Calcium in PDB 4g1e: Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag.

The structure of Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag., PDB code: 4g1e was solved by X.Dong, L.Mi, J.Zhu, W.Wang, B.Luo, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.52 / 3.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.558, 128.558, 352.859, 90.00, 90.00, 120.00
R / Rfree (%)	24.1 / 26.1

The structure of Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag. also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Chlorine	(Cl)	7 atoms

The binding sites of Calcium atom in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag. (pdb code 4g1e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag., PDB code: 4g1e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag.


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 Integrin Alpha V Beta 3 with Coil-Coiled Tag. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:1.0 occ:1.00 O A:ILE236 2.1 0.8 1.0 OD1 A:ASN232 2.3 0.3 1.0 OD1 A:ASP234 2.3 0.1 1.0 OD1 A:ASP238 2.4 99.3 1.0 OD1 A:ASP230 2.4 0.6 1.0 O A:HOH2133 2.4 0.8 1.0 OD2 A:ASP238 2.4 96.1 1.0 CG A:ASP238 2.6 0.4 1.0 C A:ILE236 3.2 0.2 1.0 CG A:ASN232 3.3 0.9 1.0 CG A:ASP234 3.4 0.2 1.0 CG A:ASP230 3.5 0.6 1.0 ND2 A:ASN232 3.7 0.4 1.0 CB A:ILE236 3.7 0.2 1.0 OD2 A:ASP234 3.8 0.8 1.0 CA A:ILE236 3.8 0.0 1.0 O A:ASP234 3.9 0.2 1.0 CB A:ASP238 4.0 93.8 1.0 N A:ASP238 4.0 0.4 1.0 N A:ILE236 4.0 0.2 1.0 C A:ASP237 4.2 0.7 1.0 N A:ASP237 4.2 1.0 1.0 CB A:ASP230 4.2 0.9 1.0 CA A:ASP230 4.2 0.5 1.0 OD1 A:ASP257 4.3 0.6 1.0 CG2 A:ILE236 4.3 0.5 1.0 OD2 A:ASP230 4.4 0.3 1.0 N A:PHE231 4.4 0.1 1.0 N A:ASN232 4.4 0.1 1.0 CA A:ASP238 4.4 98.2 1.0 CA A:ASP237 4.5 0.3 1.0 O A:ASN232 4.5 0.3 1.0 C A:ASP234 4.6 0.1 1.0 N A:GLY258 4.6 0.6 1.0 O A:ASP237 4.6 0.7 1.0 CB A:ASN232 4.7 0.5 1.0 CB A:ASP234 4.7 0.8 1.0 C A:ASP230 4.8 0.7 1.0 C A:GLY235 4.9 0.2 1.0 CA A:ASN232 4.9 0.2 1.0 C A:ASN232 5.0 0.8 1.0 CG1 A:ILE236 5.0 0.7 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag.


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 Integrin Alpha V Beta 3 with Coil-Coiled Tag. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:0.6 occ:1.00 OD1 A:ASP288 2.3 0.1 1.0 O A:TYR290 2.3 0.3 1.0 OD1 A:ASP292 2.3 0.1 1.0 OD1 A:ASN286 2.4 0.1 1.0 OD2 A:ASP292 2.4 0.7 1.0 OD2 A:ASP288 2.4 0.6 1.0 OD1 A:ASP284 2.4 98.1 1.0 CG A:ASP288 2.6 0.8 1.0 CG A:ASP292 2.7 1.0 1.0 CG A:ASN286 3.3 0.9 1.0 C A:TYR290 3.4 0.4 1.0 CG A:ASP284 3.6 0.7 1.0 ND2 A:ASN286 3.6 0.8 1.0 CB A:TYR290 4.0 0.4 1.0 CA A:TYR290 4.0 0.5 1.0 CB A:ASP288 4.1 0.9 1.0 CB A:ASP292 4.1 0.9 1.0 N A:TYR290 4.1 0.2 1.0 CA A:ASP284 4.3 97.6 1.0 N A:ASP292 4.3 0.3 1.0 CB A:ASP284 4.3 0.5 1.0 OD2 A:ASP284 4.5 0.9 1.0 C A:ALA291 4.5 0.6 1.0 N A:ASP288 4.5 1.0 1.0 N A:ALA291 4.5 0.2 1.0 N A:GLN320 4.5 0.1 1.0 N A:ASN286 4.6 0.4 1.0 N A:ILE285 4.6 99.2 1.0 O A:GLN320 4.6 0.7 1.0 CA A:ASP292 4.6 0.1 1.0 CB A:ASN286 4.7 0.4 1.0 C A:ASP284 4.7 0.5 1.0 CA A:ASP288 4.8 0.8 1.0 O A:ALA291 4.9 0.4 1.0 CA A:ALA291 4.9 0.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag.


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 Integrin Alpha V Beta 3 with Coil-Coiled Tag. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:0.7 occ:1.00 O A:PHE355 2.2 0.7 1.0 OD1 A:ASP351 2.3 0.4 1.0 OD1 A:ASP349 2.3 0.0 1.0 OD1 A:ASP353 2.3 0.7 1.0 O A:HOH2140 2.4 1.0 1.0 OD2 A:ASP357 2.4 0.2 1.0 OD1 A:ASP357 2.4 0.9 1.0 CG A:ASP357 2.7 0.2 1.0 CG A:ASP349 3.2 0.7 1.0 CG A:ASP353 3.3 0.7 1.0 C A:PHE355 3.4 0.1 1.0 CG A:ASP351 3.5 0.2 1.0 N A:LEU350 3.6 0.1 1.0 CA A:ASP349 3.7 0.8 1.0 OD2 A:ASP353 3.8 0.1 1.0 N A:ASP351 3.8 0.5 1.0 OD2 A:ASP349 3.9 0.4 1.0 C A:ASP349 3.9 98.6 1.0 CB A:ASP349 4.0 0.6 1.0 N A:PHE355 4.1 0.3 1.0 OD2 A:ASP351 4.1 0.6 1.0 N A:ASP353 4.1 0.4 1.0 CB A:ASP357 4.2 0.2 1.0 CA A:PHE355 4.2 0.2 1.0 N A:ASP357 4.2 0.1 1.0 N A:GLN352 4.2 0.6 1.0 C A:ASN356 4.3 0.5 1.0 N A:ASN356 4.4 98.8 1.0 CB A:ASP353 4.4 0.6 1.0 CA A:ASN356 4.5 96.1 1.0 CA A:ASP351 4.6 0.1 1.0 CB A:PHE355 4.6 0.3 1.0 CA A:LEU350 4.6 0.4 1.0 CB A:ASP351 4.6 0.8 1.0 C A:LEU350 4.7 0.1 1.0 C A:ASP351 4.7 0.4 1.0 O A:GLY348 4.7 0.8 1.0 CA A:ASP357 4.7 99.2 1.0 CA A:ASP353 4.8 0.7 1.0 N A:GLY354 4.8 0.4 1.0 O A:ASN356 4.8 0.1 1.0 O A:ASP349 4.9 98.9 1.0 O A:GLY378 4.9 0.8 1.0 N A:ASP349 4.9 0.6 1.0 CB A:LEU350 5.0 0.8 1.0 CA A:GLN352 5.0 0.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag.


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 Integrin Alpha V Beta 3 with Coil-Coiled Tag. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:0.5 occ:1.00 O A:TYR419 2.2 0.6 1.0 OD1 A:ASP415 2.3 0.2 1.0 OD1 A:ASP421 2.3 0.9 1.0 OD1 A:ASN417 2.4 0.6 1.0 OD1 A:ASP413 2.4 0.1 1.0 OD2 A:ASP421 2.4 0.3 1.0 CG A:ASP421 2.6 0.2 1.0 CG A:ASN417 3.1 0.3 1.0 C A:TYR419 3.3 0.0 1.0 CG A:ASP415 3.3 0.3 1.0 CG A:ASP413 3.4 0.9 1.0 ND2 A:ASN417 3.5 0.2 1.0 OD2 A:ASP415 3.7 0.8 1.0 CA A:ASP413 3.8 0.7 1.0 C A:PRO420 3.9 0.5 1.0 O A:PRO420 4.0 0.1 1.0 CB A:ASP421 4.0 0.1 1.0 CB A:ASP413 4.0 0.5 1.0 N A:ASP421 4.2 0.2 1.0 N A:ILE414 4.2 0.0 1.0 N A:PRO420 4.2 0.4 1.0 CA A:TYR419 4.2 0.8 1.0 CA A:PRO420 4.3 0.4 1.0 N A:TYR419 4.3 0.7 1.0 N A:ALA437 4.3 0.8 1.0 N A:ASP415 4.4 0.7 1.0 C A:ASP413 4.4 0.3 1.0 CB A:ASN417 4.4 0.3 1.0 OD2 A:ASP413 4.4 0.1 1.0 CB A:TYR419 4.5 0.3 1.0 CA A:ASP421 4.5 0.9 1.0 N A:ASN417 4.6 0.3 1.0 CB A:ASP415 4.6 0.2 1.0 CB A:ALA437 4.7 0.1 1.0 O A:ALA437 4.7 0.4 1.0 O A:THR412 4.8 1.0 1.0 CA A:ASP415 5.0 0.3 1.0 CA A:ASN417 5.0 0.1 1.0 N A:LYS416 5.0 0.6 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag.


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 Integrin Alpha V Beta 3 with Coil-Coiled Tag. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:0.3 occ:1.00 O A:VAL601 2.3 0.3 1.0 OD2 A:ASP599 2.3 0.7 1.0 OE2 A:GLU636 2.3 0.7 1.0 OE1 A:GLU636 2.4 0.3 1.0 OD1 A:ASP599 2.4 0.6 1.0 CD A:GLU636 2.7 0.7 1.0 CG A:ASP599 2.7 0.8 1.0 C A:VAL601 3.2 0.1 1.0 N A:VAL601 3.9 0.1 1.0 O A:CYS596 3.9 0.2 1.0 N A:CYS602 4.0 0.5 1.0 CA A:CYS602 4.0 0.5 1.0 CA A:VAL601 4.1 0.3 1.0 CB A:CYS596 4.1 0.2 1.0 CG A:GLU636 4.2 0.9 1.0 CB A:ASP599 4.2 0.8 1.0 CA A:CYS596 4.5 0.6 1.0 SG A:CYS596 4.6 0.3 1.0 C A:CYS596 4.7 0.3 1.0 N A:LYS603 4.7 1.0 1.0 N A:ASN600 4.7 0.9 1.0 CB A:VAL601 4.8 0.2 1.0 C A:CYS602 4.8 0.9 1.0 C A:ASN600 5.0 0.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Integrin Alpha V Beta 3 with Coil-Coiled Tag.


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 Integrin Alpha V Beta 3 with Coil-Coiled Tag. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:0.8 occ:1.00 O B:PRO219 2.1 0.6 1.0 OD1 B:ASP217 2.3 0.7 1.0 O B:ASP217 2.4 0.5 1.0 OD2 B:ASP158 2.4 0.2 1.0 OD1 B:ASN215 2.4 0.0 1.0 OE1 B:GLU220 2.4 0.8 1.0 CG B:ASP217 3.1 0.5 1.0 C B:PRO219 3.2 0.2 1.0 O B:ARG216 3.4 0.2 1.0 OD2 B:ASP217 3.5 0.2 1.0 CG B:ASP158 3.5 0.1 1.0 C B:ASP217 3.6 0.9 1.0 CG B:ASN215 3.6 0.8 1.0 CD B:GLU220 3.7 0.5 1.0 CA B:GLU220 3.9 0.7 1.0 O B:ALA218 3.9 0.9 1.0 CB B:ASP158 3.9 0.1 1.0 NE2 B:HIS255 4.0 0.5 1.0 C B:ALA218 4.0 0.5 1.0 N B:GLU220 4.0 0.3 1.0 N B:PRO219 4.2 0.9 1.0 CB B:ASP217 4.3 0.3 1.0 CA B:PRO219 4.3 0.9 1.0 CD2 B:HIS255 4.3 98.8 1.0 ND2 B:ASN215 4.4 0.0 1.0 OE2 B:GLU220 4.4 0.4 1.0 CA B:ASP217 4.4 0.6 1.0 C B:ARG216 4.5 0.9 1.0 N B:ALA218 4.5 0.1 1.0 CB B:TYR164 4.5 98.3 1.0 OD1 B:ASP158 4.6 94.6 1.0 CA B:ALA218 4.6 0.7 1.0 CD1 B:TYR164 4.6 0.6 1.0 CG B:GLU220 4.7 0.6 1.0 CB B:ASN215 4.7 0.8 1.0 CB B:GLU220 4.7 0.1 1.0 C B:GLU220 4.9 98.9 1.0 N B:ASP217 4.9 0.1 1.0 CB B:PRO219 4.9 0.8 1.0 CG B:TYR164 4.9 0.7 1.0 CD B:PRO219 5.0 0.1 1.0

X.Dong, L.Z.Mi, J.Zhu, W.Wang, P.Hu, B.H.Luo, T.A.Springer. Alphav BETA3 Integrin Crystal Structures and Their Functional Implications Biochemistry V. 51 8814 2012.
ISSN: ISSN 0006-2960
PubMed: 23106217
DOI: 10.1021/BI300734N