Calcium in PDB 4wk4: Metal Ion and Ligand Binding of Integrin

The structure of Metal Ion and Ligand Binding of Integrin, PDB code: 4wk4 was solved by W.Xia, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.60 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.520, 112.160, 169.540, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.6

The structure of Metal Ion and Ligand Binding of Integrin also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Metal Ion and Ligand Binding of Integrin (pdb code 4wk4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Metal Ion and Ligand Binding of Integrin, PDB code: 4wk4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metal Ion and Ligand Binding of Integrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:68.6 occ:1.00 O A:HOH606 2.3 50.7 1.0 O A:THR245 2.3 83.4 1.0 OD1 A:ASP247 2.3 66.2 1.0 OD1 A:ASP243 2.4 91.1 1.0 OG A:SER241 2.4 68.9 1.0 OE2 A:GLU239 2.4 82.4 1.0 OE1 A:GLU239 2.5 82.9 1.0 OD2 A:ASP247 2.5 61.1 1.0 CG A:ASP247 2.7 61.7 1.0 CD A:GLU239 2.8 80.5 1.0 HB3 A:SER241 3.1 81.2 1.0 H A:SER241 3.2 88.1 1.0 CG A:ASP243 3.3 92.0 1.0 CB A:SER241 3.3 67.7 1.0 C A:THR245 3.5 81.8 1.0 OD2 A:ASP243 3.5 93.0 1.0 H A:PHE240 3.7 86.3 1.0 H A:ASP243 3.8 0.4 1.0 HA A:GLU239 3.8 80.5 1.0 N A:SER241 3.9 73.5 1.0 H A:THR245 3.9 0.8 1.0 HB A:THR245 4.0 98.2 1.0 H A:GLY267 4.0 82.4 1.0 HA A:GLU246 4.0 90.5 1.0 HB2 A:SER241 4.0 81.2 1.0 CA A:SER241 4.0 70.9 1.0 CB A:ASP247 4.1 56.9 1.0 N A:ASP247 4.2 62.8 1.0 C A:GLU246 4.2 69.0 1.0 CG A:GLU239 4.3 74.8 1.0 H A:ASP247 4.3 75.4 1.0 N A:THR245 4.4 93.1 1.0 CA A:THR245 4.4 85.4 1.0 N A:GLU246 4.4 78.4 1.0 CA A:GLU246 4.4 75.4 1.0 N A:PHE240 4.5 71.9 1.0 C A:SER241 4.5 74.4 1.0 N A:ASP243 4.5 84.5 1.0 H A:GLY242 4.6 89.0 1.0 HB2 A:ASP247 4.6 68.3 1.0 HA A:ASP247 4.6 74.3 1.0 CA A:ASP247 4.6 61.9 1.0 HG3 A:GLU239 4.6 89.8 1.0 CB A:ASP243 4.6 90.9 1.0 O A:GLU246 4.6 69.3 1.0 CB A:THR245 4.6 81.8 1.0 HB3 A:ASP247 4.7 68.3 1.0 CA A:GLU239 4.7 67.1 1.0 O A:HOH620 4.7 75.6 1.0 N A:GLY242 4.7 74.1 1.0 HA3 A:GLY267 4.7 84.3 1.0 HG2 A:GLU239 4.8 89.8 1.0 OD1 A:ASN266 4.8 81.3 1.0 N A:GLY267 4.8 68.6 1.0 HG22 A:THR245 4.9 91.9 1.0 C A:ASP243 4.9 92.3 1.0 HA A:SER241 4.9 85.1 1.0 CB A:GLU239 4.9 68.9 1.0 CA A:ASP243 4.9 89.3 1.0

Calcium binding site 2 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metal Ion and Ligand Binding of Integrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:67.1 occ:1.00 OD1 A:ASN295 2.3 75.5 1.0 OD1 A:ASP297 2.4 96.5 1.0 OD1 A:ASP293 2.4 82.9 1.0 O A:LEU299 2.4 77.8 1.0 O A:HOH632 2.4 75.6 1.0 OD2 A:ASP301 2.4 74.4 1.0 OD1 A:ASP301 2.4 74.7 1.0 CG A:ASP301 2.7 71.5 1.0 CG A:ASP297 3.3 95.8 1.0 HA A:ASP293 3.3 85.5 1.0 CG A:ASP293 3.4 79.9 1.0 CG A:ASN295 3.4 75.9 1.0 HB2 A:LEU299 3.5 92.7 1.0 OD2 A:ASP297 3.5 97.1 1.0 HD21 A:ASN295 3.5 92.9 1.0 C A:LEU299 3.6 77.9 1.0 H A:VAL294 3.7 90.2 1.0 H A:ASN295 3.7 95.9 1.0 H A:LEU299 3.8 95.7 1.0 HB2 A:ASP293 3.9 88.9 1.0 ND2 A:ASN295 3.9 77.4 1.0 HD22 A:LEU328 3.9 81.7 1.0 CB A:ASP293 4.0 74.1 1.0 CA A:ASP293 4.0 71.3 1.0 H A:ASP297 4.1 0.8 1.0 H A:GLN329 4.2 81.2 1.0 CB A:ASP301 4.2 64.5 1.0 CA A:LEU299 4.2 79.0 1.0 CB A:LEU299 4.3 77.2 1.0 N A:VAL294 4.3 75.2 1.0 N A:LEU299 4.3 79.8 1.0 OD2 A:ASP293 4.4 82.2 1.0 N A:ASN295 4.4 79.9 1.0 N A:ASP301 4.5 63.5 1.0 C A:ASP293 4.5 74.7 1.0 O A:GLN329 4.6 80.4 1.0 H A:ASP301 4.6 76.2 1.0 HB2 A:ASP301 4.6 77.3 1.0 C A:ASP300 4.6 70.8 1.0 HB3 A:GLN329 4.6 78.5 1.0 HA A:ASP300 4.6 93.7 1.0 N A:ASP300 4.6 78.5 1.0 CB A:ASP297 4.7 92.2 1.0 HB3 A:LEU299 4.7 92.7 1.0 CB A:ASN295 4.7 77.6 1.0 HB3 A:LEU328 4.7 88.0 1.0 HD22 A:ASN295 4.7 92.9 1.0 HB3 A:ASP301 4.8 77.3 1.0 HG22 A:VAL294 4.8 95.9 1.0 N A:ASP297 4.8 87.3 1.0 CD2 A:LEU328 4.8 68.0 1.0 HB3 A:ASP297 4.8 0.7 1.0 CA A:ASP301 4.9 61.6 1.0 CA A:ASP300 4.9 78.1 1.0 HA A:ASP301 4.9 73.9 1.0 N A:GLN329 4.9 67.6 1.0 HB3 A:ASP293 4.9 88.9 1.0 HA A:LEU328 4.9 85.4 1.0 HD23 A:LEU328 5.0 81.7 1.0 H A:GLY298 5.0 97.2 1.0 O A:ASP300 5.0 71.8 1.0 CA A:ASN295 5.0 81.0 1.0

Calcium binding site 3 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Metal Ion and Ligand Binding of Integrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.1 occ:1.00 O A:TYR366 2.3 92.5 1.0 OD1 A:ASP362 2.3 0.8 1.0 OD1 A:ASP360 2.4 0.7 1.0 OD2 A:ASP368 2.4 0.3 1.0 OD1 A:ASP364 2.4 0.9 1.0 OD1 A:ASP368 2.4 0.8 1.0 O A:HOH618 2.5 66.9 1.0 CG A:ASP368 2.7 0.6 1.0 H A:ASP362 3.2 1.0 1.0 CG A:ASP362 3.3 0.4 1.0 CG A:ASP364 3.3 0.6 1.0 HA A:ASP360 3.4 1.0 1.0 C A:TYR366 3.5 89.0 1.0 H A:LEU361 3.5 0.9 1.0 OD2 A:ASP362 3.6 0.1 1.0 CG A:ASP360 3.6 0.9 1.0 OD2 A:ASP364 3.7 0.6 1.0 HB2 A:TYR366 3.7 0.1 1.0 H A:TYR366 3.8 0.4 1.0 H A:ASP364 3.8 0.0 1.0 N A:LEU361 4.0 0.6 1.0 H A:GLY389 4.0 0.1 1.0 N A:ASP362 4.1 0.1 1.0 CA A:ASP360 4.2 95.8 1.0 CB A:ASP368 4.2 91.8 1.0 CA A:TYR366 4.3 93.4 1.0 HB3 A:LEU361 4.3 0.6 1.0 HA A:ASN367 4.3 92.6 1.0 C A:ASN367 4.3 78.9 1.0 CB A:TYR366 4.3 91.7 1.0 C A:ASP360 4.4 99.1 1.0 N A:TYR366 4.4 99.5 1.0 OD2 A:ASP360 4.5 0.2 1.0 N A:ASP368 4.5 80.8 1.0 N A:ASN367 4.5 80.7 1.0 H A:GLN363 4.5 0.1 1.0 HB2 A:ASP368 4.5 0.2 1.0 CB A:ASP360 4.5 0.8 1.0 O A:ASN367 4.5 79.0 1.0 HB3 A:TYR366 4.6 0.1 1.0 CB A:ASP362 4.6 0.2 1.0 HA A:PRO388 4.6 98.2 1.0 CB A:ASP364 4.6 0.6 1.0 CA A:ASN367 4.6 77.1 1.0 N A:ASP364 4.6 0.2 1.0 O A:GLY389 4.7 85.7 1.0 H A:ASP368 4.7 96.9 1.0 HB3 A:ASP364 4.7 0.3 1.0 HB3 A:ASP368 4.7 0.2 1.0 N A:GLY389 4.7 85.1 1.0 CA A:ASP362 4.8 0.8 1.0 CA A:ASP368 4.8 80.5 1.0 N A:GLN363 4.9 0.9 1.0 CA A:LEU361 4.9 0.6 1.0 HA A:ASP368 4.9 96.7 1.0 HB3 A:ASP362 5.0 0.1 1.0

Calcium binding site 4 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Metal Ion and Ligand Binding of Integrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.8 occ:1.00 O A:TYR430 2.3 85.3 1.0 OD1 A:ASP424 2.3 96.5 1.0 OD1 A:ASP426 2.3 0.6 1.0 OD1 A:ASP432 2.4 0.4 1.0 OD1 A:ASN428 2.4 0.3 1.0 O A:HOH633 2.4 0.4 1.0 OD2 A:ASP432 2.4 1.0 1.0 CG A:ASP432 2.7 0.0 1.0 CG A:ASP426 3.2 0.7 1.0 CG A:ASN428 3.4 0.2 1.0 OD2 A:ASP426 3.4 0.6 1.0 CG A:ASP424 3.4 0.5 1.0 C A:TYR430 3.5 85.5 1.0 HA A:ASP424 3.5 0.4 1.0 H A:TYR430 3.7 0.9 1.0 H A:GLY448 3.7 0.7 1.0 HG3 A:ARG447 3.7 0.3 1.0 HD21 A:ASN428 3.7 1.0 1.0 H A:ASN428 3.7 1.0 1.0 HB2 A:TYR430 3.8 0.4 1.0 H A:ASP426 3.8 0.6 1.0 HG2 A:ARG447 3.9 0.3 1.0 ND2 A:ASN428 4.0 1.0 1.0 H A:GLY427 4.0 0.3 1.0 CB A:ASP432 4.2 94.3 1.0 C A:PRO431 4.2 81.0 1.0 O A:PRO431 4.2 82.7 1.0 OD2 A:ASP424 4.3 0.5 1.0 H A:LEU425 4.3 0.3 1.0 CG A:ARG447 4.3 0.4 1.0 CA A:ASP424 4.3 0.6 1.0 CB A:ASP424 4.3 0.2 1.0 CA A:TYR430 4.3 93.7 1.0 N A:TYR430 4.3 99.1 1.0 HB2 A:ASP424 4.4 0.4 1.0 HA A:PRO431 4.4 94.8 1.0 CB A:TYR430 4.4 98.6 1.0 N A:PRO431 4.4 79.4 1.0 N A:GLY448 4.4 98.0 1.0 N A:ASP432 4.5 81.8 1.0 CB A:ASP426 4.5 1.0 1.0 HB2 A:ASP432 4.5 0.1 1.0 N A:ASN428 4.5 0.5 1.0 HA A:ARG447 4.6 0.6 1.0 CA A:PRO431 4.6 79.0 1.0 HB3 A:TYR430 4.6 0.4 1.0 HB3 A:ASP426 4.6 0.4 1.0 N A:ASP426 4.6 0.3 1.0 CB A:ASN428 4.6 0.3 1.0 O A:GLY448 4.6 0.5 1.0 HB3 A:ASN428 4.6 0.4 1.0 N A:LEU425 4.6 0.6 1.0 HA A:ASP432 4.7 0.9 1.0 HG A:LEU425 4.7 0.1 1.0 HB3 A:ASP432 4.7 0.1 1.0 N A:GLY427 4.7 0.1 1.0 CA A:ASP432 4.7 84.1 1.0 C A:ASP424 4.7 0.1 1.0 HD22 A:ASN428 4.8 1.0 1.0 HA3 A:GLY448 4.8 0.7 1.0 H A:ASP432 4.8 98.2 1.0 HD2 A:ARG447 4.9 0.1 1.0

Calcium binding site 5 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Metal Ion and Ligand Binding of Integrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:0.1 occ:1.00 OD1 B:ASP138 2.4 0.2 1.0 OD1 B:ASP137 2.4 0.5 1.0 O B:SER134 2.4 91.4 1.0 HA B:MET135 2.7 0.3 1.0 O B:HOH622 2.9 55.3 1.0 CG B:ASP137 3.4 1.0 1.0 C B:SER134 3.5 89.0 1.0 CA B:MET135 3.6 83.6 1.0 CG B:ASP138 3.6 0.0 1.0 OD2 B:ASP137 3.8 0.2 1.0 H B:ASP138 3.8 0.7 1.0 OD2 B:ASP259 3.9 79.3 1.0 H B:ASP137 3.9 0.4 1.0 H B:LYS136 4.0 0.4 1.0 N B:MET135 4.0 86.7 1.0 C B:MET135 4.1 85.1 1.0 N B:LYS136 4.2 92.0 1.0 O B:ALA342 4.3 0.1 1.0 OD2 B:ASP138 4.4 0.3 1.0 HB2 B:ASP138 4.4 0.4 1.0 N B:ASP138 4.4 0.1 1.0 N B:ASP137 4.5 0.7 1.0 SD B:MET135 4.6 93.6 1.0 CB B:ASP138 4.6 0.0 1.0 HB3 B:ASP259 4.7 89.4 1.0 CG B:ASP259 4.8 76.2 1.0 CB B:MET135 4.8 79.7 1.0 CB B:ASP137 4.8 0.1 1.0 CA B:SER134 4.8 89.1 1.0 HA B:SER134 4.8 0.9 1.0 HG2 B:MET135 4.8 90.9 1.0 H B:MET135 4.8 0.0 1.0 HB2 B:SER134 4.8 0.8 1.0 O B:MET135 4.9 81.5 1.0 HB3 B:MET135 5.0 95.7 1.0 CG B:MET135 5.0 75.8 1.0

Calcium binding site 6 out of 6 in the Metal Ion and Ligand Binding of Integrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Metal Ion and Ligand Binding of Integrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:66.0 occ:1.00 OD1 B:ASP226 2.3 80.6 1.0 OD1 B:ASN224 2.3 64.8 1.0 O B:PRO228 2.4 68.5 1.0 OE2 B:GLU229 2.4 63.4 1.0 OE1 B:GLU169 2.4 69.4 1.0 O B:ASP226 2.4 64.2 1.0 HA B:GLU229 2.8 71.2 1.0 CG B:ASN224 3.3 67.0 1.0 CG B:ASP226 3.3 78.2 1.0 CD B:GLU229 3.3 65.1 1.0 HD21 B:ASN224 3.3 82.0 1.0 C B:PRO228 3.4 64.1 1.0 C B:ASP226 3.4 66.0 1.0 CD B:GLU169 3.5 70.9 1.0 HG2 B:GLU169 3.6 84.4 1.0 CA B:GLU229 3.7 59.4 1.0 ND2 B:ASN224 3.7 68.3 1.0 HB2 B:GLU169 3.8 82.0 1.0 H B:ASP226 3.9 82.3 1.0 N B:GLU229 3.9 58.5 1.0 CG B:GLU169 4.0 70.3 1.0 HD2 B:HIS263 4.0 70.0 1.0 OE1 B:GLU229 4.0 64.5 1.0 CA B:ASP226 4.1 70.5 1.0 N B:ASP226 4.1 68.6 1.0 OD2 B:ASP226 4.1 77.8 1.0 O B:SER227 4.2 61.6 1.0 CB B:ASP226 4.2 74.9 1.0 C B:SER227 4.2 63.2 1.0 NE2 B:HIS263 4.2 64.2 1.0 CG B:GLU229 4.3 65.3 1.0 CB B:GLU229 4.3 62.5 1.0 HB2 B:ASP226 4.4 89.9 1.0 HB3 B:GLU229 4.4 75.1 1.0 CB B:GLU169 4.4 68.3 1.0 N B:PRO228 4.4 67.7 1.0 HG2 B:GLU229 4.4 78.4 1.0 CD2 B:HIS263 4.4 58.3 1.0 N B:SER227 4.4 63.6 1.0 HB3 B:TYR175 4.5 73.9 1.0 CA B:PRO228 4.5 66.9 1.0 OE2 B:GLU169 4.6 72.4 1.0 HD22 B:ASN224 4.6 82.0 1.0 CB B:ASN224 4.7 67.7 1.0 HB2 B:ASN224 4.7 81.2 1.0 HB2 C:ASP5 4.7 83.2 1.0 C B:GLU229 4.7 57.7 1.0 H B:LEU225 4.7 89.3 1.0 H B:GLU229 4.8 70.2 1.0 HG2 B:PRO228 4.8 81.7 1.0 CA B:SER227 4.8 63.0 1.0 H B:GLY230 4.8 65.7 1.0 HD2 B:PRO228 4.9 84.3 1.0 HA B:SER227 4.9 75.5 1.0 HG3 B:GLU169 4.9 84.4 1.0 C B:LEU225 4.9 72.7 1.0 HB3 B:GLU169 5.0 82.0 1.0

W.Xia, T.A.Springer. Metal Ion and Ligand Binding of Integrin ALPHA5BETA1 at High Resolution To Be Published.