Calcium in PDB 4zrq: E88 Deletion Mutant of CD320 in Complex with TC2

The structure of E88 Deletion Mutant of CD320 in Complex with TC2, PDB code: 4zrq 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)	29.43 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.404, 98.404, 356.341, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.1

The structure of E88 Deletion Mutant of CD320 in Complex with TC2 also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Calcium atom in the E88 Deletion Mutant of CD320 in Complex with TC2 (pdb code 4zrq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the E88 Deletion Mutant of CD320 in Complex with TC2, PDB code: 4zrq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the E88 Deletion Mutant of CD320 in Complex with TC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E88 Deletion Mutant of CD320 in Complex with TC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:64.0 occ:1.00 OD2 C:ASP163 2.3 84.7 1.0 O C:TRP150 2.3 79.0 1.0 O C:HIS155 2.3 73.9 1.0 OD2 C:ASP157 2.4 72.3 1.0 OD1 C:ASP153 2.4 62.0 1.0 OE2 C:GLU164 2.5 73.4 1.0 CG C:ASP153 3.4 63.6 1.0 CG C:ASP163 3.4 89.9 1.0 CD C:GLU164 3.5 75.7 1.0 CG C:ASP157 3.5 71.5 1.0 C C:TRP150 3.5 78.1 1.0 C C:HIS155 3.6 72.1 1.0 OD2 C:ASP153 3.8 67.4 1.0 CG C:GLU164 3.8 78.6 1.0 N C:ASP157 3.9 78.2 1.0 CB C:ASP163 4.0 97.2 1.0 CB C:ASP157 4.1 79.2 1.0 CB C:TRP150 4.1 70.9 1.0 CA C:TRP150 4.3 70.3 1.0 N C:HIS155 4.3 63.9 1.0 N C:ASP153 4.3 69.3 1.0 NZ A:LYS114 4.4 64.0 1.0 CA C:HIS155 4.4 67.1 1.0 OD1 C:ASP163 4.5 88.9 1.0 OD1 C:ASP157 4.5 69.6 1.0 N C:PRO156 4.5 72.6 1.0 N C:ARG151 4.5 86.2 1.0 CA C:PRO156 4.6 74.0 1.0 OE1 C:GLU164 4.6 79.4 1.0 N C:CYS152 4.6 94.4 1.0 CB C:ASP153 4.6 64.7 1.0 CA C:ARG151 4.6 93.3 1.0 CA C:ASP157 4.7 78.4 1.0 C C:PRO156 4.7 74.8 1.0 CB C:HIS155 4.9 63.9 1.0 CA C:ASP153 4.9 69.2 1.0 C C:ARG151 4.9 90.6 1.0 N C:GLY154 5.0 70.6 1.0 C C:ASP163 5.0 96.2 1.0

Calcium binding site 2 out of 4 in the E88 Deletion Mutant of CD320 in Complex with TC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E88 Deletion Mutant of CD320 in Complex with TC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:0.6 occ:1.00 OD2 C:ASP79 2.4 0.2 1.0 OD1 C:ASP75 2.5 0.3 1.0 O C:ASP77 2.6 0.5 1.0 O C:TRP72 2.8 0.6 1.0 N C:ASP75 3.0 0.2 1.0 OD2 C:ASP85 3.2 0.8 1.0 OD1 C:ASP85 3.2 0.0 1.0 CG C:ASP85 3.4 0.5 1.0 CA C:CYS74 3.4 0.1 1.0 C C:ASP85 3.5 0.0 1.0 C C:CYS74 3.5 0.3 1.0 CG C:ASP75 3.5 0.5 1.0 CB C:CYS74 3.5 0.9 1.0 CG C:ASP79 3.6 0.7 1.0 C C:ASP77 3.7 0.9 1.0 C C:TRP72 4.0 0.1 1.0 CA C:ASP75 4.1 0.5 1.0 N C:ASP77 4.1 0.6 1.0 OD2 C:ASP75 4.2 0.7 1.0 O C:ASP85 4.2 0.3 1.0 OD1 C:ASP79 4.3 1.0 1.0 CA C:ASP85 4.3 0.6 1.0 C C:ASP75 4.4 0.3 1.0 CB C:ASP75 4.4 0.1 1.0 N C:ASP79 4.4 0.0 1.0 CB C:ASP85 4.4 0.5 1.0 N C:ARG76 4.4 0.3 1.0 O C:CYS74 4.4 0.4 1.0 CA C:ASP77 4.5 0.6 1.0 SG C:CYS74 4.5 0.8 1.0 CB C:ASP79 4.6 0.3 1.0 CA C:ARG73 4.6 0.2 1.0 N C:LEU78 4.8 0.1 1.0 N C:ARG73 4.8 0.2 1.0 N C:CYS74 4.9 0.8 1.0 CA C:LEU78 4.9 0.7 1.0 O C:ASP75 5.0 0.9 1.0 CA C:TRP72 5.0 0.2 1.0

Calcium binding site 3 out of 4 in the E88 Deletion Mutant of CD320 in Complex with TC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E88 Deletion Mutant of CD320 in Complex with TC2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:53.2 occ:1.00 O D:TRP150 2.3 64.3 1.0 O D:HIS155 2.3 63.0 1.0 OE2 D:GLU164 2.4 65.4 1.0 OD2 D:ASP157 2.4 59.1 1.0 OD1 D:ASP153 2.4 51.2 1.0 OD2 D:ASP163 2.5 72.3 1.0 CG D:ASP153 3.3 59.2 1.0 CD D:GLU164 3.4 63.2 1.0 CG D:ASP157 3.5 61.7 1.0 C D:TRP150 3.5 62.1 1.0 C D:HIS155 3.5 63.0 1.0 CG D:ASP163 3.5 77.7 1.0 OD2 D:ASP153 3.7 64.2 1.0 CG D:GLU164 3.8 64.9 1.0 N D:ASP157 3.9 69.9 1.0 CB D:ASP163 4.0 82.6 1.0 CB D:ASP157 4.0 67.2 1.0 CB D:TRP150 4.1 57.1 1.0 N D:ASP153 4.2 61.1 1.0 N D:HIS155 4.2 58.7 1.0 CA D:TRP150 4.3 54.4 1.0 CA D:HIS155 4.4 61.2 1.0 NZ B:LYS114 4.4 57.4 1.0 OE1 D:GLU164 4.4 67.5 1.0 OD1 D:ASP157 4.5 63.8 1.0 N D:PRO156 4.5 63.1 1.0 N D:ARG151 4.5 66.9 1.0 CB D:ASP153 4.5 59.6 1.0 N D:CYS152 4.5 71.7 1.0 CA D:PRO156 4.6 64.3 1.0 CA D:ARG151 4.6 70.7 1.0 OD1 D:ASP163 4.6 78.9 1.0 CA D:ASP157 4.6 68.7 1.0 C D:PRO156 4.7 68.5 1.0 CA D:ASP153 4.8 59.9 1.0 CB D:HIS155 4.8 60.0 1.0 C D:ARG151 4.8 68.0 1.0 O D:ASP163 4.8 77.7 1.0 C D:ASP163 4.9 79.0 1.0 N D:GLY154 4.9 59.6 1.0 C D:ASP153 5.0 60.0 1.0

Calcium binding site 4 out of 4 in the E88 Deletion Mutant of CD320 in Complex with TC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E88 Deletion Mutant of CD320 in Complex with TC2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:0.7 occ:1.00 OD1 D:ASP85 2.3 0.3 1.0 OD1 D:ASP75 2.3 0.2 1.0 OD2 D:ASP79 2.5 0.5 1.0 O D:ASP77 2.5 0.1 1.0 O D:TRP72 2.7 0.9 1.0 CG D:ASP85 2.7 0.0 1.0 OD2 D:ASP85 2.8 0.9 1.0 CG D:ASP75 3.2 0.6 1.0 N D:ASP75 3.2 0.9 1.0 C D:ASP77 3.6 0.9 1.0 OD2 D:ASP75 3.7 0.7 1.0 CG D:ASP79 3.8 0.3 1.0 CA D:CYS74 3.9 0.9 1.0 C D:TRP72 3.9 0.5 1.0 C D:CYS74 3.9 0.5 1.0 C D:ASP85 4.0 0.9 1.0 CB D:ASP85 4.1 0.4 1.0 N D:ASP77 4.1 0.1 1.0 CB D:CYS74 4.2 0.9 1.0 CA D:ASP75 4.2 0.7 1.0 CB D:ASP75 4.3 0.2 1.0 N D:ASP79 4.3 0.5 1.0 CA D:ASP85 4.3 0.0 1.0 CA D:ASP77 4.4 0.2 1.0 C D:ASP75 4.5 0.6 1.0 CB D:ASP79 4.6 0.8 1.0 OD1 D:ASP79 4.6 0.4 1.0 N D:LEU78 4.7 0.3 1.0 CA D:TRP72 4.7 1.0 1.0 N D:ARG76 4.7 0.8 1.0 CB D:TRP72 4.7 0.6 1.0 CB D:ASP77 4.8 0.2 1.0 NZ B:LYS105 4.8 88.8 1.0 N D:ARG73 4.9 0.9 1.0 CA D:LEU78 5.0 0.2 1.0 O D:CYS74 5.0 0.5 1.0 O D:ASP85 5.0 0.1 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