Calcium in PDB 6e6b: Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain

The structure of Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain, PDB code: 6e6b 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)	38.29 / 4.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	127.730, 87.580, 149.330, 90.00, 109.94, 90.00
R / Rfree (%)	23.1 / 27.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain (pdb code 6e6b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 30 binding sites of Calcium where determined in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain, PDB code: 6e6b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:0.8 occ:1.00 OE2 A:GLU10 2.4 0.8 1.0 OE1 A:GLU9 2.7 0.5 1.0 OD2 A:ASP98 2.8 0.5 1.0 OE1 A:GLU63 3.0 0.1 1.0 CD A:GLU9 3.1 0.9 1.0 OD1 A:ASP61 3.1 1.0 1.0 CD A:GLU10 3.2 0.1 1.0 CG A:GLU10 3.2 0.1 1.0 OE2 A:GLU9 3.3 0.3 1.0 CG A:ASP98 3.8 0.2 1.0 CD A:GLU63 4.0 0.5 1.0 OD1 A:ASP98 4.1 1.0 1.0 CA A:CA702 4.1 0.3 1.0 CG A:GLU9 4.2 0.0 1.0 CG A:ASP61 4.3 0.8 1.0 OE2 A:GLU63 4.3 0.2 1.0 OE1 A:GLU10 4.4 0.4 1.0 NH2 A:ARG59 4.5 0.8 1.0 CE1 A:HIS99 4.5 0.9 1.0 N A:ARG62 4.6 0.4 1.0 CB A:GLU10 4.7 0.7 1.0 CA A:ASP61 4.8 0.3 1.0 ND1 A:HIS99 4.9 0.9 1.0 CB A:GLU9 5.0 0.0 1.0

Calcium binding site 2 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:0.3 occ:1.00 OE2 A:GLU63 2.3 0.2 1.0 OD1 A:ASP95 2.5 0.2 1.0 O A:ILE96 2.6 0.5 1.0 OD1 A:ASP131 2.6 0.4 1.0 OE2 A:GLU9 2.9 0.3 1.0 OD1 A:ASP98 2.9 1.0 1.0 CD A:GLU63 3.3 0.5 1.0 CG A:ASP95 3.6 0.8 1.0 OE1 A:GLU63 3.7 0.1 1.0 CG A:ASP131 3.7 0.3 1.0 C A:ILE96 3.8 0.2 1.0 CG A:ASP98 3.9 0.2 1.0 N A:ILE96 4.0 0.9 1.0 OD2 A:ASP95 4.0 0.1 1.0 CD A:GLU9 4.0 0.9 1.0 CA A:CA701 4.1 0.8 1.0 OD2 A:ASP98 4.2 0.5 1.0 ND1 A:HIS99 4.2 0.9 1.0 CA A:ASP131 4.3 0.4 1.0 CA A:ILE96 4.4 0.0 1.0 CB A:ASP131 4.4 0.1 1.0 CG A:GLU63 4.5 0.2 1.0 N A:ASP98 4.6 0.7 1.0 OE1 A:GLU9 4.6 0.5 1.0 OD2 A:ASP131 4.7 0.2 1.0 N A:ASP131 4.7 0.4 1.0 CB A:ILE96 4.8 0.6 1.0 O A:ALA130 4.8 0.5 1.0 C A:ASP95 4.8 0.3 1.0 CB A:ASP95 4.9 0.2 1.0 N A:ASN97 4.9 0.3 1.0 C A:ALA130 4.9 0.9 1.0 CE1 A:HIS99 4.9 0.9 1.0 CA A:ASP95 5.0 0.0 1.0

Calcium binding site 3 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:0.6 occ:1.00 OD1 A:ASN97 2.5 1.0 1.0 O A:HIS99 2.9 0.4 1.0 OD2 A:ASP129 2.9 0.7 1.0 O A:ASN135 3.0 0.8 1.0 OD2 A:ASP186 3.1 0.8 1.0 OD1 A:ASP129 3.1 0.2 1.0 OD2 A:ASP131 3.1 0.2 1.0 CD A:PRO101 3.3 0.7 1.0 CG A:ASP129 3.4 0.4 1.0 CG A:ASN97 3.5 0.8 1.0 CG A:ASP186 3.8 0.0 1.0 CA A:THR100 3.8 0.9 1.0 C A:HIS99 3.9 0.6 1.0 ND2 A:ASN97 3.9 0.9 1.0 N A:PRO101 3.9 0.6 1.0 CB A:ASP186 4.0 0.6 1.0 CG A:ASP131 4.1 0.3 1.0 C A:THR100 4.2 0.5 1.0 C A:ASN135 4.2 0.3 1.0 N A:THR100 4.3 1.0 1.0 CG A:PRO101 4.5 0.1 1.0 CB A:ASP131 4.5 0.1 1.0 OD1 A:ASP186 4.7 0.6 1.0 CB A:ASN97 4.8 0.9 1.0 CB A:ASP129 4.9 0.5 1.0 CB A:THR100 4.9 0.7 1.0 CA A:ASN135 5.0 0.6 1.0

Calcium binding site 4 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:0.7 occ:1.00 OD2 A:ASP207 2.3 0.7 1.0 OE2 A:GLU114 2.4 0.9 1.0 OD1 A:ASP171 2.7 0.6 1.0 CG A:ASP207 3.2 0.2 1.0 OE1 A:GLU173 3.5 0.7 1.0 CD A:GLU114 3.6 0.1 1.0 CG A:ASP171 3.6 0.6 1.0 OD1 A:ASP207 3.8 0.8 1.0 OD2 A:ASP171 4.0 0.2 1.0 CB A:ASP207 4.2 0.3 1.0 ND2 A:ASN208 4.2 0.5 1.0 CD A:GLU173 4.2 0.3 1.0 OE1 A:GLU114 4.3 0.8 1.0 OD1 A:ASN208 4.3 0.6 1.0 CG A:ASN208 4.6 0.8 1.0 OE2 A:GLU173 4.6 0.7 1.0 CG A:GLU114 4.6 0.5 1.0 CB A:ASP171 4.7 0.4 1.0 CA A:CA705 4.8 0.1 1.0 CA A:ASP171 4.8 0.1 1.0

Calcium binding site 5 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:0.1 occ:1.00 OD1 A:ASP204 2.5 0.6 1.0 OE1 A:GLU114 2.5 0.8 1.0 OE2 A:GLU173 2.6 0.7 1.0 O A:ALA205 2.7 0.8 1.0 OD1 A:ASP207 2.8 0.8 1.0 OD1 A:ASP240 2.8 0.1 1.0 CD A:GLU173 3.4 0.3 1.0 CD A:GLU114 3.5 0.1 1.0 OE1 A:GLU173 3.5 0.7 1.0 N A:ALA205 3.6 0.1 1.0 CG A:ASP240 3.6 0.3 1.0 CG A:ASP207 3.7 0.2 1.0 CG A:ARG172 3.7 0.2 1.0 CG A:ASP204 3.7 0.2 1.0 OE2 A:GLU114 3.8 0.9 1.0 C A:ALA205 3.8 0.5 1.0 OD2 A:ASP207 3.8 0.7 1.0 CD A:ARG172 3.9 0.7 1.0 OD2 A:ASP240 4.2 0.1 1.0 CA A:ALA205 4.3 0.8 1.0 OD2 A:ASP204 4.4 0.4 1.0 CA A:ASP204 4.5 0.8 1.0 CB A:ASP240 4.5 0.3 1.0 C A:ASP204 4.6 0.8 1.0 N A:ASP207 4.6 0.9 1.0 CB A:ASP204 4.7 0.8 1.0 ND2 A:ASN208 4.7 0.5 1.0 CA A:CA704 4.8 0.7 1.0 CB A:ALA205 4.8 0.4 1.0 CG A:GLU173 4.8 0.4 1.0 CG A:GLU114 4.9 0.5 1.0 CA A:ASP240 4.9 0.0 1.0 N A:ASN206 4.9 0.2 1.0

Calcium binding site 6 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:0.0 occ:1.00 OD2 A:ASP291 2.2 0.1 1.0 O A:ASN208 2.5 0.8 1.0 OD1 A:ASN206 2.6 0.8 1.0 OD2 A:ASP240 2.7 0.1 1.0 OD2 A:ASP238 2.8 0.2 1.0 O A:ASN244 2.8 0.6 1.0 OD1 A:ASP238 3.1 0.4 1.0 CG A:ASP238 3.3 0.2 1.0 CG A:ASP291 3.3 0.7 1.0 CG A:ASN206 3.7 0.5 1.0 CG A:ASP240 3.7 0.3 1.0 C A:ASN208 3.7 0.6 1.0 CB A:ASP291 3.9 0.9 1.0 C A:ASN244 4.0 0.6 1.0 CB A:ASP240 4.2 0.3 1.0 ND2 A:ASN206 4.4 1.0 1.0 OD1 A:ASP291 4.4 0.8 1.0 CA A:PRO209 4.4 0.5 1.0 N A:PRO209 4.5 1.0 1.0 CD A:PRO210 4.6 0.0 1.0 CB A:ASN244 4.7 0.9 1.0 N A:ASN208 4.7 0.6 1.0 CA A:ASN206 4.7 0.6 1.0 CB A:ASN206 4.7 0.7 1.0 CA A:ASN208 4.7 0.1 1.0 OD1 A:ASP240 4.7 0.1 1.0 C A:PRO209 4.8 0.7 1.0 CA A:ASN244 4.8 0.3 1.0 CB A:ASP238 4.8 0.1 1.0 N A:PRO210 4.9 0.6 1.0 N A:SER245 5.0 0.3 1.0

Calcium binding site 7 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:77.3 occ:1.00 OD2 A:ASP310 2.6 71.4 1.0 OE1 A:GLU223 2.6 0.7 1.0 OD1 A:ASP276 2.8 0.8 1.0 CD A:GLU223 3.0 0.3 1.0 CG A:ASP310 3.3 0.2 1.0 OE2 A:GLU223 3.4 0.8 1.0 OD1 A:ASP310 3.5 0.0 1.0 OE1 A:GLU278 3.7 0.5 1.0 CG A:GLU223 3.8 96.7 1.0 CG A:ASP276 4.0 0.3 1.0 OE2 A:GLU278 4.2 0.1 1.0 CA A:CA708 4.3 0.4 1.0 ND2 A:ASN311 4.4 0.7 1.0 CD A:GLU278 4.4 0.3 1.0 CB A:GLU223 4.5 94.7 1.0 CA A:ASP276 4.6 0.9 1.0 CB A:ASP310 4.7 0.8 1.0 N A:PHE277 4.7 0.9 1.0 O A:GLU223 4.8 0.7 1.0 CB A:ASP276 4.8 1.0 1.0 OD2 A:ASP276 4.8 0.5 1.0 O A:LEU275 4.9 0.7 1.0

Calcium binding site 8 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:0.4 occ:1.00 OE2 A:GLU278 2.3 0.1 1.0 OD1 A:ASP307 2.5 0.1 1.0 OE2 A:GLU223 2.7 0.8 1.0 OD1 A:ASP343 2.7 0.1 1.0 ND2 A:ASN311 2.9 0.7 1.0 OD1 A:ASP310 3.2 0.0 1.0 O A:GLU308 3.2 0.7 1.0 CD A:GLU278 3.3 0.3 1.0 CG A:ASP307 3.4 0.4 1.0 CD A:GLU223 3.6 0.3 1.0 OD2 A:ASP307 3.7 0.1 1.0 OE1 A:GLU223 3.7 0.7 1.0 CG A:ASP343 3.8 0.3 1.0 OE1 A:GLU278 3.8 0.5 1.0 CA A:ASP343 4.1 0.4 1.0 CG A:ASN311 4.2 0.1 1.0 CA A:CA707 4.3 77.3 1.0 CG A:ASP310 4.3 0.2 1.0 N A:GLU308 4.3 0.9 1.0 CB A:ASP343 4.4 0.1 1.0 C A:GLU308 4.4 0.6 1.0 CG A:GLU278 4.5 0.3 1.0 N A:ASP343 4.5 0.8 1.0 CB A:ASP307 4.6 0.2 1.0 O A:LYS342 4.6 0.7 1.0 OD2 A:ASP310 4.7 71.4 1.0 C A:LYS342 4.7 0.2 1.0 CA A:ASP307 4.7 0.2 1.0 CB A:PHE277 4.8 0.5 1.0 OD2 A:ASP343 4.8 0.4 1.0 CB A:ASN311 4.8 98.6 1.0 C A:ASP307 4.8 0.6 1.0 CA A:GLU308 5.0 0.5 1.0 CG A:GLU223 5.0 96.7 1.0

Calcium binding site 9 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:0.9 occ:1.00 OD2 A:ASP343 2.3 0.4 1.0 OD2 A:ASP341 2.5 0.4 1.0 O A:ASN311 2.6 0.4 1.0 ND2 A:ASN309 2.6 0.8 1.0 OD1 A:ASP341 2.7 0.5 1.0 O A:ASN347 2.8 0.3 1.0 CG A:ASP341 3.0 0.1 1.0 OD2 A:ASP394 3.1 0.5 1.0 CG A:ASP343 3.3 0.3 1.0 C A:ASN311 3.7 0.7 1.0 CB A:ASP343 3.8 0.1 1.0 CG A:ASN309 3.9 0.9 1.0 CG A:ASP394 4.0 0.0 1.0 C A:ASN347 4.0 0.9 1.0 CD A:PRO313 4.1 0.6 1.0 CB A:ASP394 4.1 0.4 1.0 OD1 A:ASP343 4.3 0.1 1.0 CB A:ASP341 4.5 0.2 1.0 N A:PRO313 4.5 0.0 1.0 OD1 A:ASN309 4.6 0.5 1.0 CA A:ASN311 4.6 1.0 1.0 N A:ASN311 4.6 0.3 1.0 N A:VAL312 4.7 0.4 1.0 C A:VAL312 4.7 0.8 1.0 CB A:ASN311 4.7 98.6 1.0 N A:ASP343 4.8 0.8 1.0 CA A:VAL312 4.8 0.1 1.0 CA A:ASN347 4.8 0.2 1.0 CA A:GLY348 4.9 0.2 1.0 N A:GLY348 4.9 0.2 1.0 CA A:ASN309 4.9 0.9 1.0 CB A:ASN309 4.9 0.1 1.0 CA A:ASP343 4.9 0.4 1.0

Calcium binding site 10 out of 30 in the Crystal Structure of the Protocadherin GAMMAB4 Extracellular Domain


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 the Protocadherin GAMMAB4 Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:74.4 occ:1.00 OE2 A:GLU326 2.2 0.9 1.0 OE1 A:GLU381 2.8 0.2 1.0 OD1 A:ASP379 2.9 1.0 1.0 OD2 A:ASP415 2.9 84.8 1.0 ND2 A:ASN416 3.2 0.9 1.0 OD1 A:ASP415 3.3 0.8 1.0 CD A:GLU326 3.3 1.0 1.0 CG A:ASP415 3.4 0.5 1.0 CA A:CA711 3.7 63.9 1.0 CD A:GLU381 3.7 100.0 1.0 OE1 A:GLU326 3.8 0.4 1.0 CG A:ASP379 3.8 0.7 1.0 OD2 A:ASP379 4.2 86.5 1.0 OE2 A:GLU381 4.3 92.0 1.0 CG A:ASN416 4.3 0.2 1.0 CG A:GLU326 4.6 0.3 1.0 OD1 A:ASN416 4.7 0.8 1.0 CG A:GLU381 4.7 0.1 1.0 CB A:ASP415 4.8 0.3 1.0 CB A:GLU381 4.9 0.5 1.0 CB A:ASP379 5.0 0.9 1.0

J.Brasch, K.M.Goodman, A.J.Noble, M.Rapp, S.Mannepalli, F.Bahna, V.P.Dandey, T.Bepler, B.Berger, T.Maniatis, C.S.Potter, B.Carragher, B.Honig, L.Shapiro. Visualization of Clustered Protocadherin Neuronal Self-Recognition Complexes. Nature V. 569 280 2019.
ISSN: ESSN 1476-4687
PubMed: 30971825
DOI: 10.1038/S41586-019-1089-3