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Calcium in PDB 6pgw: Crystal Structure of Zebrafish Protocadherin-19 EC3-6

Protein crystallography data

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC3-6, PDB code: 6pgw was solved by S.R.Cooper, J.D.Hudson, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.92, 58.896, 70.956, 90, 117.97, 90
R / Rfree (%) 21.5 / 29.8

Other elements in 6pgw:

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC3-6 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6 (pdb code 6pgw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6, PDB code: 6pgw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6pgw

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Calcium binding site 1 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:41.9
occ:1.00
 OE2 A:GLU226 2.3 41.3 1.0
OD1 A:ASP282 2.3 45.7 1.0
O A:HOH810 2.3 43.7 1.0
OE2 A:GLU284 2.3 41.8 1.0
O A:HOH809 2.3 38.7 1.0
OD2 A:ASP318 2.3 40.3 1.0
CD A:GLU226 3.2 40.1 1.0
CG A:ASP318 3.2 39.0 1.0
OD1 A:ASP318 3.3 39.1 1.0
CG A:ASP282 3.4 46.5 1.0
CD A:GLU284 3.6 42.4 1.0
CG A:GLU226 3.9 38.6 1.0
OE1 A:GLU226 3.9 39.8 1.0
CA A:CA702 4.0 42.0 1.0
ND2 A:ASN227 4.1 37.7 1.0
OD1 A:ASN227 4.1 38.9 1.0
ND2 A:ASN319 4.1 41.4 1.0
OE1 A:GLU284 4.2 42.0 1.0
CA A:ASP282 4.2 43.8 1.0
OD2 A:ASP282 4.3 48.4 1.0
CB A:ASP282 4.3 44.4 1.0
N A:HIS283 4.4 42.8 1.0
CG A:ASN227 4.5 36.8 1.0
CB A:ASP318 4.6 37.8 1.0
C A:ASP282 4.6 42.4 1.0
CG A:GLU284 4.7 43.3 1.0
N A:GLU284 4.7 44.7 1.0
CB A:GLU284 4.9 43.4 1.0

Calcium binding site 2 out of 9 in 6pgw

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Calcium binding site 2 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:42.0
occ:1.00
 OD1 A:ASP354 2.3 38.9 1.0
OD1 A:ASP315 2.3 41.5 1.0
O A:ILE316 2.3 40.0 1.0
OE1 A:GLU226 2.4 39.8 1.0
OE1 A:GLU284 2.4 42.0 1.0
OD1 A:ASP318 2.4 39.1 1.0
CD A:GLU284 3.1 42.4 1.0
CD A:GLU226 3.2 40.1 1.0
OE2 A:GLU284 3.2 41.8 1.0
OE2 A:GLU226 3.3 41.3 1.0
CG A:ASP354 3.3 41.7 1.0
C A:ILE316 3.5 39.5 1.0
CG A:ASP318 3.5 39.0 1.0
CG A:ASP315 3.6 40.0 1.0
N A:ILE316 3.7 39.4 1.0
CB A:ASP354 4.0 42.4 1.0
ND2 A:ASN319 4.0 41.4 1.0
CA A:CA701 4.0 41.9 1.0
OD2 A:ASP318 4.1 40.3 1.0
CA A:ILE316 4.2 39.8 1.0
N A:ASP318 4.2 36.4 1.0
OD2 A:ASP354 4.3 41.5 1.0
OD2 A:ASP315 4.3 40.6 1.0
CB A:HIS283 4.4 44.3 1.0
CA A:ASP354 4.4 43.6 1.0
CA A:ASP315 4.5 39.1 1.0
C A:ASP315 4.5 38.9 1.0
CG A:GLU226 4.6 38.6 1.0
CG A:GLU284 4.6 43.3 1.0
CB A:ASP315 4.6 39.1 1.0
N A:ASN317 4.6 34.2 1.0
CB A:ASP318 4.7 37.8 1.0
CG1 A:ILE316 4.8 40.0 1.0
CA A:ASN317 4.9 33.9 1.0
CA A:ASP318 5.0 37.4 1.0

Calcium binding site 3 out of 9 in 6pgw

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Calcium binding site 3 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:41.6
occ:1.00
 O A:ASN319 2.3 40.2 1.0
OD2 A:ASP352 2.3 39.9 1.0
OD1 A:ASN317 2.3 36.5 1.0
OD2 A:ASP354 2.3 41.5 1.0
OD1 A:ASP352 2.3 40.9 1.0
O A:ASN358 2.3 45.4 1.0
OD2 A:ASP404 2.4 41.0 1.0
CG A:ASP352 2.6 41.9 1.0
CG A:ASP404 3.4 41.0 1.0
C A:ASN358 3.4 44.1 1.0
CG A:ASP354 3.5 41.7 1.0
C A:ASN319 3.5 39.4 1.0
CG A:ASN317 3.5 33.7 1.0
CB A:ASP404 3.8 42.5 1.0
CB A:ASP354 3.9 42.4 1.0
CA A:ASN358 4.1 41.2 1.0
CB A:ASP352 4.1 44.3 1.0
CB A:ASN358 4.2 39.5 1.0
ND2 A:ASN317 4.3 31.1 1.0
N A:ALA320 4.4 40.2 1.0
CA A:ALA320 4.4 40.2 1.0
OD1 A:ASP404 4.4 39.5 1.0
CA A:ASN319 4.4 39.3 1.0
N A:ASN319 4.4 39.2 1.0
CA A:ASN317 4.5 33.9 1.0
N A:GLY359 4.5 46.9 1.0
OD1 A:ASP354 4.6 38.9 1.0
CB A:ASN317 4.6 33.6 1.0
CB A:ASN319 4.7 40.1 1.0
C A:ASN317 4.8 34.6 1.0
N A:ASP354 4.8 45.4 1.0
CA A:GLY359 4.9 49.2 1.0
C A:ALA320 5.0 39.9 1.0
CA A:ASP354 5.0 43.6 1.0

Calcium binding site 4 out of 9 in 6pgw

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Calcium binding site 4 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:83.2
occ:1.00
 OE2 A:GLU337 2.3 78.2 1.0
OD2 A:ASP425 2.3 81.1 1.0
OE2 A:GLU391 2.3 81.7 1.0
O A:HOH804 2.3 75.0 1.0
O A:HOH801 2.3 78.1 1.0
OD1 A:ASP389 2.3 81.9 1.0
CG A:ASP425 3.1 80.2 1.0
OD1 A:ASP425 3.3 83.2 1.0
CD A:GLU337 3.3 79.9 1.0
CD A:GLU391 3.5 80.5 1.0
CG A:ASP389 3.5 83.2 1.0
OE1 A:GLU337 3.7 81.7 1.0
CA A:CA705 3.9 81.1 1.0
OE1 A:GLU391 4.2 80.0 1.0
N A:ARG390 4.2 89.3 1.0
OD2 A:ASP389 4.2 85.5 1.0
CA A:ASP389 4.3 85.8 1.0
CB A:ASP425 4.4 81.2 1.0
CG A:GLU337 4.4 81.1 1.0
CB A:ASP389 4.5 83.7 1.0
CG A:GLU391 4.5 81.3 1.0
N A:GLU391 4.5 81.5 1.0
ND2 A:ASN338 4.5 101.3 1.0
OD1 A:ASN426 4.5 90.9 1.0
CB A:GLU337 4.6 82.0 1.0
CB A:GLU391 4.6 80.9 1.0
ND2 A:ASN426 4.6 90.6 1.0
C A:ASP389 4.7 86.4 1.0
CG A:ASN426 4.9 89.5 1.0

Calcium binding site 5 out of 9 in 6pgw

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Calcium binding site 5 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:81.1
occ:1.00
 OE1 A:GLU337 2.3 81.7 1.0
OD1 A:ASP458 2.3 92.8 1.0
OE1 A:GLU391 2.3 80.0 1.0
O A:GLU423 2.3 78.5 1.0
OD1 A:ASP425 2.4 83.2 1.0
OD1 A:ASP422 2.4 82.2 1.0
CD A:GLU391 3.1 80.5 1.0
CD A:GLU337 3.1 79.9 1.0
OE2 A:GLU391 3.1 81.7 1.0
OE2 A:GLU337 3.3 78.2 1.0
CG A:ASP458 3.5 90.9 1.0
CG A:ASP422 3.5 81.1 1.0
CG A:ASP425 3.5 80.2 1.0
C A:GLU423 3.5 80.9 1.0
N A:GLU423 3.8 79.6 1.0
CA A:CA704 3.9 83.2 1.0
OD2 A:ASP425 4.0 81.1 1.0
OD2 A:ASP422 4.1 75.9 1.0
N A:ASP425 4.2 81.5 1.0
CB A:ASP458 4.2 90.0 1.0
CA A:GLU423 4.2 81.5 1.0
CA A:ASP458 4.3 88.6 1.0
OD2 A:ASP458 4.4 89.2 1.0
CG A:GLU337 4.5 81.1 1.0
CG A:GLU391 4.6 81.3 1.0
N A:ASN424 4.6 86.6 1.0
CB A:ARG390 4.7 94.7 1.0
CB A:ASP422 4.7 81.2 1.0
CB A:GLU423 4.8 84.5 1.0
CB A:ASP425 4.8 81.2 1.0
CA A:ASP422 4.8 78.2 1.0
C A:ASP422 4.8 77.1 1.0
CA A:ASN424 4.9 83.8 1.0
CA A:ASP425 4.9 81.3 1.0
N A:ASP458 4.9 87.2 1.0

Calcium binding site 6 out of 9 in 6pgw

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Calcium binding site 6 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:81.9
occ:1.00
 OD2 A:ASP513 2.3 92.4 1.0
O A:ASN426 2.3 85.4 1.0
OD2 A:ASP456 2.3 78.5 1.0
OD2 A:ASP458 2.3 89.2 1.0
O A:ASN462 2.3 76.0 1.0
OD1 A:ASN424 2.3 87.0 1.0
OD1 A:ASP456 3.0 77.7 1.0
CG A:ASP456 3.0 77.3 1.0
C A:ASN462 3.4 77.2 1.0
CG A:ASP458 3.4 90.9 1.0
CG A:ASP513 3.5 97.1 1.0
CG A:ASN424 3.5 85.0 1.0
C A:ASN426 3.5 86.1 1.0
CB A:ASP458 3.9 90.0 1.0
CA A:PRO427 4.0 84.5 1.0
CB A:ASP513 4.2 98.7 1.0
ND2 A:ASN424 4.2 83.7 1.0
N A:PRO427 4.2 87.3 1.0
CA A:ASN462 4.3 81.5 1.0
N A:GLY463 4.3 77.0 1.0
CB A:ASN462 4.4 81.6 1.0
CB A:ASP456 4.4 75.9 1.0
OD1 A:ASP513 4.4 96.3 1.0
CA A:GLY463 4.5 74.2 1.0
N A:ASN426 4.5 85.8 1.0
OD1 A:ASP458 4.5 92.8 1.0
CA A:ASN424 4.5 83.8 1.0
C A:PRO427 4.5 81.2 1.0
CA A:ASN426 4.6 86.3 1.0
CB A:ASN424 4.6 85.4 1.0
C A:ASN424 4.8 80.8 1.0
CD1 A:LEU519 4.9 93.0 1.0
CB A:ASN426 5.0 87.5 1.0

Calcium binding site 7 out of 9 in 6pgw

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Calcium binding site 7 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca707

b:56.2
occ:1.00
 OE2 A:GLU441 2.3 52.2 1.0
O A:HOH803 2.3 49.4 1.0
OE2 A:GLU500 2.3 54.8 1.0
OD2 A:ASP534 2.3 49.1 1.0
O A:HOH812 2.3 51.7 1.0
OD1 A:ASN498 2.3 55.0 1.0
CG A:ASP534 3.1 48.3 1.0
OD1 A:ASP534 3.2 50.5 1.0
CG A:ASN498 3.2 53.8 1.0
CD A:GLU441 3.3 54.1 1.0
CD A:GLU500 3.4 52.1 1.0
ND2 A:ASN498 3.8 53.8 1.0
ND2 A:ASN535 3.8 44.5 1.0
OE1 A:GLU441 4.0 53.0 1.0
CG A:GLU500 4.1 51.9 1.0
CG A:GLU441 4.2 55.1 1.0
CA A:CA708 4.2 52.3 1.0
CB A:GLU500 4.3 51.5 1.0
CB A:ASN498 4.3 52.7 1.0
OE1 A:GLU500 4.3 51.1 1.0
OD1 A:ASN442 4.4 60.1 1.0
CB A:ASP534 4.5 48.3 1.0
CA A:ASN498 4.6 52.2 1.0
N A:GLU500 4.6 50.3 1.0
CG A:ASN535 4.7 43.1 1.0
N A:HIS499 4.8 53.3 1.0
O A:ASP534 4.8 46.9 1.0
OD1 A:ASN535 4.9 40.8 1.0
C A:ASN498 4.9 52.7 1.0
ND2 A:ASN442 5.0 61.1 1.0

Calcium binding site 8 out of 9 in 6pgw

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Calcium binding site 8 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca708

b:52.3
occ:1.00
 OE1 A:GLU441 2.3 53.0 1.0
OE1 A:GLU500 2.3 51.1 1.0
OD1 A:ASP531 2.3 56.3 1.0
O A:VAL532 2.4 56.1 1.0
OD1 A:ASP572 2.4 49.6 1.0
OD1 A:ASP534 2.4 50.5 1.0
OE2 A:GLU500 2.9 54.8 1.0
CD A:GLU500 3.0 52.1 1.0
CD A:GLU441 3.2 54.1 1.0
CG A:ASP572 3.3 53.0 1.0
OE2 A:GLU441 3.4 52.2 1.0
CG A:ASP534 3.5 48.3 1.0
C A:VAL532 3.5 56.2 1.0
CG A:ASP531 3.6 59.0 1.0
N A:VAL532 3.7 56.6 1.0
CB A:ASP572 3.9 54.8 1.0
OD2 A:ASP534 4.1 49.1 1.0
ND2 A:ASN535 4.1 44.5 1.0
CA A:ASP572 4.2 57.1 1.0
CA A:CA707 4.2 56.2 1.0
CA A:VAL532 4.2 56.5 1.0
N A:ASP534 4.3 48.2 1.0
OD2 A:ASP572 4.3 50.2 1.0
CA A:ASP531 4.4 57.9 1.0
CB A:HIS499 4.4 54.9 1.0
CG A:GLU500 4.4 51.9 1.0
OD2 A:ASP531 4.4 60.4 1.0
C A:ASP531 4.5 58.4 1.0
CB A:ASP531 4.6 59.7 1.0
N A:ASN533 4.6 51.6 1.0
CG A:GLU441 4.6 55.1 1.0
CB A:ASP534 4.7 48.3 1.0
CG2 A:VAL532 4.7 56.8 1.0
CD2 A:HIS499 4.7 59.6 1.0
CG A:HIS499 4.8 57.2 1.0
CA A:ASN533 4.9 50.9 1.0
N A:ASP572 5.0 56.2 1.0
CA A:ASP534 5.0 47.0 1.0

Calcium binding site 9 out of 9 in 6pgw

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Calcium binding site 9 out of 9 in the Crystal Structure of Zebrafish Protocadherin-19 EC3-6


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 Zebrafish Protocadherin-19 EC3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca709

b:45.1
occ:1.00
 OD1 A:ASN533 2.3 49.0 1.0
OD2 A:ASP570 2.3 42.2 1.0
OD2 A:ASP572 2.3 50.2 1.0
OD1 A:ASP570 2.4 42.7 1.0
OD2 A:ASP622 2.4 48.0 1.0
O A:ASN535 2.4 46.2 1.0
O A:ASN576 2.4 50.9 1.0
CG A:ASP570 2.7 42.3 1.0
CG A:ASP572 3.4 53.0 1.0
CG A:ASN533 3.5 51.3 1.0
C A:ASN576 3.6 51.2 1.0
CG A:ASP622 3.6 49.0 1.0
C A:ASN535 3.7 46.1 1.0
CB A:ASP572 3.7 54.8 1.0
CB A:ASP570 4.2 44.1 1.0
CB A:ASP622 4.3 49.5 1.0
ND2 A:ASN533 4.3 50.7 1.0
CB A:ASN535 4.4 43.6 1.0
CA A:ASN535 4.4 44.7 1.0
N A:ASN535 4.4 45.0 1.0
CA A:ASN576 4.4 54.4 1.0
N A:GLY577 4.5 50.0 1.0
OD1 A:ASP572 4.5 49.6 1.0
CB A:ASN576 4.5 55.9 1.0
CA A:GLY577 4.6 50.4 1.0
CA A:ASN533 4.6 50.9 1.0
OD1 A:ASP622 4.6 48.2 1.0
CB A:ASN533 4.6 51.5 1.0
N A:ASP572 4.6 56.2 1.0
N A:THR536 4.7 49.1 1.0
CA A:ASP572 4.8 57.1 1.0
C A:ASN533 4.8 50.2 1.0
CD A:PRO537 4.9 50.8 1.0

Reference:

S.R.Cooper, J.D.Hudson, M.Sotomayor. Crystal Structure of Zebrafish Protocadherin-19 EC3-6 To Be Published.
Page generated: Wed Jul 9 16:47:16 2025

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