Atomistry » Calcium » PDB 5szl-5tac » 5szq
Atomistry »
  Calcium »
    PDB 5szl-5tac »
      5szq »

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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Go back to Calcium Binding Sites List in 5szq
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy