Calcium in PDB 5z5n: Crystal Structure of Cona-R1M

The structure of Crystal Structure of Cona-R1M, PDB code: 5z5n was solved by G.S.Chen, J.H.Gan, R.T.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.59 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.210, 118.820, 120.450, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 22.5

The structure of Crystal Structure of Cona-R1M also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Cona-R1M (pdb code 5z5n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Cona-R1M, PDB code: 5z5n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Cona-R1M


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 Cona-R1M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:26.7 occ:1.00 O A:HOH449 2.2 20.4 1.0 O A:TYR12 2.2 25.5 1.0 OD2 A:ASP19 2.3 23.2 1.0 O A:HOH441 2.4 25.3 1.0 OD1 A:ASN14 2.5 29.7 1.0 OD1 A:ASP10 2.5 21.1 1.0 OD2 A:ASP10 2.5 17.9 1.0 CG A:ASP10 2.9 20.3 1.0 CG A:ASP19 3.5 25.0 1.0 C A:TYR12 3.5 26.4 1.0 CG A:ASN14 3.6 34.7 1.0 N A:ASN14 3.9 32.3 1.0 OD1 A:ASP19 3.9 18.7 1.0 MN A:MN302 4.1 24.2 1.0 CB A:ASN14 4.3 33.8 1.0 CA A:TYR12 4.4 30.7 1.0 CB A:ASP10 4.4 22.1 1.0 N A:TYR12 4.4 27.3 1.0 N A:PRO13 4.4 25.8 1.0 CA A:PRO13 4.5 27.6 1.0 C A:PRO13 4.5 30.9 1.0 CB A:TYR12 4.6 34.4 1.0 O A:HOH425 4.6 22.9 1.0 CE1 A:HIS24 4.6 31.7 1.0 CA A:ASN14 4.7 32.5 1.0 CB A:ASP19 4.7 27.3 1.0 ND2 A:ASN14 4.7 28.6 1.0 OD2 A:ASP208 4.8 26.0 1.0 O A:ASP208 4.8 25.8 1.0 O A:ARG228 4.8 21.8 1.0 CA A:ARG228 4.8 26.2 1.0 NE2 A:HIS24 5.0 31.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Cona-R1M


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 Cona-R1M within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:21.2 occ:1.00 O B:HOH457 2.3 21.2 1.0 OD1 B:ASN14 2.3 22.4 1.0 O B:TYR12 2.4 24.9 1.0 O B:HOH439 2.4 12.7 1.0 OD2 B:ASP19 2.4 20.3 1.0 OD2 B:ASP10 2.5 18.9 1.0 OD1 B:ASP10 2.5 21.3 1.0 CG B:ASP10 2.9 18.0 1.0 CG B:ASN14 3.5 25.6 1.0 CG B:ASP19 3.6 20.6 1.0 C B:TYR12 3.6 24.7 1.0 N B:ASN14 4.0 27.1 1.0 OD1 B:ASP19 4.0 21.8 1.0 CB B:ASN14 4.1 26.2 1.0 MN B:MN302 4.2 21.2 1.0 CB B:ASP10 4.3 17.1 1.0 CA B:TYR12 4.4 25.9 1.0 N B:PRO13 4.5 27.6 1.0 CA B:PRO13 4.5 27.5 1.0 CB B:TYR12 4.5 28.8 1.0 N B:TYR12 4.5 24.6 1.0 C B:PRO13 4.6 26.5 1.0 ND2 B:ASN14 4.6 21.8 1.0 O B:ASP208 4.6 24.2 1.0 O B:HOH417 4.6 20.0 1.0 CB B:ARG228 4.7 28.6 1.0 CA B:ASN14 4.7 27.4 1.0 CE1 B:HIS24 4.7 25.4 1.0 CA B:ARG228 4.7 26.1 1.0 OD1 B:ASP208 4.8 25.8 1.0 O B:ARG228 4.8 25.8 1.0 CB B:ASP19 4.8 23.0 1.0 CD2 B:TYR12 4.9 29.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Cona-R1M


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 Cona-R1M within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:24.2 occ:1.00 O C:HOH438 2.3 21.7 1.0 O C:HOH454 2.3 21.9 1.0 O C:TYR12 2.4 21.6 1.0 OD2 C:ASP19 2.4 25.2 1.0 OD1 C:ASN14 2.4 25.5 1.0 OD1 C:ASP10 2.5 20.1 1.0 OD2 C:ASP10 2.5 20.3 1.0 CG C:ASP10 2.8 20.6 1.0 CG C:ASP19 3.5 23.9 1.0 CG C:ASN14 3.5 32.4 1.0 C C:TYR12 3.6 25.7 1.0 N C:ASN14 3.9 32.2 1.0 OD1 C:ASP19 4.0 21.3 1.0 MN C:MN302 4.1 23.1 1.0 CB C:ASN14 4.1 34.4 1.0 CB C:ASP10 4.3 21.3 1.0 CA C:TYR12 4.4 27.5 1.0 O C:HOH456 4.4 19.8 1.0 N C:TYR12 4.4 26.9 1.0 CB C:TYR12 4.5 28.2 1.0 CE1 C:HIS24 4.5 24.9 1.0 CA C:PRO13 4.6 27.0 1.0 N C:PRO13 4.6 27.0 1.0 O C:ASP208 4.6 23.4 1.0 CA C:ASN14 4.7 32.0 1.0 ND2 C:ASN14 4.7 30.7 1.0 C C:PRO13 4.7 29.2 1.0 O C:ARG228 4.7 27.6 1.0 CB C:ASP19 4.7 25.6 1.0 OD1 C:ASP208 4.8 28.4 1.0 NE2 C:HIS24 4.9 26.5 1.0 CB C:ARG228 4.9 34.9 1.0 CA C:ARG228 4.9 28.7 1.0 CD2 C:TYR12 4.9 32.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Cona-R1M


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Cona-R1M within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:28.1 occ:1.00 O D:HOH453 2.0 25.4 1.0 OD1 D:ASP10 2.2 20.5 1.0 O D:TYR12 2.3 30.2 1.0 O D:HOH441 2.3 25.4 1.0 OD1 D:ASN14 2.4 32.9 1.0 OD2 D:ASP19 2.5 27.2 1.0 CG D:ASP10 3.0 22.9 1.0 OD2 D:ASP10 3.2 19.6 1.0 C D:TYR12 3.5 32.8 1.0 CG D:ASN14 3.5 38.2 1.0 CG D:ASP19 3.5 31.4 1.0 OD1 D:ASP19 3.9 26.4 1.0 N D:ASN14 4.0 38.8 1.0 CB D:ASN14 4.0 35.4 1.0 MN D:MN302 4.2 28.9 1.0 CA D:TYR12 4.2 38.7 1.0 CB D:TYR12 4.3 42.5 1.0 N D:TYR12 4.3 36.9 1.0 CB D:ASP10 4.4 24.5 1.0 CE1 D:HIS24 4.4 30.2 1.0 O D:HOH407 4.5 26.4 1.0 N D:PRO13 4.5 37.9 1.0 CA D:PRO13 4.6 40.4 1.0 C D:PRO13 4.6 38.0 1.0 ND2 D:ASN14 4.6 31.7 1.0 CA D:ASN14 4.7 35.0 1.0 O D:ASP208 4.7 24.7 1.0 CB D:ASP19 4.8 33.4 1.0 OD1 D:ASP208 4.8 29.3 1.0 NE2 D:HIS24 4.9 28.2 1.0 CD2 D:TYR12 4.9 53.9 1.0 CA D:ASP10 5.0 24.6 1.0

G.S.Chen, J.H.Gan, R.T.Hu. Crystal Structure of Cona-R1M (Only Mannose) To Be Published.