Calcium in PDB 4p9w: Structure of Cona/RH3MAN

The structure of Structure of Cona/RH3MAN, PDB code: 4p9w was solved by F.Sakai, M.S.Weiss, M.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.40 / 2.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.000, 116.030, 84.100, 90.00, 95.03, 90.00
R / Rfree (%)	17.3 / 20.2

The structure of Structure of Cona/RH3MAN also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Structure of Cona/RH3MAN (pdb code 4p9w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Cona/RH3MAN, PDB code: 4p9w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Cona/RH3MAN


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Cona/RH3MAN within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:19.2 occ:1.00 O A:TYR12 2.2 23.8 1.0 OD1 A:ASN14 2.2 25.3 1.0 OD2 A:ASP10 2.3 24.4 1.0 O A:HOH416 2.3 2.0 1.0 O A:HOH415 2.4 6.7 1.0 OD2 A:ASP19 2.5 26.1 1.0 OD1 A:ASP10 2.5 25.0 1.0 CG A:ASP10 2.7 24.0 1.0 C A:TYR12 3.4 24.5 1.0 CG A:ASN14 3.4 25.8 1.0 CG A:ASP19 3.5 27.2 1.0 OD1 A:ASP19 3.9 26.4 1.0 N A:ASN14 4.1 26.1 1.0 CB A:ASN14 4.2 26.1 1.0 MN A:MN302 4.2 26.4 1.0 O A:HOH414 4.2 13.0 1.0 CB A:ASP10 4.3 22.9 1.0 N A:PRO13 4.3 25.6 1.0 CA A:PRO13 4.3 26.2 1.0 CA A:TYR12 4.3 24.2 1.0 C A:PRO13 4.4 26.5 1.0 N A:TYR12 4.4 23.7 1.0 ND2 A:ASN14 4.5 25.8 1.0 O A:ASP208 4.6 23.6 1.0 CB A:TYR12 4.6 24.0 1.0 OD1 A:ASP208 4.6 23.1 1.0 O A:ARG228 4.7 23.1 1.0 CE1 A:HIS24 4.7 24.2 1.0 CA A:ARG228 4.7 23.2 1.0 CB A:ARG228 4.8 23.7 1.0 CA A:ASN14 4.8 27.4 1.0 CD1 A:TYR12 4.8 24.2 1.0 CB A:ASP19 4.8 30.1 1.0 NE2 A:HIS24 4.9 23.4 1.0

Calcium binding site 2 out of 4 in the Structure of Cona/RH3MAN


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Cona/RH3MAN within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:31.5 occ:1.00 O B:HOH408 2.2 8.9 1.0 OD2 B:ASP10 2.3 33.5 1.0 O B:TYR12 2.4 32.1 1.0 OD1 B:ASN14 2.4 34.2 1.0 OD2 B:ASP19 2.4 34.5 1.0 O B:HOH409 2.4 11.9 1.0 OD1 B:ASP10 2.6 32.9 1.0 CG B:ASP10 2.8 32.1 1.0 CG B:ASP19 3.5 35.0 1.0 CG B:ASN14 3.5 35.5 1.0 C B:TYR12 3.6 32.5 1.0 OD1 B:ASP19 3.9 34.6 1.0 N B:ASN14 3.9 35.9 1.0 MN B:MN302 4.1 35.7 1.0 CB B:ASN14 4.1 35.8 1.0 O B:HOH407 4.3 5.4 1.0 CB B:ASP10 4.3 30.2 1.0 CA B:TYR12 4.4 31.4 1.0 N B:TYR12 4.5 30.2 1.0 CA B:PRO13 4.5 34.8 1.0 CE1 B:HIS24 4.6 30.4 1.0 N B:PRO13 4.6 34.3 1.0 O B:ARG228 4.6 29.4 1.0 C B:PRO13 4.6 35.9 1.0 ND2 B:ASN14 4.6 35.4 1.0 CA B:ASN14 4.7 37.2 1.0 CB B:TYR12 4.7 30.6 1.0 OD1 B:ASP208 4.7 31.2 1.0 CB B:ASP19 4.7 37.1 1.0 O B:ASP208 4.7 30.8 1.0 CB B:ARG228 4.8 31.0 1.0 CA B:ARG228 4.8 29.9 1.0 NE2 B:HIS24 4.8 30.0 1.0 CD1 B:TYR12 5.0 31.2 1.0

Calcium binding site 3 out of 4 in the Structure of Cona/RH3MAN


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Cona/RH3MAN within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:18.8 occ:1.00 O C:HOH408 2.2 4.1 1.0 O C:TYR12 2.3 20.9 1.0 O C:HOH407 2.3 6.5 1.0 OD2 C:ASP19 2.4 19.4 1.0 OD1 C:ASP10 2.4 16.9 1.0 OD1 C:ASN14 2.4 20.8 1.0 OD2 C:ASP10 2.4 16.9 1.0 CG C:ASP10 2.7 16.9 1.0 CG C:ASP19 3.5 20.4 1.0 C C:TYR12 3.5 20.7 1.0 CG C:ASN14 3.5 21.4 1.0 N C:ASN14 4.0 22.8 1.0 OD1 C:ASP19 4.1 19.4 1.0 MN C:MN302 4.1 22.5 1.0 CB C:ASN14 4.2 22.4 1.0 CB C:ASP10 4.3 17.1 1.0 CA C:TYR12 4.3 20.2 1.0 N C:TYR12 4.4 19.8 1.0 N C:PRO13 4.5 21.6 1.0 O C:HOH406 4.5 5.0 1.0 OD1 C:ASP208 4.5 17.9 1.0 ND2 C:ASN14 4.6 21.2 1.0 CB C:TYR12 4.6 19.8 1.0 CA C:PRO13 4.6 22.5 1.0 CD1 C:TYR12 4.6 19.7 1.0 O C:ASP208 4.6 19.4 1.0 C C:PRO13 4.6 22.9 1.0 CB C:ARG228 4.6 19.7 1.0 CE1 C:HIS24 4.7 21.1 1.0 CA C:ASN14 4.7 23.0 1.0 CA C:ARG228 4.7 19.5 1.0 CB C:ASP19 4.8 22.5 1.0 NE2 C:HIS24 4.8 21.0 1.0 O C:ARG228 4.8 19.4 1.0

Calcium binding site 4 out of 4 in the Structure of Cona/RH3MAN


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Cona/RH3MAN within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:20.1 occ:1.00 O D:HOH402 2.2 28.9 1.0 OD2 D:ASP19 2.3 22.3 1.0 O D:TYR12 2.3 25.0 1.0 OD1 D:ASP10 2.4 20.6 1.0 OD1 D:ASN14 2.4 24.4 1.0 O D:HOH410 2.5 22.1 1.0 OD2 D:ASP10 2.6 20.3 1.0 CG D:ASP10 2.8 20.6 1.0 CG D:ASP19 3.4 22.9 1.0 C D:TYR12 3.5 25.2 1.0 CG D:ASN14 3.6 25.3 1.0 OD1 D:ASP19 3.9 22.1 1.0 N D:ASN14 3.9 26.3 1.0 MN D:MN302 4.0 25.8 1.0 CB D:ASN14 4.2 25.8 1.0 CA D:TYR12 4.4 25.4 1.0 CB D:ASP10 4.4 20.8 1.0 CA D:PRO13 4.5 26.3 1.0 N D:PRO13 4.5 26.3 1.0 CB D:TYR12 4.5 25.3 1.0 O D:ASP208 4.5 20.9 1.0 O D:HOH408 4.5 20.8 1.0 N D:TYR12 4.6 25.0 1.0 OD1 D:ASP208 4.6 20.4 1.0 C D:PRO13 4.6 26.8 1.0 CB D:ARG228 4.6 23.4 1.0 CB D:ASP19 4.7 24.6 1.0 CA D:ASN14 4.7 26.7 1.0 ND2 D:ASN14 4.7 25.7 1.0 CE1 D:HIS24 4.7 24.0 1.0 CD1 D:TYR12 4.7 26.7 1.0 CA D:ARG228 4.8 23.2 1.0 O D:ARG228 4.9 22.7 1.0

G.Chen, F.Sakai, M.S.Weiss. Structure of Cona/RH3MAN To Be Published.