Calcium in PDB 3eto: 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr)

The structure of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr), PDB code: 3eto was solved by W.R.Gordon, S.C.Blacklow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.927, 91.759, 59.844, 90.00, 109.38, 90.00
R / Rfree (%)	21.1 / 25.2

The structure of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) (pdb code 3eto). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr), PDB code: 3eto:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:47.3 occ:1.00 O A:VAL1463 2.1 41.8 1.0 OD2 A:ASP1476 2.1 34.4 1.0 OD1 A:ASN1461 2.3 53.9 1.0 O A:ASP1458 2.4 54.8 1.0 OD2 A:ASP1479 2.5 39.7 1.0 OD2 A:ASP1458 2.7 57.2 1.0 CG A:ASP1476 2.8 32.7 1.0 OD1 A:ASP1476 2.8 36.0 1.0 CG A:ASP1458 3.2 59.8 1.0 C A:VAL1463 3.3 43.3 1.0 CG A:ASN1461 3.4 55.2 1.0 C A:ASP1458 3.4 56.6 1.0 CG A:ASP1479 3.5 37.5 1.0 OD1 A:ASP1458 3.7 63.3 1.0 CB A:ASP1479 3.8 33.9 1.0 CB A:ASP1458 3.9 58.1 1.0 ND2 A:ASN1461 4.1 56.3 1.0 N A:VAL1463 4.1 46.2 1.0 CA A:ASP1458 4.2 58.2 1.0 CB A:ASP1476 4.2 32.8 1.0 N A:ASN1461 4.2 54.7 1.0 CA A:VAL1463 4.2 45.3 1.0 N A:CYS1464 4.2 42.4 1.0 O A:ASP1476 4.2 31.3 1.0 N A:SER1465 4.3 42.1 1.0 OG A:SER1465 4.3 46.7 1.0 CA A:CYS1464 4.3 41.8 1.0 CB A:ASN1461 4.4 54.8 1.0 N A:ALA1459 4.4 55.7 1.0 N A:GLY1460 4.6 55.0 1.0 CB A:VAL1463 4.6 46.7 1.0 OD1 A:ASP1479 4.6 39.4 1.0 CB A:SER1465 4.6 41.6 1.0 CA A:ASN1461 4.6 54.0 1.0 C A:CYS1464 4.6 42.4 1.0 CA A:ALA1459 4.7 55.4 1.0 C A:ASN1461 4.8 53.3 1.0 C A:ALA1459 4.8 55.5 1.0 N A:LYS1462 4.9 52.0 1.0

Calcium binding site 2 out of 6 in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:45.4 occ:1.00 OD1 A:ASP1521 2.3 41.4 1.0 O A:TYR1500 2.3 42.8 1.0 OD1 A:ASP1507 2.3 47.8 1.0 O A:HIS1505 2.4 52.2 1.0 OD1 A:ASP1503 2.4 46.8 1.0 OD2 A:ASP1518 2.5 40.2 1.0 OD1 A:ASP1518 2.7 38.5 1.0 CG A:ASP1518 2.9 39.6 1.0 CG A:ASP1503 3.3 47.0 1.0 CG A:ASP1521 3.3 42.2 1.0 C A:TYR1500 3.4 43.8 1.0 CG A:ASP1507 3.5 48.7 1.0 C A:HIS1505 3.6 52.3 1.0 CB A:ASP1521 3.7 43.9 1.0 OD2 A:ASP1503 3.7 49.0 1.0 CB A:TYR1500 4.0 44.8 1.0 N A:ASP1507 4.0 49.0 1.0 CB A:ASP1507 4.1 47.8 1.0 N A:ASP1503 4.1 48.6 1.0 O A:ASP1518 4.1 37.2 1.0 CA A:TYR1500 4.1 44.4 1.0 N A:SER1502 4.3 44.4 1.0 N A:HIS1505 4.3 52.8 1.0 N A:PHE1501 4.4 43.5 1.0 CB A:ASP1518 4.4 37.5 1.0 OD2 A:ASP1521 4.4 41.3 1.0 CA A:HIS1505 4.4 52.6 1.0 CB A:ASP1503 4.4 49.0 1.0 OD2 A:ASP1507 4.5 48.0 1.0 C A:PHE1501 4.6 44.1 1.0 C A:CYS1506 4.6 50.3 1.0 N A:CYS1506 4.6 51.3 1.0 CA A:PHE1501 4.6 43.5 1.0 CA A:ASP1507 4.7 48.0 1.0 CA A:ASP1503 4.7 48.9 1.0 CA A:CYS1506 4.7 50.8 1.0 CB A:HIS1505 4.7 53.0 1.0 O A:HOH113 4.9 38.7 1.0 C A:ASP1503 4.9 50.3 1.0 N A:GLY1504 5.0 51.1 1.0 C A:ASP1518 5.0 37.3 1.0 CA A:SER1502 5.0 45.9 1.0

Calcium binding site 3 out of 6 in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:36.0 occ:1.00 O A:HIS1545 2.3 37.2 1.0 O A:HIS1540 2.4 37.8 1.0 OD1 A:ASP1561 2.4 32.9 1.0 OD2 A:ASP1547 2.4 32.2 1.0 OD2 A:ASP1558 2.4 34.4 1.0 OD1 A:ASP1558 2.5 34.9 1.0 OD1 A:ASP1543 2.6 36.8 1.0 CG A:ASP1558 2.8 34.2 1.0 CG A:ASP1561 3.4 36.7 1.0 CG A:ASP1543 3.5 39.1 1.0 CG A:ASP1547 3.5 37.5 1.0 C A:HIS1545 3.5 36.4 1.0 C A:HIS1540 3.5 38.6 1.0 CB A:ASP1561 3.7 37.7 1.0 OD2 A:ASP1543 3.9 37.0 1.0 CB A:ASP1547 3.9 34.4 1.0 N A:ASP1547 4.0 35.0 1.0 N A:ASP1543 4.2 39.5 1.0 CB A:HIS1540 4.2 38.5 1.0 N A:HIS1545 4.3 37.5 1.0 O A:ASP1558 4.3 32.4 1.0 CB A:ASP1558 4.3 32.4 1.0 N A:SER1542 4.3 39.2 1.0 CA A:HIS1545 4.4 37.2 1.0 CA A:HIS1540 4.4 38.6 1.0 N A:CYS1546 4.5 35.2 1.0 C A:CYS1546 4.5 36.0 1.0 N A:PHE1541 4.5 38.2 1.0 OD2 A:ASP1561 4.5 37.6 1.0 CA A:CYS1546 4.6 35.7 1.0 OD1 A:ASP1547 4.6 35.0 1.0 CA A:ASP1547 4.6 34.2 1.0 CB A:ASP1543 4.7 38.5 1.0 CA A:PHE1541 4.7 38.2 1.0 C A:PHE1541 4.7 38.3 1.0 CB A:HIS1545 4.8 37.2 1.0 O A:HOH39 4.8 35.1 1.0 CA A:ASP1543 4.9 38.5 1.0

Calcium binding site 4 out of 6 in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:46.9 occ:1.00 O B:VAL1463 2.2 43.6 1.0 OD1 B:ASP1476 2.3 35.2 1.0 O B:ASP1458 2.3 64.8 1.0 OD2 B:ASP1479 2.4 39.5 1.0 OD1 B:ASN1461 2.5 52.7 1.0 OD2 B:ASP1476 2.7 40.9 1.0 OD1 B:ASP1458 2.7 67.7 1.0 CG B:ASP1476 2.8 33.6 1.0 C B:ASP1458 3.3 65.5 1.0 C B:VAL1463 3.3 44.1 1.0 CG B:ASP1479 3.4 37.4 1.0 CG B:ASN1461 3.5 54.8 1.0 CG B:ASP1458 3.6 68.3 1.0 CB B:ASP1479 3.8 34.5 1.0 CB B:ASP1458 3.8 67.1 1.0 N B:VAL1463 4.0 48.4 1.0 CA B:ASP1458 4.1 67.0 1.0 CA B:VAL1463 4.1 46.3 1.0 CB B:ASP1476 4.2 34.2 1.0 N B:ASN1461 4.2 56.2 1.0 O B:ASP1476 4.2 30.6 1.0 N B:SER1465 4.3 42.0 1.0 ND2 B:ASN1461 4.3 52.1 1.0 N B:ALA1459 4.3 64.0 1.0 OG B:SER1465 4.3 45.9 1.0 N B:CYS1464 4.4 42.0 1.0 CB B:VAL1463 4.4 47.2 1.0 N B:GLY1460 4.5 60.0 1.0 OD1 B:ASP1479 4.5 40.3 1.0 CA B:ALA1459 4.5 62.6 1.0 CA B:CYS1464 4.5 41.7 1.0 CB B:ASN1461 4.6 54.9 1.0 OD2 B:ASP1458 4.6 69.4 1.0 CB B:SER1465 4.7 41.5 1.0 C B:ALA1459 4.7 61.7 1.0 CA B:ASN1461 4.7 54.8 1.0 C B:CYS1464 4.8 41.5 1.0 N B:LYS1462 4.8 53.4 1.0 C B:ASN1461 4.8 54.2 1.0 O B:HOH243 4.9 57.8 1.0 CG1 B:VAL1463 5.0 46.1 1.0 C B:ASP1476 5.0 32.8 1.0

Calcium binding site 5 out of 6 in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:44.0 occ:1.00 OD2 B:ASP1507 2.3 42.6 1.0 O B:TYR1500 2.4 42.0 1.0 O B:HIS1505 2.4 48.6 1.0 OD2 B:ASP1521 2.4 41.7 1.0 OD2 B:ASP1503 2.6 48.4 1.0 OD1 B:ASP1518 2.7 39.0 1.0 OD2 B:ASP1518 2.7 39.9 1.0 CG B:ASP1518 3.0 39.1 1.0 CG B:ASP1503 3.4 48.1 1.0 CG B:ASP1521 3.4 41.7 1.0 C B:TYR1500 3.4 43.3 1.0 CG B:ASP1507 3.4 44.6 1.0 C B:HIS1505 3.6 49.5 1.0 OD1 B:ASP1503 3.7 49.0 1.0 CB B:ASP1521 3.7 42.3 1.0 CB B:TYR1500 4.0 45.0 1.0 CB B:ASP1507 4.1 44.2 1.0 N B:ASP1503 4.1 48.0 1.0 N B:ASP1507 4.1 45.0 1.0 O B:HOH149 4.2 50.2 1.0 CA B:TYR1500 4.2 44.3 1.0 O B:ASP1518 4.2 38.2 1.0 N B:HIS1505 4.2 51.1 1.0 N B:SER1502 4.3 44.9 1.0 N B:PHE1501 4.4 43.4 1.0 CA B:HIS1505 4.4 50.4 1.0 CB B:ASP1518 4.5 38.5 1.0 OD1 B:ASP1507 4.5 47.0 1.0 CB B:ASP1503 4.5 48.4 1.0 OD1 B:ASP1521 4.6 43.0 1.0 N B:CYS1506 4.6 48.5 1.0 C B:PHE1501 4.6 44.2 1.0 CA B:PHE1501 4.7 43.0 1.0 C B:CYS1506 4.7 46.8 1.0 CB B:HIS1505 4.7 50.8 1.0 O B:HOH191 4.7 38.5 1.0 CA B:CYS1506 4.7 47.3 1.0 CA B:ASP1503 4.7 48.8 1.0 CA B:ASP1507 4.8 44.0 1.0 N B:GLY1504 4.8 50.1 1.0 C B:ASP1503 4.9 49.3 1.0

Calcium binding site 6 out of 6 in the 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 2 Angstrom Xray Structure of the NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:34.8 occ:1.00 O B:HIS1540 2.3 35.9 1.0 OD1 B:ASP1543 2.4 34.8 1.0 OD2 B:ASP1561 2.4 37.3 1.0 OD1 B:ASP1558 2.4 35.6 1.0 OD1 B:ASP1547 2.4 34.7 1.0 O B:HIS1545 2.4 36.2 1.0 OD2 B:ASP1558 2.5 33.5 1.0 CG B:ASP1558 2.8 33.8 1.0 CG B:ASP1561 3.4 37.8 1.0 CG B:ASP1543 3.4 38.4 1.0 CG B:ASP1547 3.5 36.2 1.0 C B:HIS1540 3.5 37.0 1.0 C B:HIS1545 3.6 36.0 1.0 CB B:ASP1561 3.7 38.5 1.0 OD2 B:ASP1543 3.9 38.3 1.0 CB B:ASP1547 3.9 33.9 1.0 N B:ASP1547 4.0 34.0 1.0 CB B:HIS1540 4.1 37.7 1.0 N B:ASP1543 4.2 39.5 1.0 O B:ASP1558 4.2 31.3 1.0 O B:HOH50 4.3 36.5 1.0 CB B:ASP1558 4.3 31.6 1.0 N B:HIS1545 4.3 36.9 1.0 CA B:HIS1540 4.3 37.4 1.0 N B:SER1542 4.3 37.6 1.0 CA B:HIS1545 4.4 37.0 1.0 C B:CYS1546 4.5 35.6 1.0 N B:PHE1541 4.5 35.8 1.0 OD1 B:ASP1561 4.5 35.8 1.0 N B:CYS1546 4.6 35.6 1.0 CB B:ASP1543 4.6 39.7 1.0 OD2 B:ASP1547 4.6 34.9 1.0 CA B:ASP1547 4.6 33.6 1.0 CA B:CYS1546 4.6 35.1 1.0 CA B:PHE1541 4.7 36.2 1.0 C B:PHE1541 4.7 36.3 1.0 CB B:HIS1545 4.8 36.5 1.0 O B:HOH46 4.8 35.2 1.0 CA B:ASP1543 4.8 38.8 1.0

W.R.Gordon, M.Roy, D.Vardar-Ulu, M.Garfinkel, M.R.Mansour, J.C.Aster, S.C.Blacklow. Structure of the NOTCH1-Negative Regulatory Region: Implications For Normal Activation and Pathogenic Signaling in T-All. Blood V. 113 4381 2009.
ISSN: ISSN 0006-4971
PubMed: 19075186
DOI: 10.1182/BLOOD-2008-08-174748