Calcium in PDB 2oo4: Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2

The structure of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2, PDB code: 2oo4 was solved by W.R.Gordon, D.Vardar-Ulu, G.Histen, C.Sanchez-Irizarry, J.C.Aster, 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	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.372, 74.706, 139.412, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.8

The structure of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 (pdb code 2oo4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2, PDB code: 2oo4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5001 b:54.2 occ:1.00 OD1 A:ASP1451 2.2 42.6 1.0 O A:VAL1438 2.4 48.8 1.0 OD1 A:ASP1436 2.4 51.7 1.0 OD2 A:ASP1454 2.4 40.1 1.0 O A:LYS1433 2.4 52.2 1.0 OD2 A:ASP1440 2.5 49.6 1.0 CG A:ASP1451 2.8 43.1 1.0 OD2 A:ASP1451 2.8 46.5 1.0 CG A:ASP1454 3.4 40.1 1.0 CG A:ASP1436 3.4 54.9 1.0 C A:LYS1433 3.4 53.9 1.0 C A:VAL1438 3.6 48.7 1.0 CG A:ASP1440 3.6 52.1 1.0 CB A:ASP1454 3.8 38.1 1.0 OD2 A:ASP1436 4.0 56.6 1.0 CB A:LYS1433 4.0 56.1 1.0 N A:ASP1440 4.2 48.5 1.0 O A:ASP1451 4.2 40.3 1.0 CB A:ASP1451 4.2 41.8 1.0 CA A:LYS1433 4.2 56.2 1.0 CB A:ASP1440 4.2 51.5 1.0 N A:ASP1436 4.2 52.0 1.0 N A:VAL1438 4.3 50.0 1.0 N A:ALA1434 4.3 54.2 1.0 CA A:VAL1438 4.4 50.0 1.0 N A:ARG1435 4.4 50.5 1.0 CA A:ALA1434 4.5 52.6 1.0 OD1 A:ASP1454 4.5 39.0 1.0 CB A:ASP1436 4.5 55.5 1.0 N A:CYS1439 4.5 47.3 1.0 OD1 A:ASP1440 4.6 54.3 1.0 C A:ALA1434 4.6 52.2 1.0 CA A:CYS1439 4.6 46.6 1.0 C A:CYS1439 4.7 48.6 1.0 CB A:VAL1438 4.7 52.9 1.0 CA A:ASP1436 4.8 53.7 1.0 CA A:ASP1440 4.9 50.1 1.0 CD A:LYS1433 4.9 60.5 1.0 C A:ASP1451 5.0 41.1 1.0

Calcium binding site 2 out of 6 in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5002 b:51.9 occ:1.00 OE1 A:GLU1495 2.2 57.1 1.0 O A:TYR1475 2.3 52.8 1.0 O A:GLN1479 2.4 59.7 1.0 OD2 A:ASP1492 2.4 52.7 1.0 OD1 A:ASN1477 2.6 58.5 1.0 OD1 A:ASP1492 2.6 50.6 1.0 OD2 A:ASP1481 2.7 60.5 1.0 CG A:ASP1492 2.9 49.2 1.0 CD A:GLU1495 3.4 55.9 1.0 C A:TYR1475 3.5 51.7 1.0 CG A:ASN1477 3.6 60.0 1.0 C A:GLN1479 3.6 62.7 1.0 CG A:ASP1481 3.7 60.7 1.0 N A:ASP1481 3.9 59.3 1.0 CB A:ASP1481 4.0 57.7 1.0 CB A:GLU1495 4.0 55.5 1.0 ND2 A:ASN1477 4.0 61.3 1.0 N A:ASN1477 4.1 56.0 1.0 CB A:TYR1475 4.2 54.8 1.0 CG A:GLU1495 4.2 54.7 1.0 N A:GLN1479 4.3 63.2 1.0 OE2 A:GLU1495 4.3 56.5 1.0 CB A:ASP1492 4.4 45.3 1.0 CA A:TYR1475 4.4 53.6 1.0 C A:CYS1480 4.5 62.1 1.0 O A:ASP1492 4.5 44.3 1.0 N A:ILE1476 4.5 53.1 1.0 CA A:GLN1479 4.5 65.2 1.0 N A:CYS1480 4.5 64.5 1.0 CA A:CYS1480 4.5 62.9 1.0 CA A:ASP1481 4.6 59.0 1.0 CA A:ILE1476 4.6 52.3 1.0 O A:HOH80 4.8 39.4 1.0 OD1 A:ASP1481 4.8 63.9 1.0 CB A:ASN1477 4.8 61.6 1.0 CA A:ASN1477 4.9 59.7 1.0 C A:ILE1476 4.9 54.7 1.0 N A:ASN1478 4.9 60.0 1.0

Calcium binding site 3 out of 6 in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5003 b:39.1 occ:1.00 ND2 A:ASN1519 2.3 43.5 1.0 OD2 A:ASP1533 2.3 36.2 1.0 O A:HIS1512 2.3 38.1 1.0 O A:HIS1517 2.4 47.8 1.0 OD1 A:ASP1530 2.4 38.9 1.0 OD1 A:ASP1515 2.4 45.4 1.0 OD2 A:ASP1530 2.5 40.0 1.0 CG A:ASP1530 2.8 36.6 1.0 CG A:ASP1533 3.3 36.7 1.0 CG A:ASP1515 3.4 47.6 1.0 C A:HIS1512 3.5 38.0 1.0 CG A:ASN1519 3.5 46.4 1.0 C A:HIS1517 3.6 50.4 1.0 CB A:ASP1533 3.6 37.7 1.0 OD2 A:ASP1515 3.8 49.3 1.0 N A:ASN1519 4.0 46.9 1.0 CB A:ASN1519 4.1 45.3 1.0 N A:ASP1515 4.1 43.1 1.0 O A:ASP1530 4.1 33.5 1.0 CB A:HIS1512 4.2 41.1 1.0 N A:HIS1517 4.2 51.6 1.0 CB A:ASP1530 4.3 34.5 1.0 N A:LYS1514 4.4 35.7 1.0 CA A:HIS1512 4.4 40.3 1.0 CA A:HIS1517 4.4 53.5 1.0 OD1 A:ASP1533 4.5 38.2 1.0 N A:PHE1513 4.5 36.4 1.0 CB A:ASP1515 4.5 47.9 1.0 OD1 A:ASN1519 4.5 50.3 1.0 N A:CYS1518 4.5 51.4 1.0 CA A:PHE1513 4.6 34.2 1.0 CA A:CYS1518 4.6 49.4 1.0 C A:CYS1518 4.6 49.8 1.0 CA A:ASN1519 4.7 47.3 1.0 CB A:HIS1517 4.7 55.9 1.0 CA A:ASP1515 4.7 47.1 1.0 C A:PHE1513 4.7 35.8 1.0 N A:ASN1516 4.9 48.7 1.0 C A:ASP1530 4.9 31.8 1.0 C A:ASP1515 5.0 49.8 1.0 CA A:ASP1530 5.0 32.4 1.0

Calcium binding site 4 out of 6 in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5004 b:90.5 occ:1.00 OD2 B:ASP1451 2.3 71.3 1.0 OD2 B:ASP1440 2.4 78.9 1.0 OD2 B:ASP1454 2.4 71.0 1.0 OD1 B:ASP1436 2.4 87.4 1.0 O B:VAL1438 2.5 78.3 1.0 CG B:ASP1451 3.0 71.7 1.0 OD1 B:ASP1451 3.2 74.0 1.0 CG B:ASP1436 3.2 89.4 1.0 OD2 B:ASP1436 3.4 89.0 1.0 CG B:ASP1454 3.5 65.2 1.0 CG B:ASP1440 3.6 79.4 1.0 C B:VAL1438 3.7 79.0 1.0 O B:ASP1436 3.8 86.9 1.0 CB B:LYS1433 3.8 86.9 1.0 CB B:ASP1454 3.9 62.9 1.0 N B:ALA1434 3.9 87.8 1.0 C B:LYS1433 4.0 87.1 1.0 N B:ASP1440 4.1 75.6 1.0 CA B:LYS1433 4.1 88.7 1.0 O B:ASP1451 4.3 73.3 1.0 CB B:ASP1451 4.3 70.5 1.0 CB B:ASP1440 4.4 78.1 1.0 O B:LYS1433 4.5 85.8 1.0 CA B:ALA1434 4.5 87.3 1.0 OD1 B:ASP1440 4.5 81.9 1.0 OD1 B:ASP1454 4.5 63.4 1.0 N B:VAL1438 4.6 84.8 1.0 CA B:VAL1438 4.6 82.7 1.0 CB B:ASP1436 4.6 93.1 1.0 C B:ASP1436 4.6 90.4 1.0 N B:CYS1439 4.7 77.3 1.0 C B:ALA1434 4.7 88.4 1.0 CA B:CYS1439 4.7 75.0 1.0 CB B:VAL1438 4.7 84.6 1.0 N B:ASP1436 4.7 92.8 1.0 CA B:ASP1436 4.9 93.1 1.0 C B:CYS1439 4.9 75.6 1.0 CA B:ASP1440 4.9 77.0 1.0 O B:ALA1434 5.0 87.0 1.0

Calcium binding site 5 out of 6 in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5005 b:69.5 occ:1.00 OE1 B:GLU1495 2.4 76.7 1.0 OD2 B:ASP1492 2.4 68.5 1.0 OD1 B:ASP1492 3.0 73.4 1.0 O B:GLN1479 3.0 90.1 1.0 OD2 B:ASP1481 3.0 84.4 1.0 CG B:ASP1492 3.0 68.9 1.0 OD1 B:ASN1477 3.1 93.3 1.0 CG B:ASN1477 3.3 97.0 1.0 CB B:ASN1477 3.4 98.2 1.0 O B:TYR1475 3.4 85.1 1.0 CG B:ASP1481 3.5 82.8 1.0 CD B:GLU1495 3.6 78.1 1.0 CB B:ASP1481 4.1 78.9 1.0 C B:TYR1475 4.1 89.7 1.0 OD1 B:ASP1481 4.1 85.1 1.0 N B:ILE1476 4.2 93.3 1.0 ND2 B:ASN1477 4.2 0.5 1.0 C B:GLN1479 4.2 94.1 1.0 N B:ASP1481 4.2 80.8 1.0 CB B:GLU1495 4.4 77.7 1.0 OE2 B:GLU1495 4.4 80.3 1.0 O B:ASP1492 4.4 65.2 1.0 CG B:GLU1495 4.5 76.5 1.0 CB B:ASP1492 4.5 65.5 1.0 C B:CYS1480 4.8 85.5 1.0 CA B:ASP1481 4.8 79.8 1.0 N B:GLN1479 4.8 0.7 1.0 N B:ASN1478 4.9 0.3 1.0 CA B:ASN1477 4.9 0.7 1.0 C B:ASP1492 5.0 61.8 1.0 CA B:CYS1480 5.0 87.0 1.0

Calcium binding site 6 out of 6 in the Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Lnr-Hd (Negative Regulatory Region) From Human Notch 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5006 b:46.7 occ:1.00 O B:HIS1512 2.2 48.3 1.0 OD1 B:ASP1515 2.3 52.1 1.0 O B:HIS1517 2.3 53.9 1.0 OD2 B:ASP1530 2.3 51.4 1.0 ND2 B:ASN1519 2.4 51.0 1.0 OD2 B:ASP1533 2.5 49.0 1.0 OD1 B:ASP1530 3.0 51.0 1.0 CG B:ASP1530 3.0 51.3 1.0 CG B:ASP1515 3.2 50.4 1.0 CG B:ASP1533 3.5 51.1 1.0 C B:HIS1512 3.5 47.5 1.0 C B:HIS1517 3.5 55.7 1.0 CG B:ASN1519 3.7 54.1 1.0 OD2 B:ASP1515 3.7 51.2 1.0 CB B:ASP1533 3.8 52.5 1.0 N B:ASP1515 3.9 48.5 1.0 CB B:HIS1512 4.2 49.1 1.0 N B:HIS1517 4.2 54.7 1.0 N B:LYS1514 4.3 47.1 1.0 CB B:ASP1515 4.3 49.3 1.0 N B:ASN1519 4.3 57.6 1.0 CA B:HIS1512 4.3 47.9 1.0 CA B:HIS1517 4.3 56.1 1.0 O B:ASP1530 4.4 49.5 1.0 N B:PHE1513 4.4 46.5 1.0 CB B:ASN1519 4.4 55.5 1.0 CA B:ASP1515 4.5 49.3 1.0 CB B:ASP1530 4.5 51.8 1.0 OD1 B:ASP1533 4.5 51.7 1.0 N B:CYS1518 4.5 58.0 1.0 C B:PHE1513 4.6 45.9 1.0 OD1 B:ASN1519 4.6 54.0 1.0 CA B:PHE1513 4.6 46.2 1.0 CA B:CYS1518 4.7 58.7 1.0 CB B:HIS1517 4.7 56.1 1.0 C B:CYS1518 4.7 58.7 1.0 C B:ASP1515 4.8 51.1 1.0 C B:LYS1514 4.9 47.6 1.0 N B:ASN1516 4.9 51.7 1.0 CA B:LYS1514 4.9 47.3 1.0

W.R.Gordon, D.Vardar-Ulu, G.Histen, C.Sanchez-Irizarry, J.C.Aster, S.C.Blacklow. Structural Basis For Autoinhibition of Notch Nat.Struct.Mol.Biol. V. 14 295 2007.
ISSN: ISSN 1545-9993
PubMed: 17401372
DOI: 10.1038/NSMB1227