Calcium in PDB 7abv: Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr)

Protein crystallography data

The structure of Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr), PDB code: 7abv was solved by M.R.Zeronian, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.89 / 2.07
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.724, 65.724, 161.683, 90, 90, 90
R / Rfree (%) 19.6 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr) (pdb code 7abv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr), PDB code: 7abv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7abv

Go back to Calcium Binding Sites List in 7abv
Calcium binding site 1 out of 3 in the Structure of the S1-Cleaved Mouse 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 Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3001

b:37.4
occ:1.00
OD2 A:ASP1546 2.3 33.7 1.0
O A:HIS1544 2.4 36.5 1.0
OD2 A:ASP1557 2.4 32.6 1.0
O A:HIS1539 2.4 35.5 1.0
OD2 A:ASP1560 2.4 39.6 1.0
OD1 A:ASP1542 2.6 36.2 1.0
OD1 A:ASP1557 2.6 34.0 1.0
CG A:ASP1557 2.8 33.3 1.0
CG A:ASP1560 3.4 41.5 1.0
CG A:ASP1546 3.5 35.0 1.0
CG A:ASP1542 3.5 36.6 1.0
C A:HIS1544 3.5 36.5 1.0
C A:HIS1539 3.5 34.5 1.0
CB A:ASP1560 3.6 39.3 1.0
OD2 A:ASP1542 3.9 37.2 1.0
CB A:ASP1546 4.0 33.9 1.0
O A:HOH3127 4.0 34.2 1.0
N A:ASP1546 4.0 36.0 1.0
CB A:HIS1539 4.1 31.4 1.0
N A:HIS1544 4.2 36.7 1.0
O A:ASP1557 4.2 33.8 1.0
N A:ASP1542 4.2 36.9 1.0
CB A:ASP1557 4.3 32.1 1.0
N A:SER1541 4.3 35.0 1.0
CA A:HIS1544 4.3 38.3 1.0
CA A:HIS1539 4.4 33.0 1.0
C A:CYS1545 4.5 36.6 1.0
N A:CYS1545 4.5 36.1 1.0
OD1 A:ASP1560 4.5 40.7 1.0
N A:PHE1540 4.5 35.8 1.0
CA A:CYS1545 4.5 36.8 1.0
OD1 A:ASP1546 4.6 34.7 1.0
CB A:ASP1542 4.6 37.1 1.0
CB A:HIS1544 4.6 39.6 1.0
CA A:ASP1546 4.7 35.7 1.0
CA A:PHE1540 4.7 34.9 1.0
C A:PHE1540 4.7 36.2 1.0
CA A:ASP1542 4.9 36.7 1.0
O A:HOH3104 5.0 34.3 1.0

Calcium binding site 2 out of 3 in 7abv

Go back to Calcium Binding Sites List in 7abv
Calcium binding site 2 out of 3 in the Structure of the S1-Cleaved Mouse 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 Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3002

b:47.4
occ:1.00
OD2 A:ASP1506 2.1 51.9 1.0
OD2 A:ASP1520 2.2 44.0 1.0
O A:HIS1504 2.3 51.5 1.0
O A:TYR1499 2.3 42.2 1.0
OD1 A:ASP1517 2.5 43.8 1.0
OD1 A:ASP1502 2.6 49.7 1.0
OD2 A:ASP1517 2.6 44.3 1.0
CG A:ASP1517 2.9 41.9 1.0
CG A:ASP1520 3.3 45.4 1.0
CG A:ASP1506 3.3 52.3 1.0
CG A:ASP1502 3.4 52.1 1.0
C A:HIS1504 3.5 53.5 1.0
C A:TYR1499 3.5 44.0 1.0
CB A:ASP1520 3.6 44.8 1.0
OD2 A:ASP1502 3.8 53.8 1.0
CB A:ASP1506 3.9 50.1 1.0
N A:ASP1506 4.0 47.7 1.0
CB A:TYR1499 4.0 45.1 1.0
O A:ASP1517 4.0 40.3 1.0
N A:ASP1502 4.1 50.2 1.0
N A:HIS1504 4.2 53.3 1.0
CA A:TYR1499 4.2 45.5 1.0
CA A:HIS1504 4.3 54.9 1.0
OD1 A:ASP1506 4.3 53.7 1.0
N A:SER1501 4.4 43.3 1.0
CB A:ASP1517 4.4 39.5 1.0
OD1 A:ASP1520 4.4 43.6 1.0
N A:CYS1505 4.5 52.0 1.0
CB A:ASP1502 4.5 51.7 1.0
N A:PHE1500 4.5 42.6 1.0
C A:CYS1505 4.5 49.8 1.0
CB A:HIS1504 4.6 57.1 1.0
CA A:ASP1506 4.6 48.8 1.0
CA A:CYS1505 4.6 49.9 1.0
CA A:ASP1502 4.7 51.1 1.0
C A:PHE1500 4.7 43.9 1.0
CA A:PHE1500 4.8 42.2 1.0
C A:ASP1502 4.9 51.5 1.0
C A:ASP1517 4.9 39.5 1.0
N A:GLY1503 4.9 50.1 1.0
O A:HOH3134 5.0 38.4 1.0

Calcium binding site 3 out of 3 in 7abv

Go back to Calcium Binding Sites List in 7abv
Calcium binding site 3 out of 3 in the Structure of the S1-Cleaved Mouse 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 Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:84.0
occ:1.00
OD1 A:ASN1460 2.3 98.0 1.0
O A:VAL1462 2.4 88.3 1.0
OD2 A:ASP1475 2.5 71.3 1.0
O A:ASP1457 2.5 83.6 1.0
OD2 A:ASP1478 2.5 71.0 1.0
OD1 A:ASN1464 2.6 88.1 1.0
CG A:ASP1475 3.2 69.6 1.0
OD1 A:ASP1475 3.3 72.2 1.0
CG A:ASN1460 3.3 100.2 1.0
CG A:ASN1464 3.4 87.6 1.0
C A:ASP1457 3.5 86.0 1.0
C A:VAL1462 3.6 86.8 1.0
CG A:ASP1478 3.6 69.5 1.0
CB A:ASP1457 3.9 91.9 1.0
ND2 A:ASN1460 3.9 103.1 1.0
N A:ASN1464 4.0 79.2 1.0
CB A:ASP1478 4.1 66.7 1.0
CA A:ASP1457 4.1 90.6 1.0
CB A:ASN1464 4.1 83.5 1.0
N A:ASN1460 4.1 92.1 1.0
ND2 A:ASN1464 4.3 89.9 1.0
N A:VAL1462 4.3 93.9 1.0
CB A:ASN1460 4.4 100.3 1.0
N A:ALA1458 4.4 84.5 1.0
CA A:VAL1462 4.5 90.3 1.0
CG1 A:VAL1462 4.5 96.3 1.0
N A:GLY1459 4.5 81.5 1.0
N A:CYS1463 4.5 82.0 1.0
O A:ASP1475 4.6 64.2 1.0
CB A:ASP1475 4.6 65.7 1.0
CA A:ASN1460 4.6 98.1 1.0
CA A:ALA1458 4.6 81.5 1.0
CA A:CYS1463 4.6 78.2 1.0
C A:CYS1463 4.7 79.2 1.0
CA A:ASN1464 4.7 80.7 1.0
OD1 A:ASP1478 4.7 68.6 1.0
CG A:ASP1457 4.8 96.3 1.0
C A:ASN1460 4.8 99.7 1.0
C A:ALA1458 4.9 82.3 1.0
N A:LYS1461 4.9 99.8 1.0
CB A:VAL1462 4.9 95.0 1.0

Reference:

M.R.Zeronian, B.J.C.Janssen. Structure of the S1-Cleaved Mouse NOTCH1 Negative Regulatory Region (Nrr) To Be Published.
Page generated: Sat Jul 10 11:12:50 2021

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