Calcium in PDB 6pol: Crystal Structure of the Human NELL1 EGF1-3-ROBO3 FN1 Complex

The structure of Crystal Structure of the Human NELL1 EGF1-3-ROBO3 FN1 Complex, PDB code: 6pol was solved by J.Wang, J.S.Pak, E.Ozkan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.47 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.000, 87.000, 211.300, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 26.7

The binding sites of Calcium atom in the Crystal Structure of the Human NELL1 EGF1-3-ROBO3 FN1 Complex (pdb code 6pol). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Human NELL1 EGF1-3-ROBO3 FN1 Complex, PDB code: 6pol:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Human NELL1 EGF1-3-ROBO3 FN1 Complex


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 NELL1 EGF1-3-ROBO3 FN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:29.9 occ:1.00 O B:ILE435 2.3 34.7 1.0 O B:HOH1006 2.4 31.8 1.0 O B:LEU454 2.4 30.1 1.0 OD1 B:ASN453 2.4 31.6 1.0 O B:LEU457 2.5 28.8 1.0 OD1 B:ASP434 2.5 32.0 1.0 OE1 B:GLU437 2.6 37.0 1.0 OD2 B:ASP434 2.6 33.6 1.0 CG B:ASP434 2.9 34.2 1.0 CG B:ASN453 3.5 34.2 1.0 C B:ILE435 3.5 33.3 1.0 CD B:GLU437 3.5 35.8 1.0 C B:LEU454 3.6 33.6 1.0 C B:LEU457 3.6 31.1 1.0 N B:LEU457 3.7 32.3 1.0 OE2 B:GLU437 3.8 35.4 1.0 N B:LEU454 3.8 33.5 1.0 ND2 B:ASN453 3.9 32.8 1.0 N B:GLY456 4.0 34.7 1.0 CA B:LEU457 4.3 36.4 1.0 N B:ILE435 4.3 33.2 1.0 CA B:LEU454 4.3 34.7 1.0 C B:GLY456 4.4 34.9 1.0 CA B:ILE435 4.4 32.9 1.0 N B:ASP436 4.4 35.3 1.0 CB B:ASP434 4.4 31.8 1.0 CA B:ASP436 4.5 37.8 1.0 N B:GLU437 4.5 33.9 1.0 CA B:GLY456 4.6 34.8 1.0 N B:PRO455 4.6 36.6 1.0 O B:GLY421 4.7 32.0 1.0 N B:TYR458 4.7 31.4 1.0 CA B:PRO455 4.7 39.1 1.0 CB B:ILE435 4.7 33.6 1.0 C B:PRO455 4.7 38.5 1.0 CB B:ASN453 4.8 36.5 1.0 C B:ASP434 4.8 33.8 1.0 O B:HOH1027 4.8 45.0 1.0 C B:ASN453 4.8 35.2 1.0 CB B:TYR458 4.9 27.1 1.0 CA B:ASN453 4.9 34.4 1.0 CG B:GLU437 4.9 33.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Human NELL1 EGF1-3-ROBO3 FN1 Complex


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 NELL1 EGF1-3-ROBO3 FN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:30.8 occ:1.00 O D:ILE435 2.3 33.1 1.0 OD1 D:ASN453 2.4 30.2 1.0 O D:HOH1020 2.4 23.8 1.0 O D:LEU454 2.5 30.2 1.0 OE1 D:GLU437 2.5 35.1 1.0 O D:LEU457 2.5 30.6 1.0 OD1 D:ASP434 2.5 33.9 1.0 OD2 D:ASP434 2.6 35.8 1.0 CG D:ASP434 2.9 36.3 1.0 CG D:ASN453 3.4 32.6 1.0 C D:ILE435 3.5 33.9 1.0 CD D:GLU437 3.5 33.4 1.0 C D:LEU457 3.7 34.0 1.0 C D:LEU454 3.7 34.7 1.0 OE2 D:GLU437 3.8 34.1 1.0 N D:LEU457 3.8 32.1 1.0 ND2 D:ASN453 3.8 32.3 1.0 N D:LEU454 3.9 32.9 1.0 N D:GLY456 4.1 35.5 1.0 CA D:LEU457 4.3 35.2 1.0 N D:ILE435 4.3 32.5 1.0 CB D:ASP434 4.4 35.1 1.0 CA D:ILE435 4.4 33.7 1.0 CA D:LEU454 4.4 33.1 1.0 C D:GLY456 4.4 34.7 1.0 N D:ASP436 4.4 36.3 1.0 N D:GLU437 4.5 34.7 1.0 CA D:ASP436 4.5 35.4 1.0 O D:GLY421 4.6 31.4 1.0 CA D:GLY456 4.7 32.3 1.0 CB D:ASN453 4.7 33.1 1.0 N D:PRO455 4.7 36.5 1.0 N D:TYR458 4.7 29.4 1.0 CB D:ILE435 4.8 32.5 1.0 C D:ASP434 4.8 32.5 1.0 C D:ASN453 4.8 33.8 1.0 CA D:PRO455 4.8 38.8 1.0 C D:PRO455 4.8 37.1 1.0 CA D:ASN453 4.8 31.8 1.0 CB D:TYR458 4.9 30.5 1.0 CG D:GLU437 4.9 32.1 1.0 O D:HOH1078 5.0 49.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Human NELL1 EGF1-3-ROBO3 FN1 Complex


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 NELL1 EGF1-3-ROBO3 FN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca902 b:29.8 occ:1.00 O F:ILE435 2.3 34.8 1.0 OD1 F:ASN453 2.4 31.9 1.0 O F:LEU454 2.4 34.3 1.0 O F:LEU457 2.5 34.8 1.0 O F:HOH1023 2.5 29.7 1.0 OD1 F:ASP434 2.5 34.3 1.0 OD2 F:ASP434 2.6 35.6 1.0 OE1 F:GLU437 2.6 32.8 1.0 CG F:ASP434 2.9 37.0 1.0 CG F:ASN453 3.4 37.4 1.0 C F:ILE435 3.5 34.2 1.0 C F:LEU457 3.6 31.5 1.0 C F:LEU454 3.6 36.3 1.0 CD F:GLU437 3.6 34.6 1.0 N F:LEU457 3.8 36.6 1.0 N F:LEU454 3.8 37.2 1.0 ND2 F:ASN453 3.9 40.3 1.0 OE2 F:GLU437 3.9 33.8 1.0 N F:GLY456 4.1 36.7 1.0 CA F:LEU457 4.2 36.3 1.0 N F:ILE435 4.3 32.8 1.0 CA F:LEU454 4.3 35.8 1.0 CB F:ASP434 4.4 37.1 1.0 CA F:ILE435 4.4 35.3 1.0 N F:ASP436 4.4 33.7 1.0 N F:GLU437 4.5 34.4 1.0 CA F:ASP436 4.5 36.1 1.0 C F:GLY456 4.5 36.8 1.0 N F:PRO455 4.6 38.4 1.0 N F:TYR458 4.7 31.4 1.0 CB F:ASN453 4.7 38.1 1.0 CA F:PRO455 4.7 37.5 1.0 CA F:GLY456 4.7 37.3 1.0 O F:GLY421 4.7 34.8 1.0 C F:ASN453 4.7 37.3 1.0 C F:ASP434 4.7 35.9 1.0 CB F:ILE435 4.8 35.7 1.0 C F:PRO455 4.8 38.3 1.0 CA F:ASN453 4.8 35.9 1.0 CB F:TYR458 4.9 33.8 1.0 CG F:GLU437 5.0 32.1 1.0 O F:HOH1088 5.0 45.9 1.0

J.S.Pak, Z.J.Deloughery, J.Wang, N.Acharya, Y.Park, A.Jaworski, E.Ozkan. NELL2-ROBO3 Complex Structure Reveals Mechanisms of Receptor Activation For Axon Guidance. Nat Commun V. 11 1489 2020.
ISSN: ESSN 2041-1723
PubMed: 32198364
DOI: 10.1038/S41467-020-15211-1