Calcium in PDB 7qbe: Tc:CD320 in Complex with Nanobody Tc-NB11

The structure of Tc:CD320 in Complex with Nanobody Tc-NB11, PDB code: 7qbe was solved by J.S.Bloch, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.96 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.717, 195.831, 198.385, 90, 90, 90
R / Rfree (%)	25.2 / 28.4

The structure of Tc:CD320 in Complex with Nanobody Tc-NB11 also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Calcium atom in the Tc:CD320 in Complex with Nanobody Tc-NB11 (pdb code 7qbe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tc:CD320 in Complex with Nanobody Tc-NB11, PDB code: 7qbe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tc:CD320 in Complex with Nanobody Tc-NB11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tc:CD320 in Complex with Nanobody Tc-NB11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:46.8 occ:1.00 OD1 B:ASP153 2.1 44.5 1.0 O B:HIS155 2.2 52.9 1.0 OD2 B:ASP157 2.3 48.4 1.0 OD2 B:ASP163 2.3 55.0 1.0 OE2 B:GLU164 2.3 45.1 1.0 O B:TRP150 2.3 45.6 1.0 CG B:ASP153 3.1 42.9 1.0 CG B:ASP157 3.3 50.3 1.0 C B:HIS155 3.4 49.5 1.0 CG B:ASP163 3.5 54.9 1.0 CD B:GLU164 3.5 48.7 1.0 C B:TRP150 3.5 47.7 1.0 OD2 B:ASP153 3.5 40.3 1.0 N B:ASP157 3.8 48.3 1.0 CB B:ASP157 3.9 43.7 1.0 CB B:TRP150 4.0 46.6 1.0 CG B:GLU164 4.0 47.1 1.0 CA B:TRP150 4.1 45.7 1.0 CB B:ASP163 4.1 50.9 1.0 N B:HIS155 4.1 40.5 1.0 NZ A:LYS114 4.2 43.4 1.0 CA B:HIS155 4.2 46.2 1.0 OD1 B:ASP157 4.2 53.2 1.0 N B:ASP153 4.3 45.1 1.0 N B:PRO156 4.4 47.5 1.0 CB B:ASP153 4.4 42.9 1.0 CA B:PRO156 4.5 47.2 1.0 OE1 B:GLU164 4.5 45.0 1.0 CA B:ASP157 4.5 47.8 1.0 C B:PRO156 4.5 51.5 1.0 OD1 B:ASP163 4.5 52.8 1.0 CB B:HIS155 4.6 46.8 1.0 N B:ARG151 4.6 51.8 1.0 N B:CYS152 4.7 46.8 1.0 CA B:ASP153 4.8 45.1 1.0 O B:ASP163 4.9 46.4 1.0 CA B:ARG151 4.9 45.5 1.0 N B:GLY154 4.9 39.3 1.0

Calcium binding site 2 out of 4 in the Tc:CD320 in Complex with Nanobody Tc-NB11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tc:CD320 in Complex with Nanobody Tc-NB11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:91.0 occ:1.00 OD1 B:ASP75 1.8 104.3 1.0 O B:ASP77 1.8 87.7 1.0 OD2 B:ASP79 2.1 92.4 1.0 O B:TRP72 2.3 89.5 1.0 OD2 B:ASP85 2.3 92.1 1.0 OE2 B:GLU86 2.4 103.7 1.0 CG B:ASP75 2.9 101.4 1.0 C B:ASP77 3.0 87.9 1.0 CG B:ASP79 3.2 85.2 1.0 C B:TRP72 3.3 98.8 1.0 OD2 B:ASP75 3.4 96.0 1.0 CD B:GLU86 3.5 100.1 1.0 CG B:ASP85 3.5 89.2 1.0 N B:ASP79 3.7 82.8 1.0 CA B:ASP77 3.7 97.2 1.0 CB B:ASP77 3.7 96.4 1.0 CB B:ASP79 3.8 86.7 1.0 CA B:TRP72 3.8 102.3 1.0 N B:ASP77 3.8 100.1 1.0 N B:ASP75 3.9 101.6 1.0 CB B:TRP72 3.9 97.2 1.0 CG B:GLU86 4.0 91.4 1.0 N B:LEU78 4.1 89.5 1.0 CB B:ASP75 4.1 100.7 1.0 OD1 B:ASP79 4.2 78.7 1.0 CB B:ASP85 4.3 91.4 1.0 CA B:LEU78 4.4 91.5 1.0 CA B:ASP79 4.4 85.1 1.0 CA B:ASP75 4.4 101.5 1.0 OD1 B:ASP85 4.4 87.8 1.0 O B:ARG73 4.4 111.4 1.0 C B:LEU78 4.5 85.8 1.0 OE1 B:GLU86 4.5 104.8 1.0 N B:ARG73 4.5 103.1 1.0 C B:ARG73 4.5 106.0 1.0 C B:ASP75 4.7 97.7 1.0 N B:ARG76 4.7 99.0 1.0 CA B:ARG73 4.8 103.4 1.0 N B:CYS74 4.9 105.6 1.0 C B:ARG76 5.0 95.4 1.0

Calcium binding site 3 out of 4 in the Tc:CD320 in Complex with Nanobody Tc-NB11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tc:CD320 in Complex with Nanobody Tc-NB11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:66.3 occ:1.00 OD1 D:ASP75 1.7 78.4 1.0 O D:ASP77 2.0 70.4 1.0 OD2 D:ASP85 2.2 75.8 1.0 O D:TRP72 2.3 72.3 1.0 OE2 D:GLU86 2.3 70.5 1.0 OD2 D:ASP79 2.8 73.9 1.0 CG D:ASP75 2.8 77.7 1.0 C D:ASP77 3.2 70.7 1.0 CD D:GLU86 3.3 72.1 1.0 CG D:ASP85 3.4 71.8 1.0 C D:TRP72 3.4 75.3 1.0 OD2 D:ASP75 3.5 84.7 1.0 CG D:ASP79 3.7 78.2 1.0 N D:ASP77 3.7 75.6 1.0 CA D:ASP77 3.9 70.3 1.0 CG D:GLU86 3.9 70.9 1.0 N D:ASP75 3.9 73.0 1.0 CB D:ASP75 4.0 66.4 1.0 N D:ASP79 4.0 73.4 1.0 CA D:TRP72 4.0 77.2 1.0 CB D:TRP72 4.1 80.8 1.0 CB D:ASP85 4.1 72.8 1.0 CB D:ASP79 4.2 76.7 1.0 CB D:ASP77 4.2 72.7 1.0 OE1 D:GLU86 4.2 70.0 1.0 OD1 D:ASP85 4.3 67.3 1.0 N D:LEU78 4.3 70.8 1.0 CA D:ASP75 4.4 70.7 1.0 N D:ARG76 4.4 74.4 1.0 N D:ARG73 4.5 80.8 1.0 N D:CYS74 4.6 72.7 1.0 CA D:LEU78 4.6 67.5 1.0 C D:ASP75 4.6 72.1 1.0 OD1 D:ASP79 4.7 79.0 1.0 C D:LEU78 4.7 70.7 1.0 CA D:ASP79 4.8 70.2 1.0 CA D:ARG73 4.8 79.8 1.0 C D:ARG76 4.9 82.7 1.0 C D:ASP85 4.9 73.8 1.0 O D:ASP85 5.0 73.4 1.0

Calcium binding site 4 out of 4 in the Tc:CD320 in Complex with Nanobody Tc-NB11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tc:CD320 in Complex with Nanobody Tc-NB11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:67.3 occ:1.00 OE2 D:GLU164 2.2 65.2 1.0 O D:HIS155 2.3 69.2 1.0 OD1 D:ASP153 2.4 60.3 1.0 O D:TRP150 2.4 67.9 1.0 OD2 D:ASP157 2.5 67.7 1.0 CG D:ASP153 3.0 64.2 1.0 CD D:GLU164 3.2 68.1 1.0 OD2 D:ASP153 3.3 68.6 1.0 C D:HIS155 3.5 66.2 1.0 CG D:ASP157 3.6 69.4 1.0 C D:TRP150 3.6 69.6 1.0 OD1 D:ASP163 3.6 82.6 1.0 CG D:ASP163 3.6 81.0 1.0 CG D:GLU164 3.8 72.6 1.0 OD2 D:ASP163 3.9 80.2 1.0 N D:HIS155 4.0 63.9 1.0 N D:ASP157 4.0 64.4 1.0 CB D:ASP163 4.1 79.4 1.0 N D:ASP153 4.2 74.2 1.0 CB D:ASP157 4.2 73.3 1.0 CB D:TRP150 4.2 64.3 1.0 CA D:HIS155 4.2 61.5 1.0 NZ C:LYS114 4.3 60.8 1.0 CA D:TRP150 4.3 67.6 1.0 CB D:ASP153 4.3 61.9 1.0 OE1 D:GLU164 4.3 66.8 1.0 N D:PRO156 4.5 63.8 1.0 N D:CYS152 4.5 73.3 1.0 OD1 D:ASP157 4.6 64.0 1.0 CB D:HIS155 4.6 58.5 1.0 CA D:PRO156 4.7 68.8 1.0 CA D:ASP153 4.7 66.1 1.0 N D:ARG151 4.7 71.3 1.0 N D:GLY154 4.7 60.8 1.0 C D:PRO156 4.7 67.6 1.0 CA D:ASP157 4.7 68.7 1.0 C D:ASP153 4.9 65.9 1.0 C D:ARG151 4.9 71.2 1.0 CA D:ARG151 4.9 74.0 1.0 C D:ASP163 4.9 78.4 1.0 O D:ASP163 4.9 71.7 1.0

J.S.Bloch, J.M.Sequeira, A.S.Ramirez, E.V.Quadros, K.P.Locher. Generation of Nanobodies Targeting the Human, Transcobalamin-Mediated Vitamin B 12 Uptake Route. Faseb J. V. 36 22222 2022.
ISSN: ESSN 1530-6860
PubMed: 35218573
DOI: 10.1096/FJ.202101376RR