Calcium in PDB 5czx: Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab

The structure of Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab, PDB code: 5czx was solved by T.Hu, C.Fryer, R.Chopra, K.Clark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.340, 123.860, 150.570, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.6

The structure of Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab (pdb code 5czx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab, PDB code: 5czx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab


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 NOTCH3 Nrr in Complex with 20358 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1702 b:71.2 occ:1.00 OD2 A:ASP1413 2.1 63.7 1.0 O A:ARG1400 2.3 75.4 1.0 OD1 A:ASP1398 2.4 91.1 1.0 O A:LYS1395 2.5 89.1 1.0 OD1 A:ASP1413 2.5 63.3 1.0 OD2 A:ASP1416 2.6 71.0 1.0 OD2 A:ASP1402 2.6 94.3 1.0 CG A:ASP1413 2.6 62.2 1.0 CG A:ASP1398 3.4 90.5 1.0 C A:ARG1400 3.5 75.4 1.0 CG A:ASP1416 3.5 69.2 1.0 C A:LYS1395 3.6 89.5 1.0 CG A:ASP1402 3.7 87.0 1.0 CB A:ASP1416 3.7 59.6 1.0 O A:ASP1413 3.9 60.4 1.0 N A:ASP1402 4.0 69.8 1.0 OD2 A:ASP1398 4.0 96.4 1.0 CB A:ASP1413 4.1 56.1 1.0 CB A:LYS1395 4.1 89.3 1.0 CB A:ASP1402 4.2 72.9 1.0 CA A:LYS1395 4.3 86.7 1.0 CA A:CYS1401 4.3 65.8 1.0 N A:CYS1401 4.3 67.9 1.0 N A:ASP1398 4.4 79.8 1.0 N A:ARG1400 4.4 76.4 1.0 CA A:ARG1400 4.4 75.7 1.0 CB A:ASP1398 4.5 81.0 1.0 C A:CYS1401 4.5 71.9 1.0 CG A:LYS1395 4.6 0.9 1.0 OD1 A:ASP1416 4.6 70.4 1.0 N A:ARG1396 4.7 84.9 1.0 OD1 A:ASP1402 4.7 88.3 1.0 N A:GLY1397 4.7 83.0 1.0 CA A:ASP1402 4.8 70.5 1.0 C A:ASP1413 4.8 60.4 1.0 CA A:ASP1398 4.8 79.3 1.0 CB A:ARG1400 4.8 78.3 1.0 CA A:ARG1396 4.9 84.3 1.0 CA A:ASP1413 4.9 55.1 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab


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 NOTCH3 Nrr in Complex with 20358 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1703 b:36.8 occ:1.00 O A:LEU1436 2.3 38.8 1.0 OD1 A:ASP1454 2.3 33.0 1.0 OD2 A:ASP1454 2.4 36.4 1.0 OD1 A:ASN1439 2.4 40.2 1.0 OD2 A:ASP1443 2.5 49.9 1.0 O A:ARG1441 2.5 40.8 1.0 CG A:ASP1454 2.7 34.3 1.0 CG A:ASN1439 3.3 56.5 1.0 CG A:ASP1443 3.4 49.6 1.0 C A:LEU1436 3.5 41.7 1.0 ND2 A:ASN1439 3.7 47.1 1.0 C A:ARG1441 3.7 42.0 1.0 CB A:ASP1443 3.9 39.8 1.0 N A:ASP1443 4.1 39.5 1.0 CB A:ASP1454 4.2 30.5 1.0 CB A:LEU1436 4.2 43.3 1.0 O A:ASP1454 4.3 35.5 1.0 OD2 A:ASP1457 4.3 51.3 1.0 N A:ARG1441 4.3 41.7 1.0 CA A:LEU1436 4.4 43.0 1.0 OD1 A:ASP1443 4.5 52.0 1.0 N A:PHE1437 4.5 36.6 1.0 C A:CYS1442 4.6 43.9 1.0 CA A:ARG1441 4.6 40.4 1.0 O A:HOH1826 4.6 40.0 1.0 CA A:ASP1443 4.6 38.5 1.0 N A:CYS1442 4.6 38.3 1.0 CB A:ASP1457 4.6 34.8 1.0 CA A:PHE1437 4.7 36.4 1.0 CB A:ASN1439 4.7 43.3 1.0 CA A:CYS1442 4.7 40.0 1.0 O A:PHE1437 4.7 43.0 1.0 C A:PHE1437 4.8 43.9 1.0 N A:ASN1439 4.8 45.1 1.0 C A:ASP1454 4.9 35.8 1.0 CA A:ASP1454 4.9 30.9 1.0 CG A:ARG1441 5.0 59.8 1.0 CG A:ASP1457 5.0 44.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab


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 NOTCH3 Nrr in Complex with 20358 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1704 b:24.6 occ:1.00 OD2 A:ASP1485 2.2 22.3 1.0 O A:HIS1478 2.3 24.8 1.0 OD2 A:ASP1499 2.3 29.9 1.0 O A:ARG1483 2.4 28.0 1.0 OD1 A:ASP1481 2.4 27.3 1.0 OD1 A:ASP1496 2.5 26.6 1.0 OD2 A:ASP1496 2.6 26.1 1.0 CG A:ASP1496 2.9 27.9 1.0 CG A:ASP1481 3.3 30.2 1.0 CG A:ASP1485 3.4 26.0 1.0 CG A:ASP1499 3.4 30.2 1.0 C A:HIS1478 3.5 26.4 1.0 C A:ARG1483 3.6 30.1 1.0 OD2 A:ASP1481 3.8 28.5 1.0 CB A:ASP1499 3.8 23.2 1.0 CB A:ASP1485 4.0 21.8 1.0 O A:HOH1801 4.0 28.2 1.0 CB A:HIS1478 4.1 27.9 1.0 N A:ASP1485 4.1 22.3 1.0 O A:ASP1496 4.2 23.3 1.0 N A:ASP1481 4.2 25.0 1.0 N A:ARG1483 4.2 27.5 1.0 CA A:HIS1478 4.2 26.8 1.0 CB A:ASP1496 4.4 22.8 1.0 OD1 A:ASP1485 4.4 30.7 1.0 CA A:ARG1483 4.4 27.6 1.0 N A:ALA1480 4.4 26.0 1.0 N A:PHE1479 4.5 22.3 1.0 OD1 A:ASP1499 4.5 28.7 1.0 CB A:ASP1481 4.5 26.2 1.0 N A:CYS1484 4.6 25.7 1.0 C A:CYS1484 4.7 26.8 1.0 CA A:PHE1479 4.7 23.5 1.0 CA A:ASP1485 4.7 21.2 1.0 C A:PHE1479 4.7 30.9 1.0 CA A:CYS1484 4.7 25.3 1.0 CB A:ARG1483 4.7 30.0 1.0 CA A:ASP1481 4.8 25.3 1.0 C A:ASP1496 5.0 25.1 1.0 N A:GLY1482 5.0 29.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab


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 NOTCH3 Nrr in Complex with 20358 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1702 b:71.7 occ:1.00 OD1 B:ASP1398 2.1 88.2 1.0 O B:ARG1400 2.4 67.6 1.0 OD2 B:ASP1413 2.4 70.2 1.0 OD2 B:ASP1416 2.6 66.4 1.0 O B:LYS1395 2.6 88.5 1.0 OD1 B:ASP1413 2.6 64.7 1.0 OD2 B:ASP1402 2.7 73.4 1.0 CG B:ASP1413 2.8 64.5 1.0 CG B:ASP1398 3.2 88.1 1.0 CG B:ASP1416 3.5 61.3 1.0 C B:ARG1400 3.6 67.9 1.0 CB B:ASP1416 3.7 53.5 1.0 C B:LYS1395 3.8 89.1 1.0 CG B:ASP1402 3.8 73.3 1.0 OD2 B:ASP1398 3.8 93.2 1.0 O B:ASP1413 3.9 56.2 1.0 N B:ASP1398 4.1 77.2 1.0 CB B:ASP1398 4.2 78.6 1.0 CB B:ASP1413 4.3 55.0 1.0 N B:ASP1402 4.3 64.6 1.0 CB B:ASP1402 4.4 67.1 1.0 N B:ARG1400 4.5 69.8 1.0 CG B:LYS1395 4.5 0.0 1.0 N B:GLY1397 4.5 79.8 1.0 N B:CYS1401 4.5 61.3 1.0 CA B:ARG1400 4.5 68.0 1.0 CA B:ASP1398 4.6 77.1 1.0 CA B:CYS1401 4.6 59.6 1.0 CA B:ARG1396 4.6 82.4 1.0 N B:ARG1396 4.6 83.6 1.0 OD1 B:ASP1416 4.7 60.3 1.0 C B:CYS1401 4.7 66.0 1.0 CA B:LYS1395 4.8 88.1 1.0 OD1 B:ASP1402 4.8 74.9 1.0 C B:ASP1413 4.8 56.2 1.0 C B:ASP1398 4.9 82.0 1.0 C B:ARG1396 4.9 84.6 1.0 CB B:LYS1395 4.9 90.4 1.0 CB B:ARG1400 5.0 69.2 1.0 N B:GLN1399 5.0 77.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab


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 NOTCH3 Nrr in Complex with 20358 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1703 b:42.4 occ:1.00 OD1 B:ASN1439 2.2 44.3 1.0 OD2 B:ASP1454 2.3 36.4 1.0 O B:LEU1436 2.3 45.2 1.0 OD1 B:ASP1454 2.4 36.8 1.0 O B:ARG1441 2.4 45.5 1.0 O B:HOH1801 2.4 31.7 1.0 OD2 B:ASP1443 2.6 60.5 1.0 CG B:ASP1454 2.6 35.4 1.0 CG B:ASN1439 3.2 59.6 1.0 C B:LEU1436 3.5 46.6 1.0 CG B:ASP1443 3.5 58.6 1.0 ND2 B:ASN1439 3.6 50.0 1.0 C B:ARG1441 3.6 46.5 1.0 CB B:ASP1443 3.9 48.6 1.0 O B:ASP1454 4.0 32.4 1.0 N B:ASP1443 4.1 46.4 1.0 CB B:ASP1454 4.1 30.4 1.0 N B:ARG1441 4.3 43.7 1.0 CB B:LEU1436 4.3 46.9 1.0 CA B:LEU1436 4.4 46.5 1.0 N B:PHE1437 4.4 40.0 1.0 CA B:ARG1441 4.5 43.9 1.0 C B:CYS1442 4.5 50.1 1.0 O B:PHE1437 4.6 42.0 1.0 OD1 B:ASP1443 4.6 59.3 1.0 N B:CYS1442 4.6 43.4 1.0 CA B:PHE1437 4.6 38.5 1.0 CB B:ASN1439 4.6 42.5 1.0 OD2 B:ASP1457 4.6 40.2 1.0 C B:PHE1437 4.6 42.4 1.0 CA B:ASP1443 4.6 46.0 1.0 CB B:ASP1457 4.6 37.6 1.0 CA B:CYS1442 4.6 43.9 1.0 O B:HOH1803 4.6 38.8 1.0 N B:ASN1439 4.7 40.9 1.0 C B:ASP1454 4.8 33.2 1.0 CA B:ASP1454 4.9 30.6 1.0 CG B:ARG1441 5.0 59.8 1.0 CA B:ASN1439 5.0 41.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of NOTCH3 Nrr in Complex with 20358 Fab


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 NOTCH3 Nrr in Complex with 20358 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1704 b:20.2 occ:1.00 OD2 B:ASP1485 2.3 18.4 1.0 OD2 B:ASP1499 2.3 23.0 1.0 O B:HIS1478 2.3 20.7 1.0 O B:ARG1483 2.4 22.0 1.0 OD1 B:ASP1496 2.4 19.4 1.0 OD1 B:ASP1481 2.4 24.2 1.0 OD2 B:ASP1496 2.5 22.5 1.0 CG B:ASP1496 2.8 22.5 1.0 CG B:ASP1499 3.4 24.1 1.0 CG B:ASP1481 3.4 25.7 1.0 CG B:ASP1485 3.4 22.8 1.0 C B:HIS1478 3.5 22.2 1.0 C B:ARG1483 3.6 23.6 1.0 CB B:ASP1499 3.8 21.0 1.0 OD2 B:ASP1481 3.9 23.2 1.0 CB B:ASP1485 4.0 18.2 1.0 O B:HOH1804 4.0 24.3 1.0 CB B:HIS1478 4.1 21.6 1.0 N B:ASP1485 4.1 18.2 1.0 O B:ASP1496 4.1 21.8 1.0 N B:ASP1481 4.2 19.6 1.0 CA B:HIS1478 4.3 19.9 1.0 N B:ARG1483 4.3 21.8 1.0 CB B:ASP1496 4.3 20.5 1.0 N B:ALA1480 4.4 20.0 1.0 OD1 B:ASP1485 4.4 26.4 1.0 CA B:ARG1483 4.4 21.4 1.0 OD1 B:ASP1499 4.4 24.1 1.0 N B:PHE1479 4.5 18.4 1.0 CB B:ASP1481 4.5 18.4 1.0 N B:CYS1484 4.6 21.1 1.0 CA B:PHE1479 4.6 18.1 1.0 C B:CYS1484 4.7 23.3 1.0 CA B:CYS1484 4.7 21.2 1.0 CA B:ASP1485 4.7 17.6 1.0 C B:PHE1479 4.7 22.9 1.0 CB B:ARG1483 4.8 21.0 1.0 CA B:ASP1481 4.8 18.6 1.0 O B:HOH1818 4.9 16.8 1.0 C B:ASP1496 4.9 21.7 1.0 CA B:ASP1496 4.9 19.8 1.0 N B:GLY1482 5.0 23.1 1.0

P.Bernasconi-Elias, T.Hu, D.Jenkins, B.Firestone, S.Gans, E.Kurth, P.Capodieci, J.Deplazes-Lauber, K.Petropoulos, P.Thiel, D.Ponsel, S.Hee Choi, P.Lemotte, A.London, M.Goetcshkes, E.Nolin, M.D.Jones, K.Slocum, M.J.Kluk, D.M.Weinstock, A.Christodoulou, O.Weinberg, J.Jaehrling, S.A.Ettenberg, A.Buckler, S.C.Blacklow, J.C.Aster, C.J.Fryer. Characterization of Activating Mutations of NOTCH3 in T-Cell Acute Lymphoblastic Leukemia and Anti-Leukemic Activity of NOTCH3 Inhibitory Antibodies. Oncogene V. 35 6077 2016.
ISSN: ISSN 0950-9232
PubMed: 27157619
DOI: 10.1038/ONC.2016.133