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Calcium in PDB 3l95: Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody

Protein crystallography data

The structure of Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody, PDB code: 3l95 was solved by S.G.Hymowitz, G.P.De Leon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.254, 163.934, 179.620, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody (pdb code 3l95). 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 Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody, PDB code: 3l95:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3l95

Go back to Calcium Binding Sites List in 3l95
Calcium binding site 1 out of 6 in the Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody


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 Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca2001

b:43.6
occ:1.00
 O X:VAL1463 2.1 20.0 1.0
OD1 X:ASN1461 2.4 13.1 1.0
OD2 X:ASP1476 2.6 31.8 1.0
OD2 X:ASP1479 2.6 21.6 1.0
O X:ASP1458 2.6 34.0 1.0
C X:VAL1463 3.3 24.8 1.0
CG X:ASN1461 3.4 20.0 1.0
CG X:ASP1476 3.4 30.3 1.0
OD1 X:ASP1476 3.6 35.3 1.0
OD1 X:ASP1458 3.6 47.4 1.0
C X:ASP1458 3.7 31.6 1.0
CG X:ASP1479 3.7 22.2 1.0
CG X:ASP1458 3.8 45.1 1.0
CB X:ASP1458 3.9 40.2 1.0
ND2 X:ASN1461 3.9 18.2 1.0
N X:VAL1463 4.1 26.4 1.0
CA X:VAL1463 4.1 26.3 1.0
CB X:VAL1463 4.1 25.1 1.0
CB X:ASP1479 4.2 20.9 1.0
N X:SER1465 4.2 24.7 1.0
N X:CYS1464 4.4 28.3 1.0
CA X:ASP1458 4.4 35.0 1.0
N X:ASN1461 4.4 24.2 1.0
OD2 X:ASP1458 4.4 47.8 1.0
CG1 X:VAL1463 4.5 27.8 1.0
CA X:CYS1464 4.5 30.9 1.0
CB X:SER1465 4.6 29.1 1.0
N X:ALA1459 4.6 29.1 1.0
CB X:ASN1461 4.6 24.2 1.0
C X:CYS1464 4.7 29.9 1.0
N X:GLY1460 4.7 20.1 1.0
O X:ASP1476 4.7 16.2 1.0
CA X:ALA1459 4.7 25.4 1.0
OD1 X:ASP1479 4.7 31.8 1.0
OG X:SER1465 4.8 27.5 1.0
CB X:ASP1476 4.8 26.8 1.0
CA X:ASN1461 4.9 21.0 1.0

Calcium binding site 2 out of 6 in 3l95

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Calcium binding site 2 out of 6 in the Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody


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 Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca2002

b:13.8
occ:1.00
 O X:HIS1505 2.3 15.4 1.0
OD2 X:ASP1507 2.3 16.4 1.0
O X:TYR1500 2.3 15.7 1.0
OD2 X:ASP1521 2.4 14.6 1.0
OD1 X:ASP1503 2.5 16.5 1.0
OD2 X:ASP1518 2.5 16.0 1.0
OD1 X:ASP1518 2.6 12.3 1.0
CG X:ASP1518 2.9 16.7 1.0
CG X:ASP1521 3.3 19.4 1.0
CG X:ASP1507 3.4 16.4 1.0
C X:TYR1500 3.4 16.2 1.0
C X:HIS1505 3.5 8.5 1.0
CG X:ASP1503 3.5 15.6 1.0
CB X:ASP1521 3.7 19.2 1.0
N X:ASP1507 4.0 13.9 1.0
OD2 X:ASP1503 4.0 12.5 1.0
CB X:ASP1507 4.1 13.0 1.0
CB X:TYR1500 4.1 17.6 1.0
O X:ASP1518 4.1 14.0 1.0
N X:ASP1503 4.2 21.0 1.0
CA X:TYR1500 4.2 15.0 1.0
N X:HIS1505 4.2 17.9 1.0
ND2 B:ASN55 4.2 27.3 1.0
N X:SER1502 4.3 16.8 1.0
CA X:HIS1505 4.3 13.2 1.0
OD1 X:ASP1507 4.4 22.0 1.0
CB X:ASP1518 4.4 19.9 1.0
OD1 X:ASP1521 4.4 13.4 1.0
N X:PHE1501 4.4 15.9 1.0
N X:CYS1506 4.5 15.8 1.0
CA X:CYS1506 4.6 13.2 1.0
CB X:ASP1503 4.6 15.6 1.0
CB X:HIS1505 4.6 16.2 1.0
C X:PHE1501 4.7 19.1 1.0
C X:CYS1506 4.7 12.0 1.0
CA X:PHE1501 4.7 19.0 1.0
CA X:ASP1507 4.7 13.2 1.0
O X:HOH6 4.8 4.4 1.0
CA X:ASP1503 4.8 19.1 1.0
N X:GLY1504 4.9 16.5 1.0
C X:ASP1518 5.0 15.3 1.0

Calcium binding site 3 out of 6 in 3l95

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Calcium binding site 3 out of 6 in the Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody


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 Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca2003

b:21.0
occ:1.00
 O X:HIS1545 2.2 27.1 1.0
OD2 X:ASP1547 2.3 24.3 1.0
OD2 X:ASP1561 2.4 21.6 1.0
O X:HIS1540 2.4 13.8 1.0
OD1 X:ASP1543 2.4 25.9 1.0
OD1 X:ASP1558 2.7 25.6 1.0
OD2 X:ASP1558 2.8 25.1 1.0
CG X:ASP1558 3.1 20.8 1.0
CG X:ASP1543 3.4 25.9 1.0
CG X:ASP1561 3.4 25.2 1.0
C X:HIS1545 3.4 29.0 1.0
CG X:ASP1547 3.5 26.2 1.0
C X:HIS1540 3.6 16.3 1.0
CB X:ASP1561 3.7 27.5 1.0
OD2 X:ASP1543 3.8 22.2 1.0
N X:ASP1547 4.1 32.6 1.0
N X:HIS1545 4.2 29.3 1.0
N X:ASP1543 4.2 30.9 1.0
CA X:HIS1545 4.2 27.0 1.0
CB X:ASP1547 4.3 29.0 1.0
O X:ASP1558 4.3 17.8 1.0
CB X:HIS1540 4.3 19.2 1.0
N X:SER1542 4.4 24.5 1.0
N X:CYS1546 4.4 33.0 1.0
OD1 X:ASP1547 4.4 26.1 1.0
OD1 X:ASP1561 4.5 25.6 1.0
CA X:HIS1540 4.5 19.3 1.0
CB X:ASP1558 4.5 22.8 1.0
CA X:CYS1546 4.5 34.6 1.0
N X:PHE1541 4.5 17.5 1.0
CB X:HIS1545 4.5 27.1 1.0
C X:CYS1546 4.6 32.9 1.0
CB X:ASP1543 4.6 27.3 1.0
CA X:PHE1541 4.6 19.8 1.0
C X:PHE1541 4.8 22.1 1.0
CA X:ASP1547 4.8 29.1 1.0
CA X:ASP1543 4.9 29.8 1.0
N X:GLY1544 4.9 31.3 1.0

Calcium binding site 4 out of 6 in 3l95

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Calcium binding site 4 out of 6 in the Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody


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 Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Ca2001

b:67.9
occ:1.00
 O Y:VAL1463 2.3 38.0 1.0
OG Y:SER1465 2.4 29.7 1.0
OD2 Y:ASP1476 2.8 35.9 1.0
OD1 Y:ASN1461 3.3 44.9 1.0
C Y:VAL1463 3.5 38.5 1.0
CB Y:SER1465 3.6 28.5 1.0
CG Y:ASP1476 3.7 34.0 1.0
OD1 Y:ASP1476 3.7 34.2 1.0
N Y:SER1465 3.8 33.8 1.0
OD2 Y:ASP1479 3.8 31.4 1.0
CG Y:ASN1461 4.1 48.1 1.0
CB Y:VAL1463 4.1 37.1 1.0
CA Y:SER1465 4.2 29.6 1.0
CA Y:VAL1463 4.2 38.7 1.0
C Y:CYS1464 4.3 34.4 1.0
ND2 Y:ASN1461 4.4 48.8 1.0
N Y:VAL1463 4.4 42.1 1.0
CG1 Y:VAL1463 4.5 37.4 1.0
N Y:CYS1464 4.5 37.6 1.0
N Y:ASN1461 4.6 49.9 1.0
CA Y:CYS1464 4.7 35.8 1.0
CG Y:ASP1479 4.7 30.5 1.0
CB Y:ASP1479 4.8 29.5 1.0

Calcium binding site 5 out of 6 in 3l95

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Calcium binding site 5 out of 6 in the Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody


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 Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Ca2002

b:21.5
occ:1.00
 OD2 Y:ASP1507 2.2 20.4 1.0
OD1 Y:ASP1503 2.3 16.5 1.0
O Y:HIS1505 2.3 21.2 1.0
O Y:TYR1500 2.4 15.8 1.0
OD1 Y:ASP1518 2.4 13.4 1.0
OD2 Y:ASP1521 2.5 25.6 1.0
OD2 Y:ASP1518 2.7 11.9 1.0
CG Y:ASP1518 2.8 16.2 1.0
CG Y:ASP1503 3.4 19.0 1.0
CG Y:ASP1507 3.4 20.0 1.0
C Y:TYR1500 3.5 18.2 1.0
CG Y:ASP1521 3.5 24.6 1.0
C Y:HIS1505 3.6 23.8 1.0
CB Y:ASP1521 3.8 22.7 1.0
OD2 Y:ASP1503 3.9 14.7 1.0
N Y:ASP1507 4.0 19.7 1.0
O Y:ASP1518 4.0 23.0 1.0
CB Y:TYR1500 4.0 18.8 1.0
CB Y:ASP1507 4.1 19.1 1.0
N Y:ASP1503 4.1 20.7 1.0
CA Y:TYR1500 4.2 16.9 1.0
N Y:HIS1505 4.2 22.5 1.0
CB Y:ASP1518 4.3 19.6 1.0
CA Y:HIS1505 4.3 23.7 1.0
OD1 Y:ASP1507 4.4 20.4 1.0
N Y:SER1502 4.4 14.4 1.0
ND2 H:ASN55 4.5 29.0 1.0
N Y:PHE1501 4.5 16.9 1.0
CB Y:HIS1505 4.5 26.2 1.0
CB Y:ASP1503 4.6 20.6 1.0
N Y:CYS1506 4.6 26.5 1.0
O Y:HOH62 4.6 15.6 1.0
OD1 Y:ASP1521 4.6 28.4 1.0
C Y:PHE1501 4.7 16.1 1.0
CA Y:CYS1506 4.7 27.1 1.0
CA Y:PHE1501 4.7 16.1 1.0
CA Y:ASP1507 4.7 19.7 1.0
C Y:CYS1506 4.7 21.2 1.0
CA Y:ASP1503 4.7 20.2 1.0
C Y:ASP1518 4.9 21.4 1.0
CA Y:ASP1518 4.9 18.9 1.0
C Y:ASP1503 4.9 23.1 1.0

Calcium binding site 6 out of 6 in 3l95

Go back to Calcium Binding Sites List in 3l95
Calcium binding site 6 out of 6 in the Crystal Structure of the Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody


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 Human NOTCH1 Negative Regulatory Region (Nrr) Bound to the Fab Fragment of An Antagonist Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Ca2003

b:23.2
occ:1.00
 O Y:HIS1545 2.4 28.3 1.0
O Y:HIS1540 2.4 17.8 1.0
OD2 Y:ASP1547 2.5 27.4 1.0
OD2 Y:ASP1558 2.5 13.9 1.0
OD2 Y:ASP1561 2.5 32.4 1.0
OD1 Y:ASP1543 2.5 31.6 1.0
OD1 Y:ASP1558 2.6 14.6 1.0
CG Y:ASP1558 2.9 16.3 1.0
CG Y:ASP1543 3.5 31.6 1.0
CG Y:ASP1561 3.5 32.7 1.0
CG Y:ASP1547 3.5 30.2 1.0
C Y:HIS1545 3.6 27.4 1.0
C Y:HIS1540 3.6 17.7 1.0
CB Y:ASP1561 3.8 30.2 1.0
OD2 Y:ASP1543 4.0 35.8 1.0
N Y:ASP1547 4.1 29.5 1.0
CB Y:ASP1547 4.1 28.6 1.0
N Y:ASP1543 4.2 26.2 1.0
CB Y:HIS1540 4.3 17.4 1.0
N Y:HIS1545 4.3 27.3 1.0
O Y:ASP1558 4.3 24.5 1.0
N Y:SER1542 4.4 24.8 1.0
CA Y:HIS1545 4.4 27.5 1.0
CB Y:ASP1558 4.4 18.5 1.0
CA Y:HIS1540 4.5 18.2 1.0
OD1 Y:ASP1547 4.5 31.7 1.0
OD1 Y:ASP1561 4.6 34.9 1.0
CB Y:HIS1545 4.6 27.6 1.0
CB Y:ASP1543 4.6 26.5 1.0
N Y:PHE1541 4.6 17.3 1.0
N Y:CYS1546 4.6 30.4 1.0
C Y:CYS1546 4.7 32.1 1.0
CA Y:PHE1541 4.7 20.6 1.0
CA Y:CYS1546 4.7 33.3 1.0
CA Y:ASP1547 4.7 27.8 1.0
C Y:PHE1541 4.8 21.5 1.0
CA Y:ASP1543 4.9 24.8 1.0
O Y:HOH2 4.9 8.3 1.0

Reference:

Y.Wu, C.Cain-Hom, L.Choy, T.J.Hagenbeek, G.P.De Leon, Y.Chen, D.Finkle, R.Venook, X.Wu, J.Ridgway, D.Schahin-Reed, G.J.Dow, A.Shelton, S.Stawicki, R.J.Watts, J.Zhang, R.Choy, P.Howard, L.Kadyk, M.Yan, J.Zha, C.A.Callahan, S.G.Hymowitz, C.W.Siebel. Therapeutic Antibody Targeting of Individual Notch Receptors. Nature V. 464 1052 2010.
ISSN: ISSN 0028-0836
PubMed: 20393564
DOI: 10.1038/NATURE08878
Page generated: Tue Jul 8 14:08:26 2025

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