Calcium in PDB 5szp: Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form

The structure of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form, PDB code: 5szp was solved by K.M.Goodman, S.Mannepalli, F.Bahna, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.813, 45.549, 127.072, 90.00, 96.91, 90.00
R / Rfree (%)	25.6 / 31

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form (pdb code 5szp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form, PDB code: 5szp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:63.4 occ:1.00 OD2 A:ASP98 2.4 75.2 1.0 OD1 A:ASP61 2.4 0.5 1.0 OE1 A:GLU63 2.6 97.0 1.0 OE1 A:GLU9 2.7 86.7 1.0 OE2 A:GLU9 2.9 0.4 1.0 CD A:GLU9 3.0 99.6 1.0 OE2 A:GLU10 3.2 0.3 1.0 CE1 A:HIS99 3.3 0.7 1.0 CG A:ASP98 3.3 96.1 1.0 CG A:GLU10 3.5 0.8 1.0 OD1 A:ASP98 3.5 98.5 1.0 CG A:ASP61 3.6 0.4 1.0 CD A:GLU63 3.7 87.5 1.0 CD A:GLU10 3.8 0.1 1.0 ND1 A:HIS99 3.9 0.1 1.0 CA A:CA502 4.0 70.2 1.0 OE2 A:GLU63 4.2 84.4 1.0 CG A:GLU9 4.2 95.4 1.0 OD2 A:ASP61 4.4 0.5 1.0 NE2 A:HIS99 4.4 98.2 1.0 N A:ARG62 4.5 93.5 1.0 CA A:ASP61 4.5 0.4 1.0 CB A:ASP61 4.6 0.6 1.0 CB A:ASP98 4.7 91.5 1.0 C A:ASP61 4.9 0.4 1.0 N A:GLU63 4.9 94.7 1.0 CG A:GLU63 4.9 90.4 1.0 CB A:GLU10 4.9 0.5 1.0 OE1 A:GLU10 5.0 0.1 1.0

Calcium binding site 2 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:70.2 occ:1.00 OE2 A:GLU63 2.3 84.4 1.0 O A:VAL96 2.3 99.0 1.0 OE2 A:GLU9 2.4 0.4 1.0 OD1 A:ASP98 2.4 98.5 1.0 OD1 A:ASP131 2.6 89.6 1.0 OD1 A:ASP95 2.6 76.2 1.0 CD A:GLU63 3.2 87.5 1.0 OE1 A:GLU63 3.4 97.0 1.0 CG A:ASP98 3.5 96.1 1.0 C A:VAL96 3.5 93.1 1.0 CG A:ASP131 3.5 85.2 1.0 CD A:GLU9 3.7 99.6 1.0 CG A:ASP95 3.8 99.3 1.0 N A:VAL96 3.8 92.3 1.0 ND1 A:HIS99 3.9 0.1 1.0 NH2 A:ARG62 4.0 0.5 1.0 CA A:CA501 4.0 63.4 1.0 OD2 A:ASP98 4.0 75.2 1.0 N A:ASP98 4.2 68.2 1.0 CA A:VAL96 4.2 84.5 1.0 OD2 A:ASP131 4.3 79.0 1.0 OD2 A:ASP95 4.3 0.5 1.0 CB A:ASP131 4.3 83.6 1.0 NE A:ARG62 4.4 0.6 1.0 OE1 A:GLU9 4.4 86.7 1.0 CG A:GLU63 4.5 90.4 1.0 CA A:ASP131 4.5 90.9 1.0 CE1 A:HIS99 4.6 0.7 1.0 N A:ASN97 4.6 98.6 1.0 CG A:GLU9 4.6 95.4 1.0 CB A:VAL96 4.6 79.1 1.0 CB A:ASP98 4.7 91.5 1.0 CZ A:ARG62 4.7 0.6 1.0 N A:HIS99 4.7 69.3 1.0 C A:ASP95 4.8 0.4 1.0 CA A:ASN97 4.9 86.1 1.0 CA A:ASP98 4.9 75.9 1.0 CG A:HIS99 4.9 86.0 1.0 CA A:ASP95 5.0 1.0 1.0 CB A:ASP95 5.0 0.7 1.0

Calcium binding site 3 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:73.8 occ:1.00 OD1 A:ASN97 2.5 0.7 1.0 O A:HIS99 2.5 66.3 1.0 OD2 A:ASP131 2.5 79.0 1.0 OD2 A:ASP186 2.5 68.7 1.0 OD2 A:ASP129 2.5 95.6 1.0 O A:ASN135 2.6 0.2 1.0 OD1 A:ASP129 2.8 98.3 1.0 CG A:ASP129 3.0 97.2 1.0 CG A:ASP131 3.4 85.2 1.0 CG A:ASP186 3.5 76.0 1.0 CG A:ASN97 3.6 0.1 1.0 C A:HIS99 3.7 69.8 1.0 CB A:ASP131 3.8 83.6 1.0 CB A:ASP186 3.8 74.0 1.0 C A:ASN135 3.8 0.9 1.0 CD A:PRO101 4.1 81.5 1.0 ND2 A:ASN97 4.3 0.5 1.0 CA A:ALA100 4.3 64.3 1.0 N A:ALA100 4.5 78.5 1.0 CB A:ASP129 4.5 99.1 1.0 OD1 A:ASP131 4.5 89.6 1.0 N A:PRO101 4.6 79.0 1.0 CB A:ASN135 4.6 0.5 1.0 CA A:ASN135 4.6 0.7 1.0 OD1 A:ASP186 4.6 87.9 1.0 C A:ALA100 4.7 71.9 1.0 CB A:ASN97 4.7 87.9 1.0 N A:SER136 4.7 0.8 1.0 CA A:HIS99 4.7 61.9 1.0 CA A:SER136 4.8 0.2 1.0 CA A:ASN97 4.8 86.1 1.0 N A:HIS99 4.8 69.3 1.0 C A:SER136 5.0 0.4 1.0 CA A:ASP131 5.0 90.9 1.0 N A:ASP131 5.0 90.5 1.0

Calcium binding site 4 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.4 occ:1.00 OE2 A:GLU114 2.4 43.7 1.0 OD2 A:ASP207 2.5 72.6 1.0 OE1 A:GLU173 2.5 73.5 1.0 OD1 A:ASP171 2.6 86.2 1.0 CG A:ASP207 3.2 73.2 1.0 OD1 A:ASP207 3.3 84.7 1.0 OD1 A:ASN208 3.4 98.0 1.0 CD A:GLU173 3.4 74.5 1.0 CG A:ASP171 3.4 98.6 1.0 CD A:GLU114 3.5 56.0 1.0 OD2 A:ASP171 3.8 0.6 1.0 CA A:CA505 3.9 60.2 1.0 OE1 A:GLU114 3.9 55.0 1.0 CG A:GLU173 4.1 84.6 1.0 CB A:GLU173 4.1 84.3 1.0 CG A:ASN208 4.1 83.3 1.0 OE2 A:GLU173 4.2 73.0 1.0 ND2 A:ASN208 4.3 82.8 1.0 CB A:ASP171 4.6 85.1 1.0 N A:GLU173 4.6 80.8 1.0 CB A:ASP207 4.6 65.9 1.0 CA A:ASP171 4.7 63.7 1.0 CG A:GLU114 4.7 58.1 1.0 N A:ARG172 4.9 34.8 1.0

Calcium binding site 5 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:60.2 occ:1.00 OE2 A:GLU173 2.5 73.0 1.0 OE1 A:GLU114 2.5 55.0 1.0 OD1 A:ASP204 2.5 68.3 1.0 OD1 A:ASP207 2.5 84.7 1.0 O A:ALA205 2.5 98.0 1.0 OD1 A:ASP240 2.7 61.5 1.0 OE1 A:GLU173 2.9 73.5 1.0 CD A:GLU173 3.0 74.5 1.0 CD A:GLU114 3.4 56.0 1.0 CG A:ASP207 3.5 73.2 1.0 C A:ALA205 3.6 89.3 1.0 N A:ALA205 3.6 78.2 1.0 OE2 A:GLU114 3.7 43.7 1.0 CG A:ASP240 3.7 64.2 1.0 CG A:ASP204 3.7 89.7 1.0 CA A:CA504 3.9 0.4 1.0 NH2 A:ARG172 3.9 91.5 1.0 OD2 A:ASP207 4.0 72.6 1.0 CA A:ALA205 4.2 84.6 1.0 NE A:ARG172 4.3 81.6 1.0 N A:ASP207 4.4 46.2 1.0 OD2 A:ASP204 4.4 0.3 1.0 CB A:ASP240 4.4 47.1 1.0 CG A:GLU173 4.5 84.6 1.0 OD2 A:ASP240 4.5 85.2 1.0 CA A:ASP240 4.6 47.8 1.0 CA A:ASP204 4.6 73.8 1.0 C A:ASP204 4.6 61.7 1.0 CZ A:ARG172 4.6 87.6 1.0 OD1 A:ASN208 4.7 98.0 1.0 CB A:ASP204 4.7 84.6 1.0 CB A:ALA205 4.7 81.6 1.0 CB A:ASP207 4.7 65.9 1.0 N A:ASN206 4.8 83.2 1.0 CG A:GLU114 4.8 58.1 1.0 CG A:ASN208 4.9 83.3 1.0

Calcium binding site 6 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:53.4 occ:1.00 O A:ASN208 2.4 69.4 1.0 OD2 A:ASP238 2.4 57.1 1.0 O A:ASN244 2.4 47.0 1.0 OD1 A:ASN206 2.6 99.6 1.0 OD2 A:ASP240 2.6 85.2 1.0 OD1 A:ASP238 2.6 58.3 1.0 OD2 A:ASP291 2.8 0.8 1.0 CG A:ASP238 2.9 56.4 1.0 CG A:ASP240 3.6 64.2 1.0 C A:ASN208 3.6 67.9 1.0 C A:ASN244 3.7 67.0 1.0 CG A:ASN206 3.7 0.5 1.0 CG A:ASP291 3.8 0.6 1.0 CB A:ASP240 3.9 47.1 1.0 CB A:ASP291 4.2 0.7 1.0 CB A:ASP238 4.3 62.3 1.0 ND2 A:ASN206 4.4 0.6 1.0 N A:ASN208 4.4 58.3 1.0 CA A:ASN208 4.5 70.9 1.0 CD A:PRO210 4.5 59.3 1.0 CA A:ALA245 4.5 67.5 1.0 N A:ARG209 4.5 52.0 1.0 CD1 A:LEU295 4.5 66.4 1.0 N A:ALA245 4.5 63.0 1.0 CA A:ARG209 4.5 49.0 1.0 CA A:ASN244 4.6 79.4 1.0 OD1 A:ASP240 4.6 61.5 1.0 CB A:ASN244 4.6 94.9 1.0 CB A:ASN208 4.7 71.2 1.0 N A:PRO210 4.8 61.0 1.0 C A:ARG209 4.8 53.5 1.0 CB A:ASN206 4.9 97.6 1.0 CA A:ASN206 4.9 87.1 1.0 OD1 A:ASP291 4.9 0.5 1.0 CB A:LEU295 5.0 64.5 1.0

Calcium binding site 7 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:83.5 occ:1.00 OD2 A:ASP310 2.4 0.7 1.0 OD1 A:ASP276 2.5 67.9 1.0 OE1 A:GLU278 2.5 52.2 1.0 OE1 A:GLU223 2.5 0.5 1.0 OD1 A:ASP310 2.8 97.8 1.0 CG A:ASP310 3.0 0.8 1.0 CD A:GLU223 3.1 0.9 1.0 CA A:CA508 3.1 54.8 1.0 OE2 A:GLU223 3.2 0.6 1.0 CD A:GLU278 3.5 69.5 1.0 CG A:ASP276 3.7 80.3 1.0 OE2 A:GLU278 3.9 51.9 1.0 ND2 A:ASN311 4.1 0.1 1.0 N A:PHE277 4.3 53.2 1.0 CG A:GLU223 4.3 89.5 1.0 OD2 A:ASP276 4.4 88.9 1.0 OD1 A:ASN311 4.5 98.6 1.0 CB A:ASP310 4.5 0.0 1.0 CA A:ASP276 4.5 70.6 1.0 CG A:ASN311 4.6 98.0 1.0 CB A:ASP276 4.6 78.1 1.0 OD1 A:ASP343 4.7 0.8 1.0 O A:GLU308 4.8 88.2 1.0 N A:GLU278 4.8 81.5 1.0 CG A:GLU278 4.8 89.3 1.0 C A:ASP276 4.8 68.3 1.0 CB A:GLU223 5.0 81.3 1.0

Calcium binding site 8 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:54.8 occ:1.00 OD1 A:ASP343 2.4 0.8 1.0 OE2 A:GLU278 2.4 51.9 1.0 OE2 A:GLU223 2.5 0.6 1.0 O A:GLU308 2.5 88.2 1.0 OD1 A:ASP310 2.5 97.8 1.0 OD1 A:ASP307 2.6 76.6 1.0 CA A:CA507 3.1 83.5 1.0 CD A:GLU278 3.2 69.5 1.0 OE1 A:GLU278 3.2 52.2 1.0 CG A:ASP343 3.2 0.5 1.0 CD A:GLU223 3.4 0.9 1.0 CG A:ASP310 3.6 0.8 1.0 OE1 A:GLU223 3.7 0.5 1.0 C A:GLU308 3.7 93.1 1.0 CG A:ASP307 3.7 89.4 1.0 OD2 A:ASP343 3.9 0.9 1.0 N A:GLU308 4.0 0.4 1.0 CB A:ASP343 4.1 82.0 1.0 OD2 A:ASP310 4.2 0.7 1.0 N A:ASP310 4.3 97.9 1.0 OD2 A:ASP307 4.3 0.3 1.0 CA A:ASP343 4.3 75.1 1.0 ND2 A:ASN311 4.3 0.1 1.0 CA A:GLU308 4.5 0.4 1.0 CG A:GLU278 4.6 89.3 1.0 CB A:PHE277 4.7 56.6 1.0 N A:ASN309 4.7 0.2 1.0 CG A:GLU223 4.8 89.5 1.0 CG A:ASN311 4.8 98.0 1.0 CB A:ASP310 4.8 0.0 1.0 C A:ASP307 4.8 0.1 1.0 CA A:ASP307 4.9 99.1 1.0 CB A:ASP307 4.9 93.2 1.0 CA A:ASN309 4.9 0.6 1.0 N A:ASN311 4.9 93.5 1.0 CA A:ASP310 5.0 0.5 1.0

Calcium binding site 9 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:80.3 occ:1.00 OD2 A:ASP394 2.3 0.9 1.0 O A:ASN311 2.3 78.2 1.0 OD2 A:ASP343 2.4 0.9 1.0 OD2 A:ASP341 2.4 0.1 1.0 OD1 A:ASP341 2.4 0.0 1.0 CG A:ASP341 2.8 0.6 1.0 OD1 A:ASN309 2.8 0.3 1.0 O A:ASN347 3.0 76.0 1.0 CG A:ASP343 3.0 0.5 1.0 CB A:ASP343 3.4 82.0 1.0 CG A:ASP394 3.5 0.7 1.0 C A:ASN311 3.5 92.9 1.0 CG A:ASN309 3.9 0.9 1.0 OD1 A:ASP343 4.1 0.8 1.0 C A:ASN347 4.1 91.9 1.0 OD1 A:ASP394 4.2 0.1 1.0 CB A:ASP341 4.3 97.3 1.0 N A:ASN311 4.3 93.5 1.0 CA A:ASN311 4.3 87.5 1.0 N A:ASP343 4.3 84.6 1.0 CB A:ASN311 4.4 81.7 1.0 CA A:ASP343 4.5 75.1 1.0 N A:ARG312 4.6 99.3 1.0 CB A:ASP394 4.6 0.8 1.0 ND2 A:ASN309 4.6 0.1 1.0 CA A:ARG312 4.7 78.4 1.0 CD A:PRO313 4.7 66.5 1.0 CA A:ASN309 4.7 0.6 1.0 N A:PRO313 4.8 70.1 1.0 C A:ARG312 4.8 68.2 1.0 CB A:ASN347 4.8 97.2 1.0 CB A:ASN309 4.8 0.2 1.0 CA A:ASN347 4.9 99.0 1.0

Calcium binding site 10 out of 18 in the Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Protocadherin Gamma B7 Extracellular Cadherin Domains 1-4 P21 Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:0.5 occ:1.00 OD2 B:ASP98 2.5 0.6 1.0 OD1 B:ASP61 2.5 0.1 1.0 OE1 B:GLU63 2.7 80.7 1.0 OE1 B:GLU9 2.7 83.6 1.0 OE2 B:GLU9 2.9 0.7 1.0 CD B:GLU9 3.0 89.2 1.0 OE2 B:GLU10 3.0 0.3 1.0 CG B:ASP98 3.2 0.5 1.0 OD1 B:ASP98 3.2 0.7 1.0 CG B:GLU10 3.3 0.2 1.0 CA B:CA502 3.4 68.8 1.0 CD B:GLU10 3.5 0.8 1.0 CG B:ASP61 3.7 0.7 1.0 CD B:GLU63 3.7 90.3 1.0 NE2 B:HIS99 4.0 0.8 1.0 OE2 B:GLU63 4.1 80.5 1.0 CE1 B:HIS99 4.1 0.1 1.0 CG B:GLU9 4.2 74.5 1.0 OD2 B:ASP61 4.4 0.7 1.0 NH1 B:ARG59 4.5 0.1 1.0 CA B:ASP61 4.5 0.3 1.0 N B:ARG62 4.6 0.2 1.0 CG2 B:VAL96 4.6 90.9 1.0 CB B:ASP61 4.6 0.9 1.0 CB B:ASP98 4.6 0.0 1.0 CD2 B:HIS99 4.7 0.8 1.0 ND1 B:HIS99 4.7 0.2 1.0 OE1 B:GLU10 4.7 0.0 1.0 CB B:GLU10 4.8 0.6 1.0 C B:ASP61 5.0 1.0 1.0

K.M.Goodman, R.Rubinstein, C.A.Thu, S.Mannepalli, F.Bahna, G.Ahlsen, C.Rittenhouse, T.Maniatis, B.Honig, L.Shapiro. Gamma-Protocadherin Structural Diversity and Functional Implications. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27782885
DOI: 10.7554/ELIFE.20930