Calcium in PDB 4um9: Crystal Structure of Alpha V Beta 6 with Peptide

The structure of Crystal Structure of Alpha V Beta 6 with Peptide, PDB code: 4um9 was solved by X.Dong, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	185.020, 168.090, 101.800, 90.00, 98.95, 90.00
R / Rfree (%)	22.2 / 26.6

The structure of Crystal Structure of Alpha V Beta 6 with Peptide 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 Alpha V Beta 6 with Peptide (pdb code 4um9). 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 Alpha V Beta 6 with Peptide, PDB code: 4um9:
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 Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:67.5 occ:1.00 O A:ILE236 2.2 58.2 1.0 OD1 A:ASN232 2.3 60.6 1.0 OD1 A:ASP230 2.4 61.2 1.0 O A:HOH4030 2.4 39.2 1.0 OD1 A:ASP234 2.4 84.2 1.0 OD2 A:ASP238 2.5 64.0 1.0 OD1 A:ASP238 2.5 56.5 1.0 CG A:ASP238 2.8 57.7 1.0 C A:ILE236 3.3 58.9 1.0 CG A:ASN232 3.4 61.9 1.0 CG A:ASP234 3.5 66.4 1.0 CG A:ASP230 3.5 59.0 1.0 ND2 A:ASN232 3.8 76.8 1.0 OD1 A:ASP257 3.9 61.0 1.0 CA A:ILE236 3.9 68.6 1.0 N A:ILE236 3.9 75.9 1.0 CB A:ILE236 4.0 68.4 1.0 OD2 A:ASP234 4.0 67.3 1.0 N A:PHE231 4.2 58.6 1.0 CB A:ASP238 4.2 55.0 1.0 CA A:ASP230 4.2 54.4 1.0 N A:ASN232 4.3 58.7 1.0 OD2 A:ASP230 4.3 65.3 1.0 N A:ASP238 4.3 52.7 1.0 CB A:ASP230 4.4 57.8 1.0 N A:ASP237 4.4 65.7 1.0 N A:ASP234 4.5 69.0 1.0 C A:ASP237 4.5 53.9 1.0 CB A:ASP234 4.6 68.7 1.0 CB A:ASN232 4.7 62.0 1.0 CG2 A:ILE236 4.7 61.6 1.0 CA A:ASP238 4.7 56.5 1.0 C A:ASP230 4.7 54.1 1.0 CA A:ASP237 4.8 54.7 1.0 N A:GLY233 4.8 77.5 1.0 N A:GLY235 4.8 65.7 1.0 CA A:ASN232 4.9 61.2 1.0 N A:GLY258 4.9 56.7 1.0 O A:ASP237 4.9 65.0 1.0 CA A:ASP234 4.9 69.9 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:58.1 occ:1.00 O A:TYR290 2.3 76.5 1.0 OD1 A:ASN286 2.3 56.4 1.0 O A:HOH4045 2.4 43.7 1.0 OD1 A:ASP284 2.4 54.4 1.0 OD1 A:ASP292 2.4 55.4 1.0 OD2 A:ASP292 2.4 47.7 1.0 OD1 A:ASP288 2.5 89.3 1.0 CG A:ASP292 2.7 47.5 1.0 CG A:ASP288 3.3 68.7 1.0 CG A:ASN286 3.4 51.7 1.0 OD2 A:ASP288 3.4 67.0 1.0 C A:TYR290 3.4 52.3 1.0 CG A:ASP284 3.5 59.2 1.0 ND2 A:ASN286 3.8 52.7 1.0 CB A:TYR290 3.9 55.2 1.0 CA A:TYR290 4.0 54.7 1.0 CA A:ASP284 4.1 48.7 1.0 N A:TYR290 4.1 62.1 1.0 CB A:ASP292 4.2 45.5 1.0 N A:ILE285 4.2 49.9 1.0 CB A:ASP284 4.2 50.8 1.0 N A:ASN286 4.3 58.8 1.0 OD2 A:ASP284 4.4 54.3 1.0 C A:ALA291 4.5 48.2 1.0 N A:ASP292 4.5 53.2 1.0 N A:ALA291 4.5 51.6 1.0 C A:ASP284 4.6 57.4 1.0 N A:GLN320 4.6 49.7 1.0 O A:GLN320 4.7 54.5 1.0 CB A:ASN286 4.7 51.5 1.0 CB A:ASP288 4.7 58.4 1.0 N A:ASP288 4.8 67.5 1.0 O A:ALA291 4.8 48.8 1.0 CA A:ASP292 4.8 51.2 1.0 CA A:ALA291 4.8 49.5 1.0 CA A:ASN286 4.9 51.4 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:53.6 occ:1.00 O A:PHE355 2.2 51.1 1.0 OD1 A:ASP351 2.3 52.0 1.0 O A:HOH4064 2.3 51.4 1.0 OD1 A:ASP353 2.3 69.1 1.0 OD1 A:ASP349 2.4 87.5 1.0 OD1 A:ASP357 2.4 67.0 1.0 OD2 A:ASP357 2.4 76.9 1.0 CG A:ASP357 2.7 63.1 1.0 CG A:ASP351 3.3 53.3 1.0 CG A:ASP353 3.4 59.2 1.0 C A:PHE355 3.4 51.5 1.0 CG A:ASP349 3.5 73.2 1.0 OD2 A:ASP351 3.7 68.8 1.0 OD2 A:ASP353 3.9 62.7 1.0 N A:ASP351 4.1 52.9 1.0 CA A:ASP349 4.2 51.6 1.0 ND2 A:ASN377 4.2 48.6 1.0 OD2 A:ASP349 4.2 77.0 1.0 N A:LEU350 4.2 50.4 1.0 CB A:ASP357 4.2 45.9 1.0 N A:PHE355 4.2 65.9 1.0 CA A:PHE355 4.3 53.2 1.0 C A:ASN356 4.3 49.9 1.0 C A:ASP349 4.3 56.9 1.0 N A:ASP353 4.4 64.2 1.0 N A:ASN356 4.4 61.8 1.0 CB A:ASP349 4.4 62.0 1.0 N A:ASP357 4.5 48.7 1.0 O A:ASN356 4.5 58.5 1.0 CA A:ASN356 4.6 53.2 1.0 CB A:PHE355 4.6 52.8 1.0 N A:GLN352 4.6 71.5 1.0 CB A:ASP351 4.6 54.3 1.0 CB A:ASP353 4.7 57.8 1.0 CA A:ASP351 4.8 58.4 1.0 N A:GLY378 4.8 54.3 1.0 CA A:ASP357 4.8 50.5 1.0 O A:GLY378 4.9 50.3 1.0 C A:ASP351 4.9 59.7 1.0 CB A:ASN377 5.0 47.7 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:45.6 occ:1.00 O A:TYR419 2.2 58.0 1.0 OD1 A:ASP415 2.3 61.2 1.0 OD1 A:ASP413 2.3 68.2 1.0 O A:HOH4071 2.4 41.3 1.0 OD2 A:ASP421 2.4 74.2 1.0 OD1 A:ASP421 2.5 57.0 1.0 OD1 A:ASN417 2.5 70.9 1.0 CG A:ASP421 2.8 55.9 1.0 CG A:ASN417 3.3 63.0 1.0 CG A:ASP415 3.3 68.6 1.0 C A:TYR419 3.4 56.4 1.0 CG A:ASP413 3.5 68.8 1.0 OD2 A:ASP415 3.7 69.5 1.0 ND2 A:ASN417 3.9 62.6 1.0 CA A:ASP413 4.1 57.2 1.0 CA A:TYR419 4.2 58.1 1.0 N A:TYR419 4.2 60.5 1.0 CB A:ASP421 4.2 52.0 1.0 CB A:ASN417 4.3 65.8 1.0 CB A:ASP413 4.3 69.0 1.0 OD2 A:ASP413 4.4 65.6 1.0 N A:ILE414 4.4 60.1 1.0 N A:ASP415 4.4 61.8 1.0 CB A:TYR419 4.4 57.9 1.0 N A:PRO420 4.4 54.6 1.0 C A:PRO420 4.4 60.0 1.0 N A:ASP421 4.4 53.6 1.0 N A:ALA437 4.4 68.8 1.0 O A:ALA437 4.4 59.2 1.0 N A:ASN417 4.5 68.7 1.0 C A:ASP413 4.5 64.8 1.0 CB A:ASP415 4.6 63.8 1.0 CA A:PRO420 4.6 52.9 1.0 CB A:ALA437 4.7 54.0 1.0 O A:PRO420 4.7 61.3 1.0 CA A:ASP421 4.8 50.9 1.0 CA A:ASN417 4.9 66.9 1.0 CA A:ASP415 4.9 64.2 1.0 N A:LYS416 4.9 65.4 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:47.8 occ:1.00 O B:PRO222 2.2 58.9 1.0 OD1 B:ASP220 2.3 76.6 1.0 OD1 B:ASN218 2.3 62.8 1.0 OE2 B:GLU162 2.4 37.9 1.0 O B:ASP220 2.4 54.3 1.0 OE1 B:GLU223 2.4 53.2 1.0 CG B:ASP220 3.2 65.9 1.0 C B:PRO222 3.3 54.9 1.0 CD B:GLU162 3.4 40.8 1.0 CG B:ASN218 3.4 51.9 1.0 C B:ASP220 3.4 59.3 1.0 CD B:GLU223 3.5 38.2 1.0 CG B:GLU162 3.6 38.3 1.0 OD2 B:ASP220 3.7 55.0 1.0 CA B:GLU223 3.8 36.6 1.0 ND2 B:ASN218 3.9 39.5 1.0 N B:GLU223 4.1 50.7 1.0 CA B:ASP220 4.1 55.9 1.0 C B:THR221 4.2 46.0 1.0 CB B:GLU162 4.2 21.9 1.0 CB B:ASP220 4.2 50.4 1.0 N B:ASP220 4.2 55.3 1.0 OE2 B:GLU223 4.2 52.5 1.0 O B:THR221 4.3 48.2 1.0 N B:PRO222 4.3 47.1 1.0 N B:THR221 4.4 40.2 1.0 NE2 B:HIS258 4.4 25.5 1.0 CA B:PRO222 4.4 55.1 1.0 OE1 B:GLU162 4.5 35.5 1.0 CG B:GLU223 4.5 32.6 1.0 CD2 B:HIS258 4.5 35.2 1.0 CB B:GLU223 4.7 47.1 1.0 CB B:ASN218 4.7 61.8 1.0 CA B:THR221 4.7 42.5 1.0 C B:GLU223 4.8 39.3 1.0 O B:PHE168 4.9 30.2 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:0.6 occ:1.00 OD1 B:ASP131 2.3 0.6 1.0 OD1 B:ASP130 2.4 0.1 1.0 O B:SER127 2.4 95.6 1.0 O B:HOH4016 2.4 66.1 1.0 CG B:ASP130 3.1 0.7 1.0 OD2 B:ASP130 3.1 0.1 1.0 O B:LYS338 3.3 39.4 1.0 CG B:ASP131 3.5 88.3 1.0 C B:SER127 3.6 87.8 1.0 CA B:MET128 4.0 94.8 1.0 OD2 B:ASP131 4.0 84.4 1.0 N B:MET128 4.2 87.2 1.0 C B:MET128 4.4 0.2 1.0 N B:ASP131 4.4 0.5 1.0 C B:LYS338 4.5 63.4 1.0 CB B:ASP130 4.5 0.9 1.0 N B:ASP130 4.6 0.1 1.0 N B:ASP129 4.6 0.7 1.0 CB B:ASP131 4.7 86.0 1.0 CA B:SER127 4.8 75.8 1.0 OD2 B:ASP254 4.9 70.5 1.0 SD B:MET128 5.0 58.9 1.0 CA B:ASP130 5.0 0.9 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2001 b:73.0 occ:1.00 OD1 C:ASN417 2.2 0.5 1.0 OD1 C:ASP415 2.2 97.3 1.0 O C:HOH4040 2.3 49.7 1.0 CG C:ASN417 2.4 0.2 1.0 ND2 C:ASN417 2.4 0.7 1.0 OD1 C:ASP421 2.5 93.5 1.0 O C:TYR419 2.5 82.3 1.0 OD2 C:ASP415 2.7 95.9 1.0 CG C:ASP415 2.8 80.3 1.0 OD2 C:ASP421 3.1 78.3 1.0 CG C:ASP421 3.1 82.3 1.0 OD1 C:ASP413 3.3 84.0 1.0 CB C:ASN417 3.5 91.9 1.0 C C:TYR419 3.6 81.3 1.0 O C:ALA437 3.8 86.5 1.0 N C:ALA437 4.1 83.2 1.0 CB C:TYR419 4.2 77.6 1.0 CA C:TYR419 4.2 75.9 1.0 N C:TYR419 4.3 79.1 1.0 CB C:ASP415 4.3 82.0 1.0 CB C:ALA437 4.4 70.7 1.0 CG C:ASP413 4.4 87.2 1.0 N C:ASN417 4.5 0.7 1.0 CA C:ASN417 4.5 94.5 1.0 CB C:ASP421 4.6 68.0 1.0 CA C:ALA437 4.6 84.7 1.0 C C:ALA437 4.6 81.4 1.0 N C:PRO420 4.6 84.1 1.0 C C:PRO420 4.7 75.5 1.0 N C:ASP415 4.7 79.7 1.0 N C:ASP421 4.8 68.5 1.0 O C:PRO420 4.9 80.9 1.0 C C:ASN417 4.9 86.0 1.0 CA C:ASP415 4.9 82.7 1.0 CB C:ARG436 5.0 73.9 1.0 CA C:PRO420 5.0 74.6 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2002 b:68.9 occ:1.00 O C:PHE355 2.1 66.3 1.0 OD1 C:ASP353 2.3 75.1 1.0 OD1 C:ASP351 2.4 66.8 1.0 OD1 C:ASP357 2.4 0.2 1.0 OD1 C:ASP349 2.4 78.8 1.0 OD2 C:ASP357 2.5 94.1 1.0 CG C:ASP357 2.7 81.9 1.0 C C:PHE355 3.3 65.8 1.0 CG C:ASP351 3.3 68.5 1.0 CG C:ASP353 3.4 77.9 1.0 CG C:ASP349 3.5 85.2 1.0 OD2 C:ASP351 3.7 70.6 1.0 OD2 C:ASP353 3.8 89.0 1.0 CA C:PHE355 4.1 67.4 1.0 N C:PHE355 4.1 70.1 1.0 OD2 C:ASP349 4.2 76.8 1.0 CA C:ASP349 4.2 66.8 1.0 C C:ASN356 4.2 60.8 1.0 CB C:ASP357 4.2 59.1 1.0 N C:ASP351 4.2 79.1 1.0 ND2 C:ASN377 4.2 78.2 1.0 N C:ASN356 4.3 64.2 1.0 N C:LEU350 4.3 71.1 1.0 CB C:PHE355 4.3 70.8 1.0 O C:ASN356 4.4 68.5 1.0 N C:ASP357 4.4 59.6 1.0 C C:ASP349 4.4 67.3 1.0 CB C:ASP349 4.4 87.9 1.0 N C:ASP353 4.4 77.6 1.0 CA C:ASN356 4.4 64.1 1.0 CB C:ASP351 4.6 75.5 1.0 CB C:ASP353 4.7 74.0 1.0 N C:GLN352 4.7 73.2 1.0 CA C:ASP357 4.8 58.0 1.0 N C:GLY378 4.8 69.6 1.0 CA C:ASP351 4.8 80.3 1.0 O C:GLY378 4.9 63.2 1.0 C C:ASP351 5.0 73.4 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2003 b:66.8 occ:1.00 O C:ILE236 2.3 81.2 1.0 OD1 C:ASN232 2.3 89.6 1.0 O C:HOH4019 2.3 44.3 1.0 OD1 C:ASP234 2.4 77.7 1.0 OD1 C:ASP238 2.4 75.6 1.0 OD2 C:ASP238 2.4 75.4 1.0 OD1 C:ASP230 2.5 67.1 1.0 CG C:ASP238 2.7 76.7 1.0 CG C:ASN232 3.4 81.9 1.0 C C:ILE236 3.4 86.1 1.0 CG C:ASP234 3.4 79.9 1.0 CG C:ASP230 3.6 68.6 1.0 ND2 C:ASN232 3.8 83.9 1.0 OD2 C:ASP234 3.9 80.8 1.0 N C:ILE236 4.0 86.5 1.0 CA C:ILE236 4.0 91.6 1.0 CB C:ILE236 4.0 83.4 1.0 CB C:ASP238 4.1 80.3 1.0 N C:PHE231 4.2 65.5 1.0 CA C:ASP230 4.3 63.1 1.0 N C:ASN232 4.3 68.7 1.0 N C:ASP238 4.3 60.5 1.0 OD2 C:ASP230 4.4 84.5 1.0 CB C:ASP230 4.4 65.8 1.0 N C:ASP237 4.5 81.9 1.0 C C:ASP237 4.5 68.4 1.0 N C:ASP234 4.6 82.7 1.0 CB C:ASP234 4.6 76.4 1.0 CA C:ASP238 4.7 64.2 1.0 OD2 C:ASP257 4.7 80.1 1.0 CB C:ASN232 4.7 68.2 1.0 CG2 C:ILE236 4.7 77.5 1.0 N C:GLY258 4.8 73.7 1.0 C C:ASP230 4.8 63.8 1.0 CA C:ASP237 4.9 69.7 1.0 N C:GLY235 4.9 75.0 1.0 CA C:ASN232 4.9 70.0 1.0 N C:GLY233 5.0 73.9 1.0 O C:ASP237 5.0 75.2 1.0 CA C:ASP234 5.0 76.8 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Alpha V Beta 6 with Peptide


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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2004 b:62.6 occ:1.00 O C:TYR290 2.3 65.5 1.0 OD1 C:ASN286 2.3 79.5 1.0 OD1 C:ASP292 2.4 68.0 1.0 OD1 C:ASP284 2.4 82.2 1.0 O C:HOH4027 2.4 66.3 1.0 OD1 C:ASP288 2.4 0.5 1.0 OD2 C:ASP292 2.4 71.0 1.0 CG C:ASP292 2.7 65.3 1.0 CG C:ASP288 3.2 99.8 1.0 OD2 C:ASP288 3.2 94.4 1.0 CG C:ASN286 3.4 79.0 1.0 C C:TYR290 3.4 62.3 1.0 CG C:ASP284 3.6 76.1 1.0 ND2 C:ASN286 3.8 84.9 1.0 CB C:TYR290 3.9 65.6 1.0 CA C:TYR290 4.0 65.6 1.0 N C:TYR290 4.1 71.4 1.0 CA C:ASP284 4.2 65.4 1.0 N C:ILE285 4.2 72.7 1.0 CB C:ASP292 4.2 54.5 1.0 CB C:ASP284 4.3 75.2 1.0 N C:ASN286 4.3 73.6 1.0 OD2 C:ASP284 4.5 66.1 1.0 C C:ALA291 4.5 66.7 1.0 N C:ALA291 4.5 63.7 1.0 N C:ASP292 4.6 55.9 1.0 C C:ASP284 4.6 78.8 1.0 N C:GLN320 4.6 57.6 1.0 CB C:ASP288 4.7 89.2 1.0 CB C:ASN286 4.7 64.5 1.0 O C:GLN320 4.7 63.1 1.0 O C:ALA291 4.8 70.4 1.0 N C:ASP288 4.8 79.2 1.0 CA C:ALA291 4.9 59.2 1.0 CA C:ASP292 4.9 54.4 1.0 CA C:ASN286 5.0 79.7 1.0

X.Dong, N.E.Hudson, C.Lu, T.A.Springer. Structural Determinants of Integrin Beta-Subunit Specificity For Latent Tgf-Beta Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
PubMed: 25383667
DOI: 10.1038/NSMB.2905