Calcium in PDB 5k8r: Structure of Human Clustered Protocadherin Gamma B3 EC1-4

Protein crystallography data

The structure of Structure of Human Clustered Protocadherin Gamma B3 EC1-4, PDB code: 5k8r was solved by J.M.Nicoludis, B.E.Vogt, R.Gaudet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.35 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 128.881, 161.229, 53.659, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.9

Other elements in 5k8r:

The structure of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4 (pdb code 5k8r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4, PDB code: 5k8r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5k8r

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Calcium binding site 1 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:32.5
occ:1.00
 O A:ASN99 2.4 28.6 1.0
OD2 A:ASP129 2.4 36.6 1.0
O A:ASN135 2.4 26.6 1.0
OD1 A:ASN97 2.4 34.9 1.0
OD2 A:ASP131 2.5 33.0 1.0
OD1 A:ASP129 2.7 44.6 1.0
OD2 A:ASP186 2.7 47.2 1.0
CG A:ASP129 2.9 33.2 1.0
CG A:ASP131 3.5 34.0 1.0
C A:ASN135 3.6 24.3 1.0
C A:ASN99 3.6 45.1 1.0
CG A:ASN97 3.6 30.0 1.0
CG A:ASP186 3.6 43.7 1.0
CB A:ASP131 3.9 30.5 1.0
CB A:ASP186 3.9 42.6 1.0
ND2 A:ASN97 4.3 16.6 1.0
CB A:ASP129 4.4 31.4 1.0
CA A:ASN135 4.4 32.3 1.0
CB A:ASN135 4.5 33.9 1.0
N A:SER136 4.5 29.0 1.0
CA A:ASN99 4.5 40.9 1.0
N A:ASN99 4.5 44.8 1.0
CA A:PRO100 4.5 33.2 1.0
N A:PRO100 4.5 41.9 1.0
CA A:SER136 4.5 32.4 1.0
C A:PRO100 4.6 30.4 1.0
OD1 A:ASP131 4.6 29.7 1.0
CB A:ASN99 4.6 38.7 1.0
OD1 A:ASP186 4.7 41.4 1.0
CD A:PRO101 4.7 27.0 1.0
N A:PRO101 4.7 27.0 1.0
CB A:ASN97 4.8 32.6 1.0
CA A:ASN97 4.8 32.8 1.0
NE2 A:GLN138 4.9 29.0 1.0

Calcium binding site 2 out of 9 in 5k8r

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Calcium binding site 2 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:42.4
occ:1.00
 OD1 A:ASP61 2.4 34.1 1.0
OE1 A:GLU63 2.4 41.8 1.0
OD2 A:ASP98 2.4 40.6 1.0
OE2 A:GLU10 2.6 58.3 1.0
OE1 A:GLU9 2.7 26.3 1.0
CG A:ASP98 3.3 29.6 1.0
OD1 A:ASP98 3.5 35.2 1.0
CD A:GLU9 3.5 30.6 1.0
CD A:GLU10 3.5 44.4 1.0
CG A:ASP61 3.5 44.1 1.0
CG A:GLU10 3.7 37.2 1.0
CD A:GLU63 3.7 38.9 1.0
OE2 A:GLU9 3.8 42.2 1.0
CA A:CA503 4.0 34.5 1.0
OD1 A:ASN99 4.2 45.8 1.0
N A:ARG62 4.3 30.8 1.0
CA A:ASP61 4.3 27.5 1.0
CB A:ASP61 4.3 30.4 1.0
NH2 A:ARG59 4.4 43.9 1.0
OD2 A:ASP61 4.4 41.5 1.0
OE2 A:GLU63 4.5 38.1 1.0
N A:GLU63 4.5 29.6 1.0
CG A:GLU63 4.6 32.1 1.0
CG A:GLU9 4.6 33.9 1.0
O A:HOH674 4.6 36.0 1.0
CB A:GLU63 4.6 31.6 1.0
C A:ASP61 4.7 38.6 1.0
OE1 A:GLU10 4.7 40.8 1.0
CB A:ASP98 4.7 28.9 1.0

Calcium binding site 3 out of 9 in 5k8r

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Calcium binding site 3 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:34.5
occ:1.00
 O A:ILE96 2.4 33.0 1.0
OE2 A:GLU63 2.4 38.1 1.0
OD1 A:ASP95 2.4 34.5 1.0
OD1 A:ASP98 2.5 35.2 1.0
OD1 A:ASP131 2.5 29.7 1.0
OE2 A:GLU9 2.5 42.2 1.0
OE1 A:GLU63 2.8 41.8 1.0
CD A:GLU63 2.9 38.9 1.0
CG A:ASP131 3.4 34.0 1.0
CD A:GLU9 3.5 30.6 1.0
CG A:ASP95 3.5 37.7 1.0
C A:ILE96 3.6 32.7 1.0
CG A:ASP98 3.6 29.6 1.0
N A:ILE96 3.9 23.3 1.0
OE1 A:GLU9 4.0 26.3 1.0
OD1 A:ASN99 4.0 45.8 1.0
CA A:CA502 4.0 42.4 1.0
OD2 A:ASP95 4.1 37.3 1.0
OD2 A:ASP98 4.1 40.6 1.0
OD2 A:ASP131 4.1 33.0 1.0
N A:ASP98 4.2 27.7 1.0
CB A:ASP131 4.2 30.5 1.0
CG A:GLU63 4.3 32.1 1.0
CA A:ILE96 4.3 31.5 1.0
CG1 A:ILE96 4.3 29.6 1.0
CA A:ASP131 4.5 27.2 1.0
NE A:ARG62 4.5 31.9 1.0
N A:ASN97 4.6 32.6 1.0
CB A:ASP95 4.7 35.8 1.0
C A:ASP95 4.7 26.5 1.0
NH2 A:ARG62 4.7 45.0 1.0
CB A:ASP98 4.8 28.9 1.0
CA A:ASP95 4.8 29.5 1.0
CG A:GLU9 4.8 33.9 1.0
CA A:ASN97 4.8 32.8 1.0
CA A:ASP98 4.9 35.0 1.0
CG A:ASN99 5.0 39.6 1.0

Calcium binding site 4 out of 9 in 5k8r

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Calcium binding site 4 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:38.7
occ:1.00
 O A:ASN313 2.4 38.2 1.0
OD1 A:ASN311 2.5 51.4 1.0
OD1 A:ASP343 2.5 45.2 1.0
O A:ASN349 2.5 49.1 1.0
OD2 A:ASP345 2.5 48.0 1.0
OD2 A:ASP343 2.6 54.3 1.0
OD2 A:ASP396 2.7 50.0 1.0
CG A:ASP343 2.9 43.2 1.0
CG A:ASP345 3.4 44.9 1.0
C A:ASN349 3.6 41.8 1.0
C A:ASN313 3.6 48.0 1.0
CG A:ASP396 3.6 50.6 1.0
CG A:ASN311 3.7 50.9 1.0
CB A:ASP345 3.7 33.7 1.0
CB A:ASP396 3.9 40.3 1.0
ND2 A:ASN311 4.3 36.9 1.0
CB A:ASP343 4.3 35.2 1.0
CA A:ASN349 4.4 46.9 1.0
N A:ASN313 4.4 49.7 1.0
CA A:ASN313 4.4 53.4 1.0
CB A:ASN349 4.4 49.9 1.0
OD1 A:ASP345 4.5 46.8 1.0
CB A:ASN313 4.5 59.0 1.0
N A:GLY350 4.6 38.0 1.0
N A:ALA314 4.6 41.4 1.0
N A:ASP345 4.7 35.0 1.0
OD1 A:ASP396 4.7 54.9 1.0
CA A:GLY350 4.7 30.5 1.0
CA A:ALA314 4.8 34.4 1.0
CB A:ASN311 4.8 52.0 1.0
CD A:PRO315 4.8 55.7 1.0
CA A:ASN311 4.8 42.5 1.0
CA A:ASP345 4.8 32.9 1.0
C A:ALA314 4.9 42.1 1.0
N A:PRO315 4.9 50.3 1.0

Calcium binding site 5 out of 9 in 5k8r

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Calcium binding site 5 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:37.4
occ:1.00
 O A:GLU310 2.4 41.0 1.0
OE2 A:GLU223 2.5 58.5 1.0
OD1 A:ASP309 2.5 31.5 1.0
OE2 A:GLU280 2.5 51.4 1.0
OD1 A:ASP345 2.5 46.8 1.0
OD1 A:ASP312 2.7 31.1 1.0
OE1 A:GLU280 2.7 45.9 1.0
CD A:GLU280 2.9 39.3 1.0
CG A:ASP345 3.4 44.9 1.0
CD A:GLU223 3.4 47.2 1.0
C A:GLU310 3.6 42.3 1.0
OE1 A:GLU223 3.6 46.8 1.0
CA A:CA506 3.7 47.1 1.0
CG A:ASP309 3.7 41.3 1.0
N A:GLU310 3.8 40.5 1.0
ND2 A:ASN313 3.9 65.0 1.0
CG A:ASP312 3.9 44.8 1.0
CB A:ASP345 4.1 33.7 1.0
OD2 A:ASP345 4.2 48.0 1.0
CA A:GLU310 4.3 42.1 1.0
CA A:ASP345 4.3 32.9 1.0
OD2 A:ASP309 4.3 37.4 1.0
N A:ASP312 4.3 37.3 1.0
CG A:GLU280 4.4 30.1 1.0
OD2 A:ASP312 4.5 44.3 1.0
CB A:PHE279 4.6 45.6 1.0
CD2 A:PHE279 4.7 40.3 1.0
N A:ASN311 4.7 47.3 1.0
C A:ASP309 4.7 31.8 1.0
CA A:ASP309 4.8 34.9 1.0
CB A:ASP309 4.8 44.6 1.0
CG A:GLU223 4.8 51.9 1.0
CB A:GLU310 4.9 56.6 1.0
CA A:ASN311 4.9 42.5 1.0
CB A:ASP312 5.0 37.9 1.0

Calcium binding site 6 out of 9 in 5k8r

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Calcium binding site 6 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:47.1
occ:1.00
 OE1 A:GLU280 2.4 45.9 1.0
OD2 A:ASP312 2.4 44.3 1.0
OE1 A:GLU223 2.5 46.8 1.0
OD1 A:ASP278 2.5 37.9 1.0
O A:HOH609 2.5 38.9 1.0
OD1 A:ASP312 2.9 31.1 1.0
CG A:ASP312 3.0 44.8 1.0
CD A:GLU223 3.3 47.2 1.0
O A:HOH685 3.5 40.6 1.0
OE2 A:GLU223 3.6 58.5 1.0
CD A:GLU280 3.6 39.3 1.0
ND2 A:ASN313 3.7 65.0 1.0
CA A:CA505 3.7 37.4 1.0
CG A:ASP278 3.7 43.2 1.0
N A:PHE279 4.3 41.3 1.0
O A:HOH688 4.4 38.1 1.0
OE2 A:GLU280 4.4 51.4 1.0
N A:GLU280 4.5 40.3 1.0
CG A:GLU223 4.5 51.9 1.0
OD2 A:ASP278 4.5 35.2 1.0
CA A:ASP278 4.5 47.1 1.0
CG A:GLU280 4.5 30.1 1.0
CB A:ASP312 4.5 37.9 1.0
CB A:GLU280 4.6 33.3 1.0
CB A:ASP278 4.7 45.7 1.0
C A:ASP278 4.8 44.5 1.0
CG A:ASN313 4.9 63.8 1.0
CB A:GLU223 5.0 44.9 1.0

Calcium binding site 7 out of 9 in 5k8r

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Calcium binding site 7 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:42.8
occ:1.00
 O A:ASN208 2.4 32.7 1.0
O A:ASN244 2.4 49.1 1.0
OD1 A:ASN206 2.4 41.2 1.0
OD2 A:ASP238 2.4 53.8 1.0
OD1 A:ASP238 2.5 44.4 1.0
OD2 A:ASP293 2.7 36.5 1.0
CG A:ASP238 2.8 45.4 1.0
OD2 A:ASP240 2.8 54.9 1.0
CG A:ASP240 3.5 44.0 1.0
CG A:ASN206 3.5 48.7 1.0
C A:ASN208 3.6 42.5 1.0
C A:ASN244 3.6 54.8 1.0
CG A:ASP293 3.7 53.9 1.0
CB A:ASP240 3.8 30.2 1.0
CB A:ASP293 4.1 43.2 1.0
ND2 A:ASN206 4.1 63.3 1.0
CB A:ASP238 4.3 40.5 1.0
CA A:ASN244 4.3 44.4 1.0
CB A:ASN244 4.3 49.2 1.0
OD1 A:ASP240 4.3 49.5 1.0
CA A:ASN208 4.4 42.0 1.0
N A:ASN208 4.4 44.6 1.0
CB A:ASN208 4.5 46.3 1.0
N A:PRO209 4.5 46.9 1.0
CA A:PRO209 4.6 41.2 1.0
N A:ALA245 4.6 53.9 1.0
CA A:ASN206 4.6 40.6 1.0
CB A:ASN206 4.6 36.2 1.0
CA A:ALA245 4.8 49.5 1.0
C A:PRO209 4.8 45.0 1.0
OD1 A:ASP293 4.8 58.9 1.0
N A:ASP240 4.8 42.4 1.0
CD2 A:HIS297 4.8 46.3 1.0
C A:ASN206 4.9 44.1 1.0
CA A:ASP240 5.0 38.7 1.0

Calcium binding site 8 out of 9 in 5k8r

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Calcium binding site 8 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:51.6
occ:1.00
 OE1 A:GLU173 1.8 41.0 1.0
OD1 A:ASP171 2.4 38.5 1.0
O A:HOH663 2.5 38.4 1.0
OD2 A:ASP207 2.5 56.4 1.0
OE1 A:GLU114 2.5 43.7 1.0
CD A:GLU173 2.8 43.7 1.0
CG A:ASP207 3.0 50.2 1.0
OD1 A:ASP207 3.1 50.0 1.0
OE2 A:GLU173 3.2 43.6 1.0
CG A:ASP171 3.5 48.5 1.0
CD A:GLU114 3.5 39.6 1.0
CA A:CA509 3.8 44.6 1.0
ND2 A:ASN208 4.0 51.3 1.0
OE2 A:GLU114 4.0 55.5 1.0
CG A:GLU173 4.1 39.2 1.0
CA A:ASP171 4.2 34.0 1.0
OD2 A:ASP171 4.2 44.1 1.0
CB A:ASP171 4.3 43.1 1.0
CB A:ASP207 4.3 39.8 1.0
CB A:GLU173 4.5 36.2 1.0
N A:ARG172 4.5 38.4 1.0
CG A:GLU114 4.5 43.2 1.0
N A:GLU173 4.6 41.7 1.0
C A:ASP171 4.7 37.8 1.0
CB A:GLU114 4.8 40.3 1.0

Calcium binding site 9 out of 9 in 5k8r

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Calcium binding site 9 out of 9 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:44.6
occ:1.00
 OE2 A:GLU173 1.8 43.6 1.0
OE2 A:GLU114 2.4 55.5 1.0
O A:ALA205 2.4 44.1 1.0
OD1 A:ASP207 2.5 50.0 1.0
OD1 A:ASP204 2.6 42.3 1.0
OD1 A:ASP240 2.8 49.5 1.0
CD A:GLU173 2.9 43.7 1.0
CD A:GLU114 3.3 39.6 1.0
CG A:ASP207 3.3 50.2 1.0
CG A:ASP240 3.3 44.0 1.0
OE1 A:GLU114 3.5 43.7 1.0
ND2 A:ASN208 3.5 51.3 1.0
OD2 A:ASP207 3.5 56.4 1.0
OE1 A:GLU173 3.6 41.0 1.0
C A:ALA205 3.6 49.2 1.0
CG A:ASP204 3.7 53.6 1.0
CA A:CA508 3.8 51.6 1.0
N A:ALA205 3.8 43.3 1.0
OD2 A:ASP240 3.8 54.9 1.0
CB A:ASP240 4.0 30.2 1.0
CG A:GLU173 4.1 39.2 1.0
N A:ASP207 4.1 41.5 1.0
OD2 A:ASP204 4.3 54.9 1.0
CA A:ALA205 4.3 49.3 1.0
CA A:ASP240 4.3 38.7 1.0
CB A:ASP207 4.6 39.8 1.0
CG A:GLU114 4.6 43.2 1.0
N A:ASN206 4.7 43.7 1.0
CG A:ASN208 4.7 48.4 1.0
C A:ASP204 4.8 37.0 1.0
NE A:ARG172 4.8 60.1 1.0
CA A:ASP204 4.8 36.5 1.0
CA A:ASP207 4.8 39.4 1.0
CB A:ASP204 4.8 37.0 1.0
CB A:ALA205 4.9 46.5 1.0
CA A:ASN206 4.9 40.6 1.0
N A:ASN208 5.0 44.6 1.0

Reference:

J.M.Nicoludis, B.E.Vogt, A.G.Green, C.P.Scharfe, D.S.Marks, R.Gaudet. Antiparallel Protocadherin Homodimers Use Distinct Affinity- and Specificity-Mediating Regions in Cadherin Repeats 1-4. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27472898
DOI: 10.7554/ELIFE.18449
Page generated: Sat Dec 12 05:33:06 2020

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