Atomistry » Calcium » PDB 3eqf-3f45 » 3eto
Atomistry »
  Calcium »
    PDB 3eqf-3f45 »
      3eto »

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

Protein crystallography data

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

Other elements in 3eto:

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

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

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 3eto

Go back to Calcium Binding Sites List in 3eto
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 3eto

Go back to Calcium Binding Sites List in 3eto
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 3eto

Go back to Calcium Binding Sites List in 3eto
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 3eto

Go back to Calcium Binding Sites List in 3eto
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 3eto

Go back to Calcium Binding Sites List in 3eto
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 3eto

Go back to Calcium Binding Sites List in 3eto
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

Reference:

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
Page generated: Sat Dec 12 04:10:43 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy