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Calcium in PDB 5szq: Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6

Protein crystallography data

The structure of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6, PDB code: 5szq 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) 19.96 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.890, 63.640, 344.310, 90.00, 90.00, 90.00
R / Rfree (%) 25.1 / 28.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 (pdb code 5szq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6, PDB code: 5szq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5szq

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Calcium binding site 1 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca710

b:88.4
occ:1.00
 OD1 A:ASP280 2.3 81.5 1.0
OE1 A:GLU282 2.5 73.8 1.0
OD1 A:ASP314 2.5 0.7 1.0
OE1 A:GLU225 2.6 95.4 1.0
OD2 A:ASP314 2.8 0.0 1.0
CG A:ASP314 3.0 0.5 1.0
CD A:GLU225 3.1 94.2 1.0
OE2 A:GLU225 3.2 99.1 1.0
CA A:CA711 3.4 65.5 1.0
CG A:ASP280 3.4 82.5 1.0
CD A:GLU282 3.7 76.6 1.0
OD2 A:ASP280 4.0 81.0 1.0
OE2 A:GLU282 4.4 62.8 1.0
CG A:GLU225 4.4 94.6 1.0
CB A:ASP314 4.5 0.9 1.0
CA A:ASP280 4.5 85.5 1.0
N A:TYR281 4.5 62.0 1.0
CB A:ASP280 4.5 84.7 1.0
ND2 A:ASN315 4.6 0.5 1.0
CG A:GLU282 4.8 81.5 1.0
OD1 A:ASN315 4.9 0.6 1.0
N A:GLU282 4.9 81.3 1.0
CG A:ASN315 4.9 0.0 1.0
C A:ASP280 5.0 86.5 1.0

Calcium binding site 2 out of 9 in 5szq

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Calcium binding site 2 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca711

b:65.5
occ:1.00
 OE2 A:GLU282 2.2 62.8 1.0
OE2 A:GLU225 2.3 99.1 1.0
OD1 A:ASP347 2.4 0.7 1.0
OE1 A:GLU282 2.6 73.8 1.0
O A:VAL312 2.7 96.0 1.0
CD A:GLU282 2.7 76.6 1.0
OD2 A:ASP311 3.0 69.3 1.0
OD2 A:ASP314 3.0 0.0 1.0
CD A:GLU225 3.2 94.2 1.0
CA A:CA710 3.4 88.4 1.0
OE1 A:GLU225 3.5 95.4 1.0
CG A:ASP314 3.6 0.5 1.0
CG A:ASP347 3.7 0.5 1.0
OD1 A:ASP314 3.7 0.7 1.0
C A:VAL312 3.9 95.3 1.0
N A:VAL312 4.1 98.2 1.0
CG A:GLU282 4.2 81.5 1.0
CG A:ASP311 4.2 70.6 1.0
N A:ASP314 4.3 91.9 1.0
CB A:ASP347 4.4 0.8 1.0
CB A:TYR281 4.5 69.2 1.0
OD2 A:ASP347 4.6 0.2 1.0
CA A:VAL312 4.6 99.5 1.0
CA A:ASP347 4.6 0.8 1.0
CG A:GLU225 4.6 94.6 1.0
ND2 A:ASN315 4.8 0.5 1.0
CB A:ASP314 4.8 0.9 1.0
N A:ASN313 4.9 0.9 1.0
OD1 A:ASP311 5.0 70.9 1.0
C A:ASP311 5.0 93.0 1.0
CA A:ASP311 5.0 89.5 1.0
N A:GLU282 5.0 81.3 1.0

Calcium binding site 3 out of 9 in 5szq

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Calcium binding site 3 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca712

b:60.4
occ:1.00
 OD2 A:ASP398 2.2 0.3 1.0
O A:ASN315 2.4 0.1 1.0
OD1 A:ASN313 2.5 0.1 1.0
OD2 A:ASP345 2.5 0.5 1.0
OD2 A:ASP347 2.6 0.2 1.0
O A:ASN351 2.6 92.1 1.0
OD1 A:ASP345 3.2 0.7 1.0
CG A:ASP345 3.2 0.5 1.0
CG A:ASP398 3.3 0.5 1.0
CG A:ASP347 3.4 0.5 1.0
CG A:ASN313 3.6 0.7 1.0
CB A:ASP347 3.6 0.8 1.0
C A:ASN315 3.6 0.3 1.0
C A:ASN351 3.8 98.6 1.0
OD1 A:ASP398 3.9 1.0 1.0
ND2 A:ASN313 4.2 0.1 1.0
CB A:ASP398 4.3 0.4 1.0
N A:ASN315 4.5 0.4 1.0
N A:ALA316 4.5 0.9 1.0
CA A:ASN315 4.5 0.4 1.0
CA A:ALA316 4.5 0.5 1.0
OD1 A:ASP347 4.6 0.7 1.0
CA A:ASN351 4.6 0.9 1.0
CD A:PRO317 4.6 0.4 1.0
CB A:ASN351 4.7 0.3 1.0
CB A:ASP345 4.7 0.8 1.0
CB A:ASN313 4.7 0.2 1.0
C A:ALA316 4.7 0.1 1.0
N A:PRO317 4.7 0.2 1.0
CB A:ASN315 4.8 0.4 1.0
N A:GLY352 4.8 0.9 1.0
CA A:ASP347 4.8 0.8 1.0
N A:ASP347 4.8 1.0 1.0
CA A:ASN313 4.9 0.2 1.0
CA A:GLY352 4.9 0.6 1.0

Calcium binding site 4 out of 9 in 5szq

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Calcium binding site 4 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca713

b:82.8
occ:1.00
 OD2 A:ASP419 2.5 0.2 1.0
OD2 A:ASP383 2.5 0.0 1.0
OE1 A:GLU330 2.6 0.7 1.0
OE1 A:GLU385 3.1 0.8 1.0
CG A:ASP383 3.1 0.8 1.0
OD1 A:ASP383 3.1 0.7 1.0
CG A:ASP419 3.4 0.1 1.0
OD1 A:ASP419 3.6 0.7 1.0
OD1 A:ASN420 3.7 0.5 1.0
CD A:GLU330 3.7 0.4 1.0
CD A:GLU385 4.1 0.1 1.0
CB A:ASP383 4.4 0.6 1.0
CG A:GLU330 4.5 0.1 1.0
OE2 A:GLU330 4.5 0.4 1.0
CG A:ASN420 4.6 0.9 1.0
CG A:GLU385 4.6 0.6 1.0
CB A:ASP419 4.7 0.3 1.0
ND2 A:ASN420 4.7 0.9 1.0
CB A:GLU385 4.8 0.8 1.0
CA A:CA714 4.9 62.7 1.0

Calcium binding site 5 out of 9 in 5szq

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Calcium binding site 5 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca714

b:62.7
occ:1.00
 OE2 A:GLU385 2.3 0.3 1.0
OD1 A:ASP416 2.3 0.1 1.0
O A:ILE417 2.4 0.7 1.0
OE2 A:GLU330 2.6 0.4 1.0
OD1 A:ASP452 2.8 0.5 1.0
CD A:GLU385 3.0 0.1 1.0
OD1 A:ASP419 3.0 0.7 1.0
OE1 A:GLU385 3.0 0.8 1.0
CD A:GLU330 3.4 0.4 1.0
CG A:ASP452 3.4 0.2 1.0
OE1 A:GLU330 3.4 0.7 1.0
CG A:ASP416 3.5 0.3 1.0
C A:ILE417 3.6 0.9 1.0
N A:ILE417 3.9 0.6 1.0
CB A:ASP452 4.1 0.7 1.0
CG A:ASP419 4.1 0.1 1.0
OD2 A:ASP452 4.1 0.7 1.0
OD2 A:ASP416 4.2 0.6 1.0
CG A:GLU385 4.3 0.6 1.0
CA A:ILE417 4.3 0.8 1.0
CA A:ASP452 4.4 0.7 1.0
C A:ASP416 4.4 0.1 1.0
CD A:ARG384 4.4 0.1 1.0
N A:ASP419 4.5 0.4 1.0
CA A:ASP416 4.5 0.0 1.0
CB A:ASP416 4.6 0.4 1.0
OD2 A:ASP419 4.6 0.2 1.0
N A:ASN418 4.7 0.7 1.0
NH1 A:ARG384 4.7 0.8 1.0
CB A:ARG384 4.8 0.1 1.0
CG A:GLU330 4.8 0.1 1.0
OD1 A:ASN420 4.9 0.5 1.0
CA A:CA713 4.9 82.8 1.0
CA A:ASN418 4.9 0.3 1.0

Calcium binding site 6 out of 9 in 5szq

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Calcium binding site 6 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca715

b:72.8
occ:1.00
 OD1 A:ASN418 2.4 0.4 1.0
O A:ASN420 2.4 0.1 1.0
O A:ASN456 2.4 0.4 1.0
OD2 A:ASP450 2.5 0.0 1.0
OD2 A:ASP508 2.6 0.2 1.0
OD2 A:ASP452 2.8 0.7 1.0
OD1 A:ASP450 2.9 0.9 1.0
CG A:ASP450 3.0 0.6 1.0
CG A:ASN418 3.5 0.7 1.0
C A:ASN420 3.7 0.9 1.0
C A:ASN456 3.7 0.1 1.0
CG A:ASP508 3.7 0.8 1.0
CG A:ASP452 3.8 0.2 1.0
CB A:ASP508 4.1 1.0 1.0
ND2 A:ASN418 4.1 0.5 1.0
CA A:PRO421 4.3 0.7 1.0
CB A:ASP452 4.3 0.7 1.0
CB A:ASP450 4.4 0.0 1.0
N A:PRO421 4.5 0.2 1.0
CD A:PRO422 4.5 0.3 1.0
CA A:ASN456 4.5 0.9 1.0
C A:PRO421 4.6 0.3 1.0
N A:ALA457 4.6 0.5 1.0
CB A:ASN456 4.6 0.6 1.0
CD2 A:LEU514 4.6 0.5 1.0
CA A:ALA457 4.6 0.6 1.0
N A:ASN420 4.7 0.2 1.0
CA A:ASN420 4.7 0.3 1.0
CB A:ASN418 4.7 0.7 1.0
OD1 A:ASP508 4.7 0.3 1.0
CB A:LEU514 4.8 0.6 1.0
N A:PRO422 4.8 0.5 1.0
OD1 A:ASP452 4.8 0.5 1.0
CA A:ASN418 4.9 0.3 1.0

Calcium binding site 7 out of 9 in 5szq

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Calcium binding site 7 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca716

b:74.3
occ:1.00
 OD2 A:ASP529 2.1 76.3 1.0
OD1 A:ASP493 2.3 60.5 1.0
OE2 A:GLU435 2.3 77.7 1.0
CG A:ASP529 3.1 67.5 1.0
CG A:ASP493 3.2 61.9 1.0
OE1 A:GLU495 3.3 44.2 1.0
CD A:GLU435 3.4 81.8 1.0
OD1 A:ASP529 3.4 52.1 1.0
OD2 A:ASP493 3.7 76.1 1.0
OD1 A:ASN436 4.0 71.7 1.0
CG A:GLU435 4.2 79.4 1.0
CB A:ASP493 4.3 71.8 1.0
OE1 A:GLU435 4.3 87.6 1.0
CD A:GLU495 4.5 60.5 1.0
CB A:ASP529 4.5 67.6 1.0
ND2 A:ASN530 4.5 80.1 1.0
CA A:CA717 4.6 41.6 1.0
CA A:ASP493 4.7 60.6 1.0
O A:ASP529 4.9 66.5 1.0
N A:TYR494 4.9 59.4 1.0
CG A:ASN436 5.0 72.4 1.0

Calcium binding site 8 out of 9 in 5szq

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Calcium binding site 8 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca717

b:41.6
occ:1.00
 OE2 A:GLU495 2.1 43.0 1.0
OE1 A:GLU435 2.4 87.6 1.0
O A:GLN527 2.4 39.8 1.0
OD1 A:ASP529 2.6 52.1 1.0
OD1 A:ASP526 2.6 46.8 1.0
OD1 A:ASP569 2.7 57.5 1.0
CD A:GLU495 2.8 60.5 1.0
OE1 A:GLU495 2.9 44.2 1.0
OE2 A:GLU435 3.0 77.7 1.0
CD A:GLU435 3.0 81.8 1.0
C A:GLN527 3.6 80.6 1.0
N A:GLN527 3.7 41.1 1.0
CG A:ASP529 3.7 67.5 1.0
CG A:ASP569 3.7 56.4 1.0
CG A:ASP526 3.7 41.4 1.0
CB A:ASP569 4.1 48.8 1.0
CA A:GLN527 4.2 67.3 1.0
ND2 A:ASN530 4.3 80.1 1.0
CG A:GLU495 4.3 69.1 1.0
OD2 A:ASP529 4.3 76.3 1.0
N A:ASP529 4.3 47.4 1.0
CA A:ASP569 4.4 56.8 1.0
OD2 A:ASP526 4.4 40.3 1.0
CB A:TYR494 4.4 46.2 1.0
CG A:GLU435 4.4 79.4 1.0
CA A:CA716 4.6 74.3 1.0
N A:ASN528 4.7 63.7 1.0
C A:ASP526 4.7 41.5 1.0
OD2 A:ASP569 4.7 66.2 1.0
CB A:GLN527 4.7 40.5 1.0
CB A:ASP529 4.8 67.6 1.0
CA A:ASP526 4.8 42.9 1.0
CB A:ASP526 4.8 98.4 1.0
CD2 A:TYR494 5.0 47.1 1.0
CB A:GLU435 5.0 78.7 1.0
CA A:ASN528 5.0 50.4 1.0
CA A:ASP529 5.0 58.6 1.0

Calcium binding site 9 out of 9 in 5szq

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Calcium binding site 9 out of 9 in the Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin Gamma A4 Extracellular Cadherin Domains 3-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca718

b:87.0
occ:1.00
 OD2 A:ASP569 2.3 66.2 1.0
OD2 A:ASP620 2.4 72.4 1.0
OD1 A:ASN528 2.4 50.3 1.0
OD1 A:ASP567 2.5 81.8 1.0
O A:ASN530 2.5 46.2 1.0
O A:ASN573 2.7 31.6 1.0
OD2 A:ASP567 2.9 71.0 1.0
CG A:ASP567 3.1 71.0 1.0
CG A:ASP620 3.4 60.5 1.0
CG A:ASP569 3.5 56.4 1.0
CG A:ASN528 3.5 49.3 1.0
CB A:ASP620 3.6 62.5 1.0
C A:ASN530 3.7 59.9 1.0
C A:ASN573 3.8 36.8 1.0
CB A:ASP569 4.0 48.8 1.0
CB A:ASN573 4.2 28.9 1.0
ND2 A:ASN528 4.2 62.1 1.0
CA A:ASN573 4.3 32.4 1.0
N A:ASN530 4.4 67.2 1.0
CA A:ASN530 4.5 69.2 1.0
OD1 A:ASP620 4.5 47.4 1.0
OD1 A:ASP569 4.5 57.5 1.0
CD1 A:LEU626 4.5 35.7 1.0
CB A:ASP567 4.5 67.5 1.0
CB A:ASN528 4.6 52.1 1.0
CD A:PRO532 4.6 54.3 1.0
CB A:ASN530 4.6 76.9 1.0
CA A:ASN528 4.6 50.4 1.0
N A:THR531 4.8 60.1 1.0
N A:ALA574 4.9 40.3 1.0
CA A:THR531 4.9 58.4 1.0
C A:THR531 5.0 60.2 1.0
N A:PRO532 5.0 54.1 1.0

Reference:

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
Page generated: Mon Jul 15 10:38:17 2024

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