Calcium in PDB 3i08: Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr)

The structure of Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr), PDB code: 3i08 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)	46.32 / 3.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.868, 65.868, 322.586, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.6

The structure of Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) (pdb code 3i08). 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 the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr), PDB code: 3i08:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of the S1-Cleaved 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 Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:75.3 occ:1.00 OD1 A:ASP1476 2.3 86.5 1.0 OD2 A:ASP1479 2.4 84.7 1.0 O A:ASP1458 2.5 0.5 1.0 O A:VAL1463 2.5 1.0 1.0 OD1 A:ASN1461 2.5 0.2 1.0 OG A:SER1465 2.8 99.5 1.0 CG A:ASP1476 3.0 86.8 1.0 OD2 A:ASP1476 3.0 88.5 1.0 CG A:ASN1461 3.1 0.2 1.0 C A:ASP1458 3.4 0.8 1.0 OD1 A:ASP1458 3.4 1.0 1.0 ND2 A:ASN1461 3.5 0.8 1.0 CG A:ASP1479 3.6 85.5 1.0 C A:VAL1463 3.7 0.1 1.0 CB A:ASP1458 3.9 1.0 1.0 N A:SER1465 3.9 99.8 1.0 CB A:SER1465 3.9 0.1 1.0 CG A:ASP1458 3.9 0.6 1.0 N A:VAL1463 4.0 0.7 1.0 CB A:ASN1461 4.1 0.5 1.0 CB A:ASP1479 4.2 85.3 1.0 N A:ALA1459 4.2 0.1 1.0 CA A:ASP1458 4.2 0.6 1.0 N A:ASN1461 4.3 0.4 1.0 N A:GLY1460 4.4 0.1 1.0 CA A:VAL1463 4.4 0.9 1.0 CB A:ASP1476 4.5 86.2 1.0 CA A:ALA1459 4.5 0.2 1.0 CA A:SER1465 4.5 100.0 1.0 OD1 A:ASP1479 4.6 86.3 1.0 N A:CYS1464 4.7 0.2 1.0 CG2 A:VAL1463 4.8 0.3 1.0 O A:ASP1476 4.8 85.2 1.0 CA A:ASN1461 4.8 0.7 1.0 CA A:CYS1464 4.8 99.5 1.0 C A:CYS1464 4.9 99.7 1.0 C A:ALA1459 4.9 0.6 1.0 OD2 A:ASP1458 5.0 0.4 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the S1-Cleaved 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 Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1666 b:64.3 occ:1.00 OD1 A:ASP1507 2.1 78.7 1.0 OD2 A:ASP1521 2.2 72.8 1.0 O A:TYR1500 2.4 74.8 1.0 O A:HIS1505 2.5 82.0 1.0 OD2 A:ASP1518 2.5 65.8 1.0 OD1 A:ASP1518 2.5 66.1 1.0 CG A:ASP1518 2.9 65.1 1.0 OD2 A:ASP1503 3.0 77.5 1.0 CG A:ASP1521 3.2 74.8 1.0 CG A:ASP1507 3.2 79.7 1.0 CG A:ASP1503 3.5 77.0 1.0 C A:TYR1500 3.5 74.4 1.0 CB A:ASP1521 3.5 76.3 1.0 C A:HIS1505 3.7 81.9 1.0 OD1 A:ASP1503 3.7 77.8 1.0 OD2 A:ASP1507 3.9 82.4 1.0 CB A:TYR1500 3.9 74.2 1.0 N A:ASP1503 4.0 76.2 1.0 O A:ASP1518 4.1 65.3 1.0 N A:ASP1507 4.1 79.4 1.0 CA A:TYR1500 4.2 74.4 1.0 N A:SER1502 4.3 74.7 1.0 CB A:ASP1518 4.3 64.0 1.0 CB A:ASP1507 4.3 78.7 1.0 OD1 A:ASP1521 4.4 73.0 1.0 CB A:ASP1503 4.5 77.2 1.0 N A:PHE1501 4.5 74.2 1.0 CA A:CYS1506 4.5 81.3 1.0 N A:CYS1506 4.5 81.7 1.0 C A:PHE1501 4.6 74.2 1.0 CA A:ASP1503 4.6 77.0 1.0 C A:CYS1506 4.7 80.3 1.0 CA A:HIS1505 4.7 82.2 1.0 CA A:PHE1501 4.7 73.8 1.0 N A:HIS1505 4.7 81.4 1.0 CA A:ASP1507 4.8 78.3 1.0 C A:ASP1518 4.9 65.0 1.0 C A:SER1502 4.9 75.1 1.0 N A:GLY1504 4.9 78.3 1.0 CA A:SER1502 4.9 74.8 1.0 C A:ASP1503 5.0 77.5 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the S1-Cleaved 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 Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1667 b:47.5 occ:1.00 O A:HIS1545 2.2 61.0 1.0 OD1 A:ASP1558 2.3 61.1 1.0 OD1 A:ASP1547 2.4 64.0 1.0 OD2 A:ASP1558 2.5 64.6 1.0 O A:HIS1540 2.5 62.8 1.0 OD2 A:ASP1543 2.6 66.5 1.0 OD2 A:ASP1561 2.7 66.1 1.0 CG A:ASP1558 2.7 63.7 1.0 CG A:ASP1543 3.3 63.5 1.0 C A:HIS1545 3.4 61.3 1.0 CG A:ASP1547 3.5 61.2 1.0 OD1 A:ASP1543 3.5 66.9 1.0 CG A:ASP1561 3.6 67.1 1.0 C A:HIS1540 3.6 63.0 1.0 CB A:ASP1561 3.7 66.9 1.0 N A:ASP1547 3.9 59.7 1.0 CB A:HIS1540 4.1 63.1 1.0 CB A:ASP1547 4.2 59.4 1.0 N A:ASP1543 4.2 60.1 1.0 CB A:ASP1558 4.3 63.6 1.0 N A:HIS1545 4.3 61.6 1.0 CA A:HIS1545 4.3 61.2 1.0 O A:ASP1558 4.3 62.9 1.0 N A:CYS1546 4.4 61.5 1.0 CA A:HIS1540 4.4 63.2 1.0 C A:CYS1546 4.4 60.6 1.0 CA A:CYS1546 4.4 61.8 1.0 OD2 A:ASP1547 4.4 62.9 1.0 CB A:HIS1545 4.5 61.4 1.0 N A:SER1542 4.5 61.4 1.0 N A:PHE1541 4.6 63.0 1.0 CB A:ASP1543 4.6 61.1 1.0 CA A:ASP1547 4.7 59.0 1.0 OD1 A:ASP1561 4.7 68.9 1.0 CA A:PHE1541 4.8 62.5 1.0 C A:PHE1541 4.8 61.7 1.0 CA A:ASP1543 4.9 60.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the S1-Cleaved 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 Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:76.7 occ:1.00 OD1 C:ASP1476 2.3 86.4 1.0 OD2 C:ASP1479 2.5 84.2 1.0 O C:ASP1458 2.5 0.6 1.0 OD1 C:ASN1461 2.6 0.2 1.0 O C:VAL1463 2.6 0.1 1.0 OG C:SER1465 2.8 99.7 1.0 OD2 C:ASP1476 3.0 88.8 1.0 CG C:ASP1476 3.0 87.0 1.0 CG C:ASN1461 3.1 0.2 1.0 OD1 C:ASP1458 3.3 0.0 1.0 C C:ASP1458 3.4 0.8 1.0 ND2 C:ASN1461 3.5 0.9 1.0 CG C:ASP1479 3.7 85.3 1.0 C C:VAL1463 3.8 0.2 1.0 CB C:ASP1458 3.8 0.1 1.0 CG C:ASP1458 3.9 0.8 1.0 CB C:SER1465 3.9 0.2 1.0 N C:SER1465 3.9 100.0 1.0 N C:VAL1463 4.1 0.6 1.0 N C:ALA1459 4.2 0.9 1.0 CB C:ASN1461 4.2 0.5 1.0 CA C:ASP1458 4.2 0.6 1.0 CB C:ASP1479 4.3 85.3 1.0 N C:ASN1461 4.4 0.5 1.0 N C:GLY1460 4.4 0.1 1.0 CA C:ALA1459 4.5 0.1 1.0 CB C:ASP1476 4.5 86.0 1.0 CA C:VAL1463 4.5 0.9 1.0 CA C:SER1465 4.5 0.1 1.0 OD1 C:ASP1479 4.7 86.2 1.0 N C:CYS1464 4.8 0.2 1.0 O C:ASP1476 4.8 85.0 1.0 CG2 C:VAL1463 4.8 0.3 1.0 CA C:ASN1461 4.8 0.6 1.0 C C:ALA1459 4.8 0.6 1.0 CA C:CYS1464 4.9 99.5 1.0 C C:CYS1464 4.9 99.8 1.0 OD2 C:ASP1458 4.9 0.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the S1-Cleaved 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 Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1666 b:67.8 occ:1.00 OD2 C:ASP1521 2.2 73.1 1.0 OD1 C:ASP1507 2.2 78.5 1.0 O C:TYR1500 2.4 74.9 1.0 O C:HIS1505 2.5 81.9 1.0 OD1 C:ASP1518 2.5 66.2 1.0 OD2 C:ASP1518 2.7 65.2 1.0 OD2 C:ASP1503 2.9 77.4 1.0 CG C:ASP1518 2.9 64.8 1.0 CG C:ASP1521 3.2 75.0 1.0 CG C:ASP1507 3.3 79.4 1.0 CG C:ASP1503 3.4 77.1 1.0 C C:TYR1500 3.5 74.4 1.0 CB C:ASP1521 3.5 76.2 1.0 OD1 C:ASP1503 3.6 77.9 1.0 C C:HIS1505 3.7 81.9 1.0 OD2 C:ASP1507 3.8 82.2 1.0 N C:ASP1503 3.9 76.1 1.0 CB C:TYR1500 3.9 74.1 1.0 O C:ASP1518 4.0 65.3 1.0 N C:ASP1507 4.1 79.4 1.0 CA C:TYR1500 4.2 74.4 1.0 N C:SER1502 4.2 74.5 1.0 OD1 C:ASP1521 4.3 73.3 1.0 CB C:ASP1518 4.4 63.9 1.0 CB C:ASP1503 4.4 77.1 1.0 CB C:ASP1507 4.4 78.6 1.0 N C:PHE1501 4.4 74.2 1.0 C C:PHE1501 4.5 74.2 1.0 CA C:CYS1506 4.5 81.2 1.0 N C:CYS1506 4.6 81.7 1.0 CA C:ASP1503 4.6 77.1 1.0 N C:HIS1505 4.6 81.4 1.0 CA C:PHE1501 4.7 73.8 1.0 CA C:HIS1505 4.7 82.2 1.0 C C:CYS1506 4.7 80.3 1.0 CA C:SER1502 4.9 74.7 1.0 C C:SER1502 4.9 75.0 1.0 N C:GLY1504 4.9 78.3 1.0 C C:ASP1518 4.9 65.1 1.0 CA C:ASP1507 4.9 78.3 1.0 C C:ASP1503 4.9 77.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the S1-Cleaved 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 Crystal Structure of the S1-Cleaved NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1667 b:51.5 occ:1.00 O C:HIS1545 2.3 60.3 1.0 OD2 C:ASP1558 2.4 67.0 1.0 OD1 C:ASP1547 2.4 56.3 1.0 O C:HIS1540 2.5 65.0 1.0 OD2 C:ASP1543 2.5 68.7 1.0 OD2 C:ASP1561 2.6 65.0 1.0 OD1 C:ASP1558 2.6 62.1 1.0 CG C:ASP1558 2.8 64.7 1.0 CG C:ASP1543 3.4 66.1 1.0 C C:HIS1545 3.5 60.9 1.0 CG C:ASP1561 3.5 66.1 1.0 CG C:ASP1547 3.5 56.8 1.0 C C:HIS1540 3.6 65.7 1.0 OD1 C:ASP1543 3.6 67.1 1.0 CB C:ASP1561 3.7 66.3 1.0 N C:ASP1547 3.9 58.9 1.0 O C:ASP1558 4.1 64.8 1.0 CB C:ASP1547 4.2 57.5 1.0 N C:HIS1545 4.3 62.1 1.0 CB C:HIS1540 4.3 66.0 1.0 CB C:ASP1558 4.3 65.2 1.0 CA C:HIS1545 4.4 61.5 1.0 N C:CYS1546 4.4 60.5 1.0 N C:SER1542 4.4 64.2 1.0 OD2 C:ASP1547 4.4 56.5 1.0 N C:ASP1543 4.4 63.7 1.0 CA C:CYS1546 4.5 60.8 1.0 C C:CYS1546 4.5 59.8 1.0 CA C:HIS1540 4.5 65.9 1.0 N C:PHE1541 4.6 65.6 1.0 OD1 C:ASP1561 4.7 67.0 1.0 CB C:HIS1545 4.7 62.0 1.0 CB C:ASP1543 4.7 63.9 1.0 CA C:ASP1547 4.7 57.9 1.0 CA C:PHE1541 4.7 65.0 1.0 C C:PHE1541 4.9 64.4 1.0 C C:ASP1558 4.9 64.9 1.0 CA C:ASP1558 5.0 65.5 1.0

W.R.Gordon, D.Vardar-Ulu, S.L'heureux, T.Ashworth, M.J.Malecki, C.Sanchez-Irizarry, D.G.Mcarthur, G.Histen, J.L.Mitchell, J.C.Aster, S.C.Blacklow. Effects of S1 Cleavage on the Structure, Surface Export, and Signaling Activity of Human NOTCH1 and NOTCH2. Plos One V. 4 E6613 2009.
ISSN: ESSN 1932-6203
PubMed: 19701457
DOI: 10.1371/JOURNAL.PONE.0006613