Calcium in PDB 4zrp: Tc:CD320

The structure of Tc:CD320, PDB code: 4zrp was solved by A.Alam, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.099, 98.099, 355.979, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.8

The structure of Tc:CD320 also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Calcium atom in the Tc:CD320 (pdb code 4zrp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Tc:CD320, PDB code: 4zrp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Tc:CD320


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tc:CD320 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:63.9 occ:1.00 O A:HOH650 2.3 52.6 1.0 O A:HOH799 2.5 49.2 1.0 OE2 A:GLU375 2.5 48.7 1.0 O A:HOH631 2.5 50.0 1.0 CD A:GLU375 3.2 45.4 1.0 OE1 A:GLU375 3.3 46.3 1.0 O A:HOH642 4.3 55.8 1.0 NZ A:LYS369 4.5 43.2 1.0 CG A:GLU375 4.7 37.9 1.0 CE A:LYS369 5.0 39.0 1.0

Calcium binding site 2 out of 6 in the Tc:CD320


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tc:CD320 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:60.8 occ:1.00 N A:ASN267 3.2 43.3 1.0 NE2 A:GLN389 3.2 42.0 1.0 N33 A:CNC501 3.3 32.3 1.0 O A:ALA264 3.4 48.9 1.0 CB A:ASN267 3.4 33.8 1.0 N A:GLN266 3.4 48.1 1.0 OH A:TYR226 3.6 41.5 1.0 CZ A:TYR226 3.9 41.0 1.0 CA A:ASN267 3.9 37.9 1.0 CE1 A:TYR226 3.9 36.2 1.0 CA A:GLN266 4.1 52.3 1.0 CG A:GLN389 4.1 34.4 1.0 C A:GLN266 4.1 46.1 1.0 CB A:GLN266 4.2 58.1 1.0 CD A:GLN389 4.2 42.0 1.0 CA A:PHE265 4.4 44.6 1.0 C A:PHE265 4.4 48.0 1.0 C A:ALA264 4.5 46.6 1.0 OD2 A:ASP393 4.5 47.3 1.0 O A:HOH617 4.5 34.1 1.0 CG A:ASP393 4.6 46.6 1.0 CB A:ASP393 4.6 42.2 1.0 C32 A:CNC501 4.6 37.2 1.0 CG A:GLN266 4.7 62.2 1.0 CG A:ASN267 4.7 38.7 1.0 CG A:MET270 4.7 33.2 1.0 CE2 A:TYR226 4.7 34.5 1.0 O34 A:CNC501 4.8 36.9 1.0 CD1 A:TYR226 4.8 37.2 1.0 N A:PHE265 4.9 41.7 1.0 CB A:MET270 4.9 29.8 1.0 CB A:GLN389 5.0 32.5 1.0

Calcium binding site 3 out of 6 in the Tc:CD320


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tc:CD320 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:45.6 occ:1.00 O C:HIS155 2.3 51.1 1.0 OD1 C:ASP153 2.3 46.4 1.0 O C:TRP150 2.3 54.2 1.0 OD2 C:ASP157 2.4 48.3 1.0 OD2 C:ASP163 2.4 54.9 1.0 OE2 C:GLU164 2.4 52.0 1.0 CG C:ASP153 3.2 46.0 1.0 CD C:GLU164 3.4 52.8 1.0 CG C:ASP157 3.5 44.5 1.0 C C:HIS155 3.5 50.6 1.0 C C:TRP150 3.5 55.6 1.0 OD2 C:ASP153 3.5 43.0 1.0 CG C:ASP163 3.5 58.5 1.0 CG C:GLU164 3.9 51.2 1.0 N C:ASP157 4.0 52.4 1.0 CB C:TRP150 4.1 48.7 1.0 N C:ASP153 4.1 48.3 1.0 N C:HIS155 4.1 52.3 1.0 CB C:ASP163 4.2 63.3 1.0 CA C:TRP150 4.2 48.5 1.0 CB C:ASP157 4.2 49.9 1.0 NZ A:LYS114 4.3 43.0 1.0 CA C:HIS155 4.3 46.8 1.0 OD1 C:ASP157 4.4 46.7 1.0 CB C:ASP153 4.4 41.4 1.0 OD1 C:ASP163 4.5 59.4 1.0 N C:PRO156 4.5 54.3 1.0 OE1 C:GLU164 4.5 52.0 1.0 N C:ARG151 4.6 56.2 1.0 CA C:PRO156 4.6 56.5 1.0 N C:CYS152 4.6 58.2 1.0 O C:ASP163 4.6 63.0 1.0 CA C:ASP153 4.7 47.2 1.0 C C:PRO156 4.7 53.1 1.0 CA C:ASP157 4.7 50.9 1.0 CB C:HIS155 4.8 43.3 1.0 CA C:ARG151 4.8 59.4 1.0 N C:GLY154 4.8 57.8 1.0 C C:ASP163 4.8 62.3 1.0 C C:ARG151 4.9 57.8 1.0 C C:ASP153 5.0 51.2 1.0

Calcium binding site 4 out of 6 in the Tc:CD320


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tc:CD320 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:77.7 occ:1.00 O C:ASP77 2.4 85.3 1.0 O C:TRP72 2.4 0.5 1.0 OD1 C:ASP75 2.4 81.4 1.0 OE2 C:GLU86 2.5 98.7 1.0 OD2 C:ASP85 2.5 98.7 1.0 OD2 C:ASP79 2.5 91.8 1.0 C C:ASP77 3.4 82.6 1.0 CG C:ASP79 3.4 93.0 1.0 CG C:ASP85 3.5 0.6 1.0 CG C:ASP75 3.5 81.8 1.0 C C:TRP72 3.5 0.5 1.0 CD C:GLU86 3.6 99.8 1.0 CB C:ASP85 3.9 0.3 1.0 CB C:ASP79 3.9 97.0 1.0 N C:ASP79 3.9 89.8 1.0 CB C:TRP72 4.0 99.2 1.0 OD2 C:ASP75 4.0 75.4 1.0 CA C:ASP77 4.1 79.0 1.0 N C:ASP77 4.1 84.5 1.0 CA C:TRP72 4.1 99.9 1.0 CG C:GLU86 4.1 1.0 1.0 CB C:ASP77 4.1 75.3 1.0 OD1 C:ASP79 4.4 92.8 1.0 N C:LEU78 4.5 80.1 1.0 N C:ASP75 4.5 95.8 1.0 OD1 C:ASP85 4.5 0.7 1.0 O C:ASP85 4.6 0.2 1.0 CA C:ASP79 4.6 93.4 1.0 OE1 C:GLU86 4.6 0.1 1.0 CB C:ASP75 4.6 86.1 1.0 N C:ARG73 4.7 0.6 1.0 CA C:LEU78 4.7 85.0 1.0 C C:ASP85 4.7 0.0 1.0 N C:CYS74 4.8 0.3 1.0 C C:LEU78 4.8 84.6 1.0 CA C:ASP75 4.9 91.2 1.0 C C:ASP75 5.0 91.9 1.0 CA C:ASP85 5.0 0.8 1.0 CA C:ARG73 5.0 0.4 1.0

Calcium binding site 5 out of 6 in the Tc:CD320


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tc:CD320 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:42.8 occ:1.00 O D:TRP150 2.3 48.6 1.0 O D:HIS155 2.3 48.4 1.0 OD1 D:ASP153 2.3 42.0 1.0 OD2 D:ASP157 2.3 46.4 1.0 OE2 D:GLU164 2.3 46.6 1.0 OD2 D:ASP163 2.4 50.4 1.0 CG D:ASP153 3.2 42.8 1.0 CD D:GLU164 3.4 47.3 1.0 C D:TRP150 3.4 44.2 1.0 CG D:ASP157 3.5 47.4 1.0 C D:HIS155 3.5 46.6 1.0 CG D:ASP163 3.6 53.4 1.0 OD2 D:ASP153 3.6 40.1 1.0 N D:ASP157 4.0 51.3 1.0 CG D:GLU164 4.0 48.4 1.0 N D:ASP153 4.1 50.6 1.0 CB D:ASP157 4.1 48.9 1.0 CB D:TRP150 4.1 42.1 1.0 N D:HIS155 4.2 47.5 1.0 CA D:TRP150 4.2 42.0 1.0 CB D:ASP163 4.3 55.9 1.0 CA D:HIS155 4.3 45.1 1.0 NZ B:LYS114 4.4 41.9 1.0 OE1 D:GLU164 4.4 51.1 1.0 OD1 D:ASP157 4.4 47.5 1.0 N D:ARG151 4.4 48.1 1.0 N D:CYS152 4.4 55.7 1.0 CB D:ASP153 4.5 43.9 1.0 CA D:ARG151 4.5 52.4 1.0 N D:PRO156 4.5 50.5 1.0 OD1 D:ASP163 4.5 53.4 1.0 O D:ASP163 4.6 55.0 1.0 CA D:PRO156 4.6 52.2 1.0 CA D:ASP153 4.7 46.9 1.0 CA D:ASP157 4.7 51.6 1.0 C D:ARG151 4.7 53.2 1.0 C D:PRO156 4.7 55.1 1.0 CB D:HIS155 4.8 42.1 1.0 N D:GLY154 4.8 44.2 1.0 C D:ASP163 4.9 56.9 1.0 C D:ASP153 4.9 49.8 1.0

Calcium binding site 6 out of 6 in the Tc:CD320


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Tc:CD320 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:80.4 occ:1.00 O D:ASP77 2.3 84.7 1.0 OD2 D:ASP75 2.3 88.5 1.0 O D:TRP72 2.4 98.3 1.0 OD2 D:ASP79 2.5 89.5 1.0 OD2 D:ASP85 2.5 97.5 1.0 OE1 D:GLU86 2.6 93.3 1.0 CG D:ASP75 3.3 92.4 1.0 C D:ASP77 3.4 82.6 1.0 CG D:ASP79 3.4 87.5 1.0 C D:TRP72 3.5 0.6 1.0 CG D:ASP85 3.5 0.4 1.0 OD1 D:ASP75 3.7 91.0 1.0 CD D:GLU86 3.8 98.0 1.0 CB D:ASP79 3.9 90.1 1.0 N D:ASP79 3.9 86.7 1.0 CB D:TRP72 4.0 94.3 1.0 CB D:ASP85 4.0 0.0 1.0 CA D:ASP77 4.0 83.3 1.0 N D:ASP77 4.0 89.7 1.0 CA D:TRP72 4.0 96.0 1.0 CB D:ASP77 4.1 79.9 1.0 OD1 D:ASP79 4.4 85.1 1.0 CG D:GLU86 4.4 0.1 1.0 N D:LEU78 4.4 79.4 1.0 OD1 D:ASP85 4.6 0.1 1.0 CB D:ASP75 4.6 96.7 1.0 CA D:ASP79 4.6 88.0 1.0 N D:ARG73 4.6 0.4 1.0 CA D:LEU78 4.7 80.2 1.0 OE2 D:GLU86 4.7 0.7 1.0 NZ B:LYS105 4.7 86.8 1.0 N D:ASP75 4.7 0.6 1.0 O D:ASP85 4.7 0.2 1.0 C D:LEU78 4.8 82.2 1.0 N D:CYS74 4.9 0.9 1.0 C D:ASP85 5.0 0.0 1.0 C D:ASP75 5.0 90.4 1.0 CA D:ARG73 5.0 0.8 1.0 CG D:TRP72 5.0 90.1 1.0

A.Alam, J.S.Woo, J.Schmitz, B.Prinz, K.Root, F.Chen, J.S.Bloch, R.Zenobi, K.P.Locher. Structural Basis of Transcobalamin Recognition By Human CD320 Receptor. Nat Commun V. 7 12100 2016.
ISSN: ESSN 2041-1723
PubMed: 27411955
DOI: 10.1038/NCOMMS12100