Calcium in PDB 4g1m: Re-Refinement of Alpha V Beta 3 Structure

The structure of Re-Refinement of Alpha V Beta 3 Structure, PDB code: 4g1m was solved by T.A.Springer, L.Mi, J.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.00 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.870, 129.870, 305.900, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 23.3

The structure of Re-Refinement of Alpha V Beta 3 Structure also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Re-Refinement of Alpha V Beta 3 Structure (pdb code 4g1m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Re-Refinement of Alpha V Beta 3 Structure, PDB code: 4g1m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:82.3 occ:1.00 O A:ILE236 2.1 81.7 1.0 OD1 A:ASN232 2.3 81.6 1.0 OD1 A:ASP234 2.4 76.1 1.0 OD1 A:ASP238 2.4 66.0 1.0 O A:HOH4001 2.4 71.7 1.0 OD2 A:ASP230 2.5 78.7 1.0 OD2 A:ASP238 2.9 77.4 1.0 CG A:ASP238 2.9 71.6 1.0 C A:ILE236 3.2 81.0 1.0 CG A:ASN232 3.3 72.1 1.0 O A:ASP234 3.5 0.3 1.0 CG A:ASP234 3.6 100.0 1.0 CG A:ASP230 3.6 86.6 1.0 ND2 A:ASN232 3.7 66.7 1.0 N A:ILE236 3.7 87.9 1.0 CA A:ILE236 3.8 84.2 1.0 CB A:ILE236 3.9 81.6 1.0 OD2 A:ASP234 4.2 0.7 1.0 N A:ASP238 4.3 76.7 1.0 C A:ASP234 4.3 83.0 1.0 CB A:ASP238 4.3 73.4 1.0 N A:ASP237 4.4 89.8 1.0 N A:PHE231 4.4 77.5 1.0 CA A:ASP230 4.4 72.3 1.0 C A:ASP237 4.4 89.8 1.0 OD1 A:ASP230 4.5 80.8 1.0 N A:ASN232 4.5 94.9 1.0 CB A:ASP230 4.5 92.1 1.0 CG2 A:ILE236 4.7 72.0 1.0 CB A:ASN232 4.7 71.1 1.0 CB A:ASP234 4.7 99.5 1.0 CA A:ASP238 4.7 66.2 1.0 CA A:ASP237 4.7 92.8 1.0 O A:ASP237 4.9 88.6 1.0 CA A:ASP234 4.9 92.1 1.0 C A:GLY235 4.9 86.6 1.0 C A:ASP230 4.9 75.9 1.0 N A:ASP234 5.0 0.6 1.0 CA A:ASN232 5.0 87.2 1.0 O A:ASN232 5.0 86.5 1.0

Calcium binding site 2 out of 7 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:80.5 occ:1.00 O A:TYR290 2.2 92.2 1.0 OD1 A:ASN286 2.3 69.9 1.0 O A:HOH4002 2.3 60.4 1.0 OD2 A:ASP284 2.4 72.7 1.0 OD2 A:ASP292 2.4 67.1 1.0 OD1 A:ASP288 2.4 0.1 1.0 OD1 A:ASP292 2.6 77.3 1.0 CG A:ASP292 2.8 72.4 1.0 C A:TYR290 3.3 87.1 1.0 CG A:ASP284 3.4 77.6 1.0 CG A:ASN286 3.5 78.3 1.0 CG A:ASP288 3.5 96.0 1.0 OD2 A:ASP288 3.9 96.1 1.0 CA A:ASP284 3.9 58.0 1.0 N A:ILE285 3.9 71.5 1.0 CA A:TYR290 3.9 82.9 1.0 CB A:TYR290 4.0 85.4 1.0 N A:TYR290 4.0 74.4 1.0 N A:ASN286 4.0 69.9 1.0 CB A:ASP284 4.1 70.0 1.0 ND2 A:ASN286 4.1 92.6 1.0 OD1 A:ASP284 4.3 88.0 1.0 C A:ASP284 4.3 66.5 1.0 CB A:ASP292 4.3 64.3 1.0 N A:ALA291 4.4 70.1 1.0 C A:ALA291 4.5 72.0 1.0 N A:ASP292 4.6 63.2 1.0 N A:ASP288 4.6 87.9 1.0 CB A:ASN286 4.6 75.8 1.0 CA A:ASN286 4.7 71.3 1.0 CA A:ALA291 4.7 68.4 1.0 CB A:ASP288 4.8 86.0 1.0 C A:ASN286 4.8 84.0 1.0 O A:GLN320 4.8 81.2 1.0 O A:ALA291 4.9 79.7 1.0 N A:GLY287 4.9 90.7 1.0 CA A:ASP292 5.0 64.8 1.0 CA A:ILE285 5.0 77.1 1.0

Calcium binding site 3 out of 7 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:80.8 occ:1.00 O A:PHE355 2.3 84.3 1.0 OD1 A:ASP351 2.3 79.5 1.0 OD1 A:ASP353 2.4 94.3 1.0 OD2 A:ASP349 2.4 90.8 1.0 O A:HOH4003 2.4 97.9 1.0 OD2 A:ASP357 2.4 82.1 1.0 OD1 A:ASP357 2.5 95.9 1.0 CG A:ASP357 2.8 85.2 1.0 CG A:ASP353 3.1 94.4 1.0 CG A:ASP349 3.4 87.7 1.0 CG A:ASP351 3.4 75.9 1.0 C A:PHE355 3.5 71.2 1.0 OD2 A:ASP353 3.5 0.3 1.0 N A:ASP351 4.0 79.4 1.0 OD2 A:ASP351 4.0 89.3 1.0 N A:LEU350 4.0 85.5 1.0 OD1 A:ASP349 4.1 75.4 1.0 CA A:ASP349 4.1 79.7 1.0 N A:ASP353 4.2 74.4 1.0 C A:ASN356 4.2 73.3 1.0 CB A:ASP357 4.3 68.8 1.0 O A:ASN356 4.3 80.5 1.0 N A:PHE355 4.3 76.8 1.0 C A:ASP349 4.3 83.2 1.0 CB A:ASP353 4.3 80.5 1.0 CA A:PHE355 4.3 70.2 1.0 CB A:ASP349 4.3 89.0 1.0 N A:ASN356 4.4 59.5 1.0 N A:GLN352 4.4 91.6 1.0 CA A:ASN356 4.5 62.9 1.0 N A:ASP357 4.5 72.8 1.0 CB A:ASP351 4.6 66.9 1.0 CB A:PHE355 4.6 71.8 1.0 CA A:ASP351 4.7 70.6 1.0 C A:ASP351 4.8 85.0 1.0 CA A:ASP353 4.8 75.7 1.0 ND2 A:ASN377 4.8 77.6 1.0 N A:GLY378 4.8 73.4 1.0 CA A:ASP357 4.9 74.5 1.0 CA A:LEU350 4.9 78.0 1.0 O A:GLY378 5.0 0.5 1.0 CB A:ASN377 5.0 77.8 1.0 C A:LEU350 5.0 76.6 1.0

Calcium binding site 4 out of 7 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:78.2 occ:1.00 O A:TYR419 2.2 62.7 1.0 OD1 A:ASP415 2.3 88.4 1.0 OD1 A:ASP413 2.4 85.8 1.0 OD1 A:ASN417 2.4 85.8 1.0 O A:HOH4004 2.4 64.1 1.0 OD2 A:ASP421 2.4 84.9 1.0 OD1 A:ASP421 2.5 88.7 1.0 CG A:ASP421 2.8 82.1 1.0 CG A:ASN417 3.3 80.2 1.0 CG A:ASP415 3.4 84.8 1.0 C A:TYR419 3.4 69.0 1.0 CG A:ASP413 3.5 82.5 1.0 ND2 A:ASN417 3.8 75.6 1.0 CA A:ASP413 3.9 77.1 1.0 OD2 A:ASP415 3.9 75.2 1.0 N A:ILE414 4.1 68.1 1.0 N A:ASP415 4.1 84.5 1.0 CB A:ASP413 4.1 83.7 1.0 N A:TYR419 4.2 74.4 1.0 CA A:TYR419 4.2 77.0 1.0 C A:ASP413 4.2 73.3 1.0 CB A:ASP421 4.3 57.7 1.0 CB A:ASN417 4.3 74.9 1.0 N A:ASN417 4.3 78.1 1.0 C A:PRO420 4.3 69.4 1.0 N A:PRO420 4.4 65.3 1.0 CB A:TYR419 4.4 87.7 1.0 N A:ASP421 4.5 74.8 1.0 OD2 A:ASP413 4.5 72.8 1.0 O A:ALA437 4.6 86.1 1.0 CA A:PRO420 4.6 64.1 1.0 CB A:ASP415 4.6 75.2 1.0 N A:ALA437 4.6 75.9 1.0 O A:PRO420 4.6 62.8 1.0 N A:LYS416 4.7 86.2 1.0 CA A:ASP415 4.7 77.2 1.0 CA A:ASN417 4.8 72.2 1.0 CA A:ASP421 4.8 62.1 1.0 C A:ASP415 4.9 82.7 1.0 CB A:ALA437 5.0 72.1 1.0 N A:GLY418 5.0 81.5 1.0

Calcium binding site 5 out of 7 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2008 b:90.6 occ:1.00 O A:VAL601 2.2 87.8 1.0 OD1 A:ASP599 2.3 0.1 1.0 O A:CYS596 2.4 0.8 1.0 OE2 A:GLU636 2.4 90.2 1.0 O A:HOH4006 2.4 1.0 1.0 O A:HOH4005 2.4 94.4 1.0 OE1 A:GLU636 2.5 0.5 1.0 CD A:GLU636 2.8 93.6 1.0 CG A:ASP599 3.2 0.0 1.0 C A:CYS596 3.3 0.1 1.0 OD2 A:ASP599 3.4 0.1 1.0 C A:VAL601 3.4 90.3 1.0 CA A:GLY597 3.8 0.6 1.0 N A:GLY597 3.9 0.0 1.0 N A:VAL601 4.0 72.5 1.0 CG1 A:VAL601 4.2 85.3 1.0 CA A:VAL601 4.3 84.6 1.0 CG A:GLU636 4.3 88.6 1.0 CA A:CYS596 4.3 97.2 1.0 N A:CYS602 4.4 81.5 1.0 C A:GLY597 4.4 0.5 1.0 CA A:CYS602 4.5 88.9 1.0 N A:LYS603 4.5 85.5 1.0 CB A:ASP599 4.6 0.6 1.0 N A:ASP599 4.7 0.9 1.0 CB A:CYS596 4.8 0.3 1.0 CB A:VAL601 4.9 81.8 1.0 N A:GLU598 4.9 0.3 1.0 N A:ASN600 4.9 0.6 1.0 CG A:LYS603 4.9 0.1 1.0 CE A:LYS603 5.0 0.1 1.0 C A:CYS602 5.0 92.2 1.0

Calcium binding site 6 out of 7 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:0.5 occ:1.00 OG B:SER121 2.4 94.1 1.0 OG B:SER123 2.4 85.3 1.0 OD1 B:ASP251 2.4 68.7 1.0 OE2 B:GLU220 3.0 74.6 1.0 CG B:ASP251 3.3 75.9 1.0 CB B:SER121 3.3 81.2 1.0 OD2 B:ASP251 3.5 91.2 1.0 OD2 B:ASP119 3.6 69.8 1.0 CB B:SER123 3.7 74.2 1.0 CB B:ALA252 4.0 80.8 1.0 CD B:GLU220 4.2 75.2 1.0 CG B:ASP119 4.3 77.4 1.0 OD1 B:ASP119 4.4 81.5 1.0 CG B:MET124 4.6 72.0 1.0 CA B:SER121 4.7 61.0 1.0 C B:ASP251 4.7 67.8 1.0 N B:SER123 4.7 66.5 1.0 CB B:ASP251 4.7 61.1 1.0 N B:ALA252 4.7 64.7 1.0 CA B:SER123 4.8 68.9 1.0 OE1 B:GLU220 4.9 86.8 1.0 O B:ASP251 4.9 73.2 1.0 C B:SER121 4.9 75.6 1.0 N B:ASP251 4.9 72.2 1.0 CA B:ALA252 5.0 70.9 1.0 SD B:MET124 5.0 0.2 1.0

Calcium binding site 7 out of 7 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:86.7 occ:1.00 OD1 B:ASP127 2.3 90.7 1.0 O B:SER123 2.3 78.3 1.0 O B:HOH1033 2.4 66.2 1.0 O B:MET335 2.5 88.4 1.0 OD1 B:ASP126 2.5 1.0 1.0 CG B:ASP126 3.2 0.5 1.0 OD2 B:ASP126 3.2 0.2 1.0 CG B:ASP127 3.4 90.9 1.0 C B:SER123 3.5 67.7 1.0 C B:MET335 3.7 89.5 1.0 OD2 B:ASP127 3.8 95.2 1.0 CA B:MET124 4.0 87.9 1.0 N B:MET124 4.2 81.4 1.0 SD B:MET124 4.2 0.2 1.0 OD2 B:ASP251 4.2 91.2 1.0 CA B:MET335 4.5 96.6 1.0 N B:ASP127 4.5 94.4 1.0 CA B:SER123 4.6 68.9 1.0 CB B:ASP127 4.6 83.0 1.0 N B:ASP336 4.7 87.6 1.0 CB B:ASP126 4.7 76.6 1.0 C B:MET124 4.7 88.7 1.0 CB B:SER123 4.7 74.2 1.0 CB B:MET335 4.8 0.5 1.0 CA B:ASP336 4.8 81.0 1.0 N B:ASP126 5.0 72.0 1.0

X.Dong, L.Z.Mi, J.Zhu, W.Wang, P.Hu, B.H.Luo, T.A.Springer. Alpha V Beta 3 Integrin Crystal Structures and Their Functional Implications Biochemistry V. 51 8814 2012.
ISSN: ISSN 0006-2960
PubMed: 23106217
DOI: 10.1021/BI300734N