Calcium in PDB 7qbf: Tc:CD320 in Complex with Nanobody Tc-NB34

The structure of Tc:CD320 in Complex with Nanobody Tc-NB34, PDB code: 7qbf 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)	49.27 / 1.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.822, 104.822, 167.46, 90, 90, 90
R / Rfree (%)	17.4 / 20.5

The structure of Tc:CD320 in Complex with Nanobody Tc-NB34 also contains other interesting chemical elements:

Iodine	(I)	16 atoms
Cobalt	(Co)	2 atoms

The binding sites of Calcium atom in the Tc:CD320 in Complex with Nanobody Tc-NB34 (pdb code 7qbf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tc:CD320 in Complex with Nanobody Tc-NB34, PDB code: 7qbf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB34


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-NB34 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:25.9 occ:1.00 OD2 C:ASP163 2.2 29.7 1.0 OD2 C:ASP157 2.2 27.0 1.0 O C:HIS155 2.3 25.6 1.0 O C:TRP150 2.3 23.8 1.0 OE2 C:GLU164 2.3 29.2 1.0 OD1 C:ASP153 2.4 28.3 1.0 CG C:ASP153 3.2 27.5 1.0 H C:ASP157 3.2 30.7 1.0 HB3 C:TRP150 3.3 30.7 1.0 H C:ASP153 3.3 36.8 1.0 CG C:ASP163 3.4 32.0 1.0 CD C:GLU164 3.4 26.8 1.0 CG C:ASP157 3.4 24.3 1.0 H C:HIS155 3.4 37.6 1.0 C C:HIS155 3.5 29.4 1.0 HG2 C:GLU164 3.5 37.8 1.0 C C:TRP150 3.5 30.4 1.0 OD2 C:ASP153 3.6 24.4 1.0 HB2 C:ASP163 3.7 33.2 1.0 HZ3 A:LYS114 3.7 32.7 1.0 HB2 C:ASP157 3.9 30.3 1.0 CG C:GLU164 3.9 31.5 1.0 N C:ASP157 3.9 25.6 1.0 HB3 C:HIS155 4.0 32.7 1.0 HA C:PRO156 4.1 33.9 1.0 N C:HIS155 4.1 31.3 1.0 CB C:ASP163 4.1 27.7 1.0 HZ2 A:LYS114 4.1 32.7 1.0 CB C:TRP150 4.1 25.6 1.0 HA C:ARG151 4.1 34.3 1.0 CB C:ASP157 4.2 25.3 1.0 N C:ASP153 4.2 30.7 1.0 HG3 C:GLU164 4.2 37.8 1.0 H C:CYS152 4.3 33.3 1.0 CA C:TRP150 4.3 24.1 1.0 CA C:HIS155 4.3 27.9 1.0 NZ A:LYS114 4.3 27.3 1.0 HA C:TRP150 4.3 29.0 1.0 OD1 C:ASP163 4.3 31.2 1.0 OD1 C:ASP157 4.3 23.5 1.0 CB C:ASP153 4.4 30.4 1.0 OE1 C:GLU164 4.4 32.6 1.0 HZ1 A:LYS114 4.5 32.7 1.0 N C:PRO156 4.5 26.6 1.0 N C:ARG151 4.5 30.1 1.0 HB2 C:TRP150 4.5 30.7 1.0 H C:GLY154 4.5 36.5 1.0 N C:CYS152 4.6 27.8 1.0 CA C:PRO156 4.6 28.2 1.0 O C:ASP163 4.6 30.6 1.0 CB C:HIS155 4.6 27.2 1.0 HB3 C:ASP153 4.6 36.5 1.0 HD12 C:ILE146 4.7 42.5 1.0 CA C:ARG151 4.7 28.6 1.0 CA C:ASP153 4.7 27.6 1.0 C C:PRO156 4.7 29.7 1.0 CA C:ASP157 4.7 25.1 1.0 HB3 C:ASP163 4.7 33.2 1.0 C C:ASP163 4.8 33.1 1.0 N C:GLY154 4.8 30.4 1.0 C C:ARG151 4.8 30.1 1.0 HD2 C:HIS155 4.9 29.9 1.0 C C:ASP153 4.9 30.2 1.0 HD13 C:ILE146 5.0 42.5 1.0

Calcium binding site 2 out of 2 in the Tc:CD320 in Complex with Nanobody Tc-NB34


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-NB34 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:30.5 occ:1.00 O C:ASP77 2.2 28.9 1.0 O C:TRP72 2.2 37.1 1.0 OD2 C:ASP79 2.3 27.7 1.0 OD1 C:ASP85 2.3 32.0 1.0 OD1 C:ASP75 2.3 32.6 1.0 OE2 C:GLU86 2.4 34.0 1.0 H C:ASP75 3.2 46.7 1.0 H C:ASP79 3.2 34.5 1.0 HG2 C:GLU86 3.3 42.7 1.0 CG C:ASP75 3.4 41.7 1.0 CD C:GLU86 3.4 33.8 1.0 C C:ASP77 3.4 27.5 1.0 CG C:ASP79 3.4 32.5 1.0 C C:TRP72 3.4 35.8 1.0 CG C:ASP85 3.5 33.0 1.0 HB3 C:TRP72 3.5 42.5 1.0 HB2 C:ASP79 3.5 31.9 1.0 HB2 C:ASP85 3.6 36.5 1.0 HB2 C:ASP77 3.6 35.4 1.0 CG C:GLU86 3.8 35.6 1.0 HZ3 A:LYS105 3.9 39.7 1.0 N C:ASP79 3.9 28.8 1.0 H C:ASP77 3.9 42.7 1.0 OD2 C:ASP75 4.0 33.8 1.0 CB C:ASP79 4.0 26.6 1.0 HA C:TRP72 4.0 42.6 1.0 N C:ASP75 4.0 39.0 1.0 HG3 C:GLU86 4.0 42.7 1.0 HA C:LEU78 4.1 40.9 1.0 CB C:ASP85 4.1 30.4 1.0 N C:ASP77 4.1 35.6 1.0 CA C:ASP77 4.1 31.6 1.0 H C:CYS74 4.1 40.7 1.0 CA C:TRP72 4.2 35.5 1.0 HA C:ARG73 4.2 40.9 1.0 CB C:TRP72 4.3 35.4 1.0 CB C:ASP77 4.3 29.5 1.0 H C:ARG76 4.4 44.6 1.0 N C:LEU78 4.4 31.5 1.0 CB C:ASP75 4.4 38.0 1.0 OE1 C:GLU86 4.4 33.3 1.0 OD1 C:ASP79 4.4 27.5 1.0 OD2 C:ASP85 4.5 32.0 1.0 N C:ARG73 4.5 38.0 1.0 N C:CYS74 4.5 34.0 1.0 CA C:ASP75 4.5 36.6 1.0 N C:ARG76 4.6 37.2 1.0 C C:ASP75 4.6 42.9 1.0 CA C:LEU78 4.6 34.0 1.0 HB3 C:ASP75 4.6 45.6 1.0 HB3 C:ASP77 4.6 35.4 1.0 CA C:ASP79 4.6 26.2 1.0 HZ2 A:LYS105 4.6 39.7 1.0 O C:ASP85 4.6 36.6 1.0 NZ A:LYS105 4.7 33.1 1.0 CA C:ARG73 4.7 34.1 1.0 C C:LEU78 4.7 32.4 1.0 HB3 C:ASP85 4.7 36.5 1.0 HB3 C:ASP79 4.8 31.9 1.0 C C:ASP85 4.8 36.0 1.0 C C:ARG73 4.8 38.2 1.0 HB2 C:TRP72 4.8 42.5 1.0 C C:ARG76 4.8 43.5 1.0 HZ1 A:LYS105 5.0 39.7 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