Calcium in PDB 4zlp: Crystal Structure of NOTCH3 Negative Regulatory Region

The structure of Crystal Structure of NOTCH3 Negative Regulatory Region, PDB code: 4zlp was solved by X.Xu, S.C.Blacklow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.18 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.482, 64.310, 83.089, 90.00, 105.23, 90.00
R / Rfree (%)	17.8 / 20.4

The binding sites of Calcium atom in the Crystal Structure of NOTCH3 Negative Regulatory Region (pdb code 4zlp). 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 Negative Regulatory Region, PDB code: 4zlp:
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 Negative Regulatory Region


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 Negative Regulatory Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5001 b:52.6 occ:1.00 OD1 A:ASP1398 2.3 69.4 1.0 OD2 A:ASP1402 2.4 55.0 1.0 OD2 A:ASP1416 2.4 50.8 1.0 O A:LYS1395 2.4 58.0 1.0 OD2 A:ASP1413 2.4 42.2 1.0 O A:ARG1400 2.4 44.7 1.0 OD1 A:ASP1413 2.4 37.3 1.0 CG A:ASP1413 2.7 37.7 1.0 CG A:ASP1416 3.4 46.7 1.0 CG A:ASP1402 3.4 55.7 1.0 CG A:ASP1398 3.5 71.1 1.0 C A:LYS1395 3.5 61.7 1.0 C A:ARG1400 3.6 46.1 1.0 CB A:ASP1416 3.7 43.2 1.0 CB A:ASP1402 3.9 45.8 1.0 OD2 A:ASP1398 4.0 72.3 1.0 N A:ASP1402 4.0 38.8 1.0 CB A:ASP1413 4.1 33.1 1.0 CB A:LYS1395 4.2 68.9 1.0 O A:ASP1413 4.2 34.2 1.0 CA A:ARG1396 4.4 58.1 1.0 CA A:LYS1395 4.4 67.6 1.0 N A:ARG1400 4.4 53.6 1.0 N A:ARG1396 4.4 60.3 1.0 OD1 A:ASP1402 4.4 61.6 1.0 N A:GLY1397 4.5 59.8 1.0 CA A:ARG1400 4.5 50.7 1.0 N A:ASP1398 4.5 62.9 1.0 N A:CYS1401 4.5 45.8 1.0 C A:CYS1401 4.5 42.4 1.0 OD1 A:ASP1416 4.5 47.7 1.0 CA A:CYS1401 4.5 42.4 1.0 CA A:ASP1402 4.6 39.3 1.0 CB A:ASP1398 4.7 69.6 1.0 O A:HOH5134 4.8 47.0 1.0 C A:ARG1396 4.8 62.5 1.0 CB A:ARG1400 4.8 54.5 1.0 C A:ASP1413 4.9 35.1 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of NOTCH3 Negative Regulatory Region


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 Negative Regulatory Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5002 b:25.2 occ:1.00 OD2 A:ASP1443 2.4 29.9 1.0 O A:ARG1441 2.4 28.4 1.0 OD1 A:ASP1454 2.4 24.0 1.0 O A:LEU1436 2.4 26.2 1.0 OD2 A:ASP1457 2.4 27.2 1.0 OD2 A:ASP1454 2.4 22.4 1.0 OD1 A:ASN1439 2.4 28.7 1.0 CG A:ASP1454 2.7 21.6 1.0 CG A:ASN1439 3.3 27.2 1.0 CG A:ASP1457 3.4 34.3 1.0 CG A:ASP1443 3.5 29.1 1.0 C A:LEU1436 3.5 23.5 1.0 C A:ARG1441 3.6 29.6 1.0 ND2 A:ASN1439 3.6 29.0 1.0 CB A:ASP1457 3.8 33.1 1.0 N A:ASP1443 4.0 21.7 1.0 CB A:ASP1443 4.1 22.3 1.0 N A:ARG1441 4.1 29.0 1.0 O A:ASP1454 4.2 21.5 1.0 CB A:ASP1454 4.2 18.4 1.0 CB A:LEU1436 4.3 18.5 1.0 CA A:ARG1441 4.4 30.3 1.0 N A:PHE1437 4.4 21.1 1.0 CA A:LEU1436 4.4 24.4 1.0 CA A:PHE1437 4.5 19.9 1.0 O A:PHE1437 4.5 29.0 1.0 OD1 A:ASP1443 4.5 29.7 1.0 C A:CYS1442 4.5 21.3 1.0 C A:PHE1437 4.5 22.9 1.0 N A:CYS1442 4.6 27.1 1.0 OD1 A:ASP1457 4.6 33.1 1.0 N A:ASN1439 4.6 18.7 1.0 CA A:CYS1442 4.7 24.4 1.0 CB A:ASN1439 4.7 20.9 1.0 CA A:ASP1443 4.7 23.5 1.0 O A:HOH5139 4.8 28.9 1.0 CB A:ARG1441 4.8 34.2 1.0 N A:SER1440 4.9 27.4 1.0 C A:ASP1454 4.9 20.7 1.0 CA A:ASP1454 4.9 23.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of NOTCH3 Negative Regulatory Region


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 Negative Regulatory Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5003 b:21.8 occ:1.00 OD2 A:ASP1485 2.3 26.2 1.0 OD2 A:ASP1499 2.4 30.1 1.0 OD1 A:ASP1481 2.4 37.8 1.0 O A:ARG1483 2.4 30.5 1.0 OD2 A:ASP1496 2.4 23.3 1.0 O A:HIS1478 2.4 29.2 1.0 OD1 A:ASP1496 2.4 27.6 1.0 CG A:ASP1496 2.7 22.6 1.0 CG A:ASP1481 3.3 34.5 1.0 CG A:ASP1499 3.4 31.0 1.0 CG A:ASP1485 3.5 27.1 1.0 C A:HIS1478 3.6 29.7 1.0 C A:ARG1483 3.6 31.0 1.0 OD2 A:ASP1481 3.7 35.1 1.0 CB A:ASP1499 3.7 30.7 1.0 N A:ASP1485 4.0 22.1 1.0 O A:HOH5119 4.1 35.6 1.0 CB A:HIS1478 4.1 28.5 1.0 CB A:ASP1485 4.1 23.6 1.0 O A:ASP1496 4.1 24.5 1.0 CB A:ASP1496 4.2 19.8 1.0 N A:ASP1481 4.2 26.3 1.0 N A:ARG1483 4.3 32.2 1.0 CA A:HIS1478 4.3 30.7 1.0 OD1 A:ASP1499 4.4 31.4 1.0 CA A:ARG1483 4.5 31.8 1.0 C A:CYS1484 4.5 26.3 1.0 N A:CYS1484 4.5 28.4 1.0 CA A:CYS1484 4.5 25.9 1.0 N A:ALA1480 4.5 27.4 1.0 OD1 A:ASP1485 4.5 27.9 1.0 N A:PHE1479 4.6 29.0 1.0 CB A:ASP1481 4.6 28.9 1.0 CA A:ASP1485 4.7 23.8 1.0 CA A:PHE1479 4.8 26.7 1.0 CA A:ASP1481 4.9 27.1 1.0 C A:PHE1479 4.9 28.0 1.0 O A:HOH5150 4.9 26.1 1.0 N A:GLY1482 4.9 26.6 1.0 C A:ASP1496 4.9 23.3 1.0 CA A:ASP1496 4.9 19.4 1.0 CB A:ARG1483 4.9 34.6 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of NOTCH3 Negative Regulatory Region


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 Negative Regulatory Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5001 b:0.7 occ:1.00 CG B:ASP1398 2.1 0.2 1.0 OD2 B:ASP1413 2.3 1.0 1.0 OD2 B:ASP1398 2.3 0.7 1.0 OD2 B:ASP1402 2.3 0.5 1.0 OD1 B:ASP1413 2.4 0.8 1.0 OD1 B:ASP1398 2.4 0.7 1.0 OD2 B:ASP1416 2.4 0.8 1.0 O B:ARG1400 2.4 0.9 1.0 CG B:ASP1413 2.6 0.1 1.0 CB B:ASP1398 3.0 0.2 1.0 CG B:ASP1402 3.4 0.7 1.0 CG B:ASP1416 3.7 1.0 1.0 C B:ARG1400 3.7 0.5 1.0 CB B:ASP1402 4.0 0.7 1.0 CB B:ASP1413 4.1 97.6 1.0 N B:ASP1402 4.2 0.4 1.0 CA B:ASP1398 4.3 0.1 1.0 CB B:ASP1416 4.4 97.3 1.0 OD1 B:ASP1402 4.5 0.9 1.0 O B:ASP1413 4.5 93.0 1.0 N B:ASP1398 4.6 0.6 1.0 N B:ARG1400 4.6 0.6 1.0 CA B:ARG1400 4.6 0.0 1.0 OD1 B:ASP1416 4.7 98.0 1.0 N B:CYS1401 4.7 0.2 1.0 C B:CYS1401 4.7 1.0 1.0 CA B:ASP1402 4.8 0.2 1.0 CB B:ARG1400 4.8 0.1 1.0 CA B:CYS1401 4.8 0.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of NOTCH3 Negative Regulatory Region


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 Negative Regulatory Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5002 b:72.5 occ:1.00 OD2 B:ASP1454 2.4 73.8 1.0 OD2 B:ASP1443 2.4 83.6 1.0 OD1 B:ASP1454 2.4 77.4 1.0 OD2 B:ASP1457 2.4 87.7 1.0 OD1 B:ASN1439 2.4 78.1 1.0 O B:LEU1436 2.4 80.6 1.0 O B:ARG1441 2.4 76.7 1.0 CG B:ASP1454 2.7 77.7 1.0 CG B:ASP1457 3.4 84.3 1.0 CG B:ASN1439 3.4 83.0 1.0 CG B:ASP1443 3.5 85.8 1.0 C B:ARG1441 3.6 78.2 1.0 C B:LEU1436 3.6 83.4 1.0 CB B:ASP1457 3.7 81.1 1.0 ND2 B:ASN1439 3.7 84.1 1.0 O B:ASP1454 4.0 66.6 1.0 N B:ASP1443 4.0 82.0 1.0 N B:ARG1441 4.0 79.0 1.0 CB B:ASP1443 4.1 85.1 1.0 CB B:ASP1454 4.1 70.7 1.0 CB B:LEU1436 4.4 87.1 1.0 CA B:ARG1441 4.4 77.8 1.0 O B:PHE1437 4.5 85.1 1.0 CA B:LEU1436 4.5 87.5 1.0 N B:PHE1437 4.5 83.9 1.0 OD1 B:ASP1457 4.5 84.6 1.0 N B:CYS1442 4.5 77.5 1.0 C B:PHE1437 4.5 85.6 1.0 OD1 B:ASP1443 4.5 90.3 1.0 CA B:PHE1437 4.6 82.4 1.0 C B:CYS1442 4.6 81.6 1.0 CA B:CYS1442 4.6 77.0 1.0 N B:ASN1439 4.6 87.7 1.0 CA B:ASP1443 4.7 84.6 1.0 C B:ASP1454 4.7 66.4 1.0 CB B:ASN1439 4.7 87.3 1.0 N B:SER1440 4.8 82.3 1.0 CA B:ASP1454 4.8 71.7 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of NOTCH3 Negative Regulatory Region


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 Negative Regulatory Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5003 b:31.8 occ:1.00 OD2 B:ASP1485 2.4 31.5 1.0 OD2 B:ASP1496 2.4 33.6 1.0 OD1 B:ASP1481 2.4 35.1 1.0 OD2 B:ASP1499 2.4 32.4 1.0 OD1 B:ASP1496 2.4 35.8 1.0 O B:ARG1483 2.4 30.4 1.0 O B:HIS1478 2.4 34.2 1.0 CG B:ASP1496 2.7 32.4 1.0 CG B:ASP1481 3.3 35.0 1.0 CG B:ASP1499 3.4 33.1 1.0 CG B:ASP1485 3.5 29.7 1.0 C B:HIS1478 3.5 34.3 1.0 C B:ARG1483 3.6 32.5 1.0 OD2 B:ASP1481 3.7 33.1 1.0 CB B:ASP1499 3.8 31.7 1.0 N B:ASP1485 4.0 28.5 1.0 O B:ASP1496 4.1 31.4 1.0 CB B:ASP1485 4.1 25.9 1.0 CB B:HIS1478 4.1 31.9 1.0 N B:ASP1481 4.2 37.0 1.0 CB B:ASP1496 4.2 30.3 1.0 N B:ARG1483 4.3 30.7 1.0 O B:HOH5104 4.3 30.5 1.0 CA B:HIS1478 4.4 34.1 1.0 N B:ALA1480 4.4 37.1 1.0 OD1 B:ASP1499 4.4 34.4 1.0 CA B:ARG1483 4.5 30.5 1.0 N B:PHE1479 4.5 34.9 1.0 C B:CYS1484 4.5 30.9 1.0 N B:CYS1484 4.5 31.4 1.0 CB B:ASP1481 4.5 33.2 1.0 CA B:CYS1484 4.6 32.7 1.0 OD1 B:ASP1485 4.6 29.7 1.0 O B:HOH5105 4.6 29.8 1.0 CA B:PHE1479 4.7 35.6 1.0 CA B:ASP1485 4.7 26.2 1.0 C B:PHE1479 4.8 36.0 1.0 CA B:ASP1481 4.8 35.4 1.0 C B:ASP1496 4.9 33.2 1.0 N B:GLY1482 4.9 34.8 1.0 CA B:ASP1496 4.9 30.7 1.0 CB B:ARG1483 4.9 31.2 1.0

X.Xu, S.H.Choi, T.Hu, K.Tiyanont, R.Habets, A.J.Groot, M.Vooijs, J.C.Aster, R.Chopra, C.Fryer, S.C.Blacklow. Insights Into Autoregulation of NOTCH3 From Structural and Functional Studies of Its Negative Regulatory Region. Structure V. 23 1227 2015.
ISSN: ISSN 0969-2126
PubMed: 26051713
DOI: 10.1016/J.STR.2015.05.001