Calcium in PDB 6pog: Crystal Structure of the NELL2 EGF1-6-ROBO3 FN1 Complex

The structure of Crystal Structure of the NELL2 EGF1-6-ROBO3 FN1 Complex, PDB code: 6pog 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)	48.34 / 2.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.873, 90.439, 171.576, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 26.4

The binding sites of Calcium atom in the Crystal Structure of the NELL2 EGF1-6-ROBO3 FN1 Complex (pdb code 6pog). 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 NELL2 EGF1-6-ROBO3 FN1 Complex, PDB code: 6pog:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the NELL2 EGF1-6-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 NELL2 EGF1-6-ROBO3 FN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca905 b:87.5 occ:1.00 OD1 B:ASN459 2.4 0.7 1.0 O B:THR460 2.4 0.3 1.0 OE1 B:GLU443 2.5 0.6 1.0 OD1 B:ASP440 2.5 1.0 1.0 O B:SER463 2.5 72.4 1.0 OD2 B:ASP440 2.5 0.6 1.0 O B:ILE441 2.6 0.0 1.0 CG B:ASP440 2.9 0.9 1.0 N B:SER463 3.4 84.0 1.0 CD B:GLU443 3.4 0.6 1.0 C B:SER463 3.5 89.5 1.0 CG B:ASN459 3.5 90.9 1.0 OE2 B:GLU443 3.6 0.6 1.0 C B:THR460 3.6 99.1 1.0 N B:GLY462 3.7 98.6 1.0 C B:ILE441 3.8 0.7 1.0 CA B:SER463 4.0 86.4 1.0 C B:GLY462 4.0 85.2 1.0 N B:THR460 4.0 87.4 1.0 ND2 B:ASN459 4.1 0.1 1.0 CA B:GLY462 4.3 66.6 1.0 CG2 B:ILE441 4.3 0.3 1.0 N B:ILE441 4.4 97.2 1.0 CB B:ASP440 4.4 0.8 1.0 CA B:THR460 4.5 96.4 1.0 C B:PRO461 4.5 0.7 1.0 N B:PRO461 4.6 0.4 1.0 CA B:PRO461 4.6 0.8 1.0 O B:GLY427 4.6 0.2 1.0 CA B:ILE441 4.6 0.3 1.0 N B:GLU443 4.6 92.2 1.0 N B:PHE464 4.7 79.1 1.0 N B:ASP442 4.7 0.2 1.0 OG1 B:THR460 4.8 0.4 1.0 CB B:ASN459 4.8 70.8 1.0 CA B:ASP442 4.8 0.1 1.0 C B:ASN459 4.8 70.6 1.0 CG B:GLU443 4.8 0.5 1.0 C B:ASP440 4.9 1.0 1.0 O B:GLY462 4.9 89.4 1.0 CA B:ASN459 4.9 77.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the NELL2 EGF1-6-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 NELL2 EGF1-6-ROBO3 FN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca906 b:86.5 occ:1.00 OD1 B:ASN574 2.4 0.4 1.0 OE1 B:GLU558 2.4 0.9 1.0 OD2 B:ASP555 2.4 99.3 1.0 OD1 B:ASP555 2.4 0.3 1.0 O B:ILE556 2.4 89.7 1.0 OE2 B:GLU558 2.4 0.7 1.0 O B:LEU575 2.6 98.8 1.0 O B:TRP578 2.7 81.0 1.0 CG B:ASP555 2.8 89.3 1.0 CD B:GLU558 2.8 0.9 1.0 N B:TRP578 3.5 95.7 1.0 CG B:ASN574 3.5 93.9 1.0 C B:TRP578 3.6 88.6 1.0 C B:ILE556 3.6 88.4 1.0 C B:LEU575 3.8 77.3 1.0 N B:GLY577 3.9 95.9 1.0 ND2 B:ASN574 3.9 98.2 1.0 CA B:TRP578 3.9 92.4 1.0 C B:GLY577 4.0 87.3 1.0 N B:LEU575 4.1 72.8 1.0 N B:ILE556 4.2 84.8 1.0 CB B:ASP555 4.3 71.4 1.0 CG B:GLU558 4.3 98.4 1.0 CA B:GLY577 4.4 86.4 1.0 CA B:ILE556 4.5 88.1 1.0 N B:GLU558 4.5 92.7 1.0 N B:ASP557 4.5 88.2 1.0 O B:GLY546 4.6 78.4 1.0 CA B:LEU575 4.6 58.4 1.0 CA B:ASP557 4.6 95.0 1.0 C B:PRO576 4.7 88.0 1.0 O B:GLY577 4.7 84.5 1.0 CA B:PRO576 4.7 79.0 1.0 N B:PRO576 4.7 75.8 1.0 C B:ASP555 4.8 82.4 1.0 CB B:ASN574 4.8 77.0 1.0 N B:TYR579 4.8 92.2 1.0 CB B:ILE556 5.0 84.3 1.0 CA B:ASP555 5.0 65.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the NELL2 EGF1-6-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 NELL2 EGF1-6-ROBO3 FN1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca907 b:0.2 occ:1.00 OE1 B:GLU605 2.2 0.6 1.0 OD1 B:ASP602 2.4 0.8 1.0 O B:LEU622 2.4 0.5 1.0 OD1 B:ASN621 2.5 0.9 1.0 OD2 B:ASP602 2.5 0.5 1.0 O B:ILE603 2.7 0.7 1.0 CG B:ASP602 2.8 0.4 1.0 O B:GLY625 3.1 0.2 1.0 CD B:GLU605 3.4 0.3 1.0 N B:LEU622 3.4 0.3 1.0 CG B:ASN621 3.5 0.0 1.0 C B:LEU622 3.5 0.1 1.0 CB B:GLU605 3.7 0.1 1.0 N B:GLU605 3.8 0.7 1.0 C B:ILE603 3.9 0.5 1.0 CG B:GLU605 4.1 0.5 1.0 ND2 B:ASN621 4.1 0.6 1.0 CA B:LEU622 4.1 0.4 1.0 N B:GLY625 4.1 0.2 1.0 C B:GLY625 4.2 0.4 1.0 CB B:ASP602 4.3 0.9 1.0 OE2 B:GLU605 4.4 0.8 1.0 CA B:GLU605 4.4 0.4 1.0 C B:ASN621 4.4 0.9 1.0 CA B:ASN621 4.4 0.8 1.0 N B:ILE603 4.5 0.8 1.0 CB B:ASN621 4.6 0.4 1.0 C B:GLY624 4.6 0.3 1.0 N B:GLY624 4.6 0.7 1.0 C B:ASP623 4.6 0.5 1.0 CA B:ASP604 4.7 0.5 1.0 N B:ASP623 4.7 0.3 1.0 C B:ASP604 4.7 0.3 1.0 CA B:GLY624 4.7 0.6 1.0 CA B:GLY625 4.7 0.3 1.0 N B:ASP604 4.7 0.3 1.0 O B:ASP623 4.8 0.0 1.0 CA B:ILE603 4.9 0.4 1.0 CB B:LEU622 5.0 0.7 1.0 C B:ASP602 5.0 0.2 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