Calcium in PDB 6wrv: Crystal Structure of Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain

The structure of Crystal Structure of Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain, PDB code: 6wrv was solved by J.Abraham, D.Baker, D.D.Sahtoe, A.Coscia, L.Clark, D.Olal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	128.04 / 2.47
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	256.079, 256.079, 128.084, 90, 90, 90
R / Rfree (%)	22.1 / 23.6

The binding sites of Calcium atom in the Crystal Structure of Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain (pdb code 6wrv). 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 Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain, PDB code: 6wrv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain


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 Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca810 b:40.8 occ:0.00 OE2 A:GLU465 2.1 80.9 1.0 O A:THR310 2.2 61.8 1.0 O A:PHE313 2.2 73.6 1.0 OE1 A:GLU465 2.4 76.4 1.0 OE1 A:GLU468 2.5 59.7 1.0 OG1 A:THR310 2.5 53.6 1.0 CD A:GLU465 2.6 69.3 1.0 C A:PHE313 3.2 59.1 1.0 CB A:THR310 3.2 60.0 1.0 C A:THR310 3.3 59.2 1.0 CD A:GLU468 3.7 57.2 1.0 N A:PHE313 3.7 54.8 1.0 OG A:SER315 3.9 58.9 1.0 CA A:THR310 3.9 63.0 1.0 CA A:PRO314 4.0 50.6 1.0 N A:PRO314 4.0 53.5 1.0 CG A:GLU465 4.1 60.6 1.0 N A:SER315 4.1 57.5 1.0 C A:PRO314 4.1 57.5 1.0 CA A:PHE313 4.1 58.8 1.0 OE2 A:GLU468 4.2 58.3 1.0 N A:GLY312 4.3 64.3 1.0 O A:ASP307 4.4 61.3 1.0 N A:PRO311 4.5 59.3 1.0 CG2 A:THR310 4.6 54.7 1.0 C A:GLY312 4.7 65.8 1.0 CB A:ASP307 4.7 64.4 1.0 N A:THR310 4.8 60.8 1.0 O A:PRO314 4.8 62.5 1.0 CA A:PRO311 4.8 57.9 1.0 C A:PRO311 4.8 65.8 1.0 CG A:GLU468 4.8 63.4 1.0 CB A:GLU468 4.9 62.4 1.0 CB A:GLU465 4.9 57.4 1.0 N A:ASP307 4.9 55.0 1.0 CB A:SER315 4.9 55.0 1.0 CA A:SER315 4.9 58.9 1.0 CA A:GLY312 5.0 59.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain


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 Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca809 b:13.5 occ:0.00 O B:THR310 2.3 68.6 1.0 OE1 B:GLU468 2.3 68.8 1.0 N B:GLY312 2.4 61.6 1.0 N B:PHE313 2.5 52.5 1.0 OE2 B:GLU468 2.5 57.7 1.0 CD B:GLU468 2.6 58.6 1.0 O B:PHE313 2.8 61.8 1.0 C B:GLY312 3.0 60.4 1.0 CA B:GLY312 3.0 60.7 1.0 C B:PRO311 3.3 67.4 1.0 C B:PHE313 3.4 53.9 1.0 C B:THR310 3.4 64.2 1.0 CA B:PHE313 3.5 57.6 1.0 OE2 B:GLU465 3.7 84.5 1.0 CA B:PRO311 3.7 58.1 1.0 CG B:GLU468 3.9 52.1 1.0 N B:PRO311 4.0 61.7 1.0 O B:GLY312 4.0 62.6 1.0 O B:PRO311 4.3 72.3 1.0 OG1 B:THR310 4.3 57.0 1.0 CB B:GLU468 4.3 44.5 1.0 OE1 B:GLU465 4.4 84.5 1.0 CD B:GLU465 4.4 75.5 1.0 N B:PRO314 4.4 52.3 1.0 CB B:THR310 4.6 59.1 1.0 CA B:THR310 4.6 63.0 1.0 CB B:PHE313 4.7 54.6 1.0 CG B:PHE313 4.9 52.5 1.0 CD1 B:PHE313 4.9 48.6 1.0 CA B:PRO314 5.0 46.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain


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 Computationally Designed Protein 3DS18 in Complex with the Human Transferrin Receptor Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca810 b:44.0 occ:0.00 O E:THR310 2.5 72.6 1.0 OE1 E:GLU468 2.5 60.4 1.0 OE2 E:GLU468 2.6 55.0 1.0 OE2 E:GLU465 2.7 71.5 1.0 CD E:GLU468 2.9 53.2 1.0 N E:GLY312 3.2 56.2 1.0 C E:THR310 3.5 56.3 1.0 CA E:PRO311 3.7 48.9 1.0 O E:ASP307 3.7 44.9 1.0 CD E:GLU465 3.8 65.3 1.0 C E:PRO311 3.9 59.4 1.0 O E:PHE313 4.0 60.2 1.0 N E:PRO311 4.1 55.0 1.0 OG1 E:THR310 4.1 44.0 1.0 CA E:GLY312 4.2 49.9 1.0 N E:PHE313 4.2 45.6 1.0 OE1 E:GLU465 4.3 73.9 1.0 N E:ASP307 4.3 45.9 1.0 CG E:GLU468 4.4 53.1 1.0 CG2 E:THR464 4.5 42.5 1.0 CA E:GLY306 4.5 37.7 1.0 C E:GLY312 4.6 48.4 1.0 O E:THR305 4.6 37.7 1.0 C E:GLY306 4.7 46.9 1.0 C E:ASP307 4.7 52.0 1.0 CA E:THR310 4.7 46.8 1.0 CB E:THR310 4.8 45.9 1.0 C E:PHE313 4.8 45.5 1.0 CG E:GLU465 4.9 55.4 1.0 CA E:ASP307 5.0 41.2 1.0

D.D.Sahtoe, A.Coscia, N.Mustafaoglu, L.M.Miller, D.Olal, I.Vulovic, T.Y.Yu, I.Goreshnik, Y.R.Lin, L.Clark, F.Busch, L.Stewart, V.H.Wysocki, D.E.Ingber, J.Abraham, D.Baker. Transferrin Receptor Targeting By De Novo Sheet Extension. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33879614
DOI: 10.1073/PNAS.2021569118