C C:ASP424 4.7 79.0 1.0 CA C:PRO431 4.7 67.0 1.0 N C:ASP432 4.7 67.2 1.0 O C:PRO431 4.7 64.6 1.0 N C:GLY448 4.8 78.3 1.0

M.Nagae, S.Re, E.Mihara, T.Nogi, Y.Sugita, J.Takagi. Crystal Structure of ALPHA5BETA1 Integrin Ectodomain: Atomic Details of the Fibronectin Receptor J.Cell Biol. V. 197 131 2012.
ISSN: ISSN 0021-9525
PubMed: 22451694
DOI: 10.1083/JCB.201111077