Calcium in PDB 9hmu: DUF4465 Domain Containing Protein in Complex with Vitamin B12.

The structure of DUF4465 Domain Containing Protein in Complex with Vitamin B12., PDB code: 9hmu was solved by C.Clarke, M.Banasik, R.W.Pickersgill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.38 / 1.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.72, 113.72, 162.593, 90, 90, 120
R / Rfree (%)	19 / 21.3

The structure of DUF4465 Domain Containing Protein in Complex with Vitamin B12. also contains other interesting chemical elements:

Cobalt

(Co)

3 atoms

The binding sites of Calcium atom in the DUF4465 Domain Containing Protein in Complex with Vitamin B12. (pdb code 9hmu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the DUF4465 Domain Containing Protein in Complex with Vitamin B12., PDB code: 9hmu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the DUF4465 Domain Containing Protein in Complex with Vitamin B12.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DUF4465 Domain Containing Protein in Complex with Vitamin B12. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:36.6 occ:1.00 O A:ASN119 2.3 29.5 1.0 O A:SER30 2.4 29.2 1.0 OG1 A:THR117 2.4 25.8 1.0 OD1 A:ASP243 2.5 25.8 1.0 OD2 A:ASP243 2.5 24.7 1.0 OE1 A:GLN244 2.6 29.8 1.0 OE1 A:GLU32 2.7 43.8 1.0 CG A:ASP243 2.8 25.4 1.0 HB A:THR117 3.2 28.8 1.0 CB A:THR117 3.4 28.8 1.0 C A:ASN119 3.5 29.3 1.0 C A:SER30 3.5 29.3 1.0 HA A:SER30 3.6 30.3 1.0 HB2 A:SER30 3.6 32.3 1.0 CD A:GLN244 3.7 31.9 1.0 HG21 A:THR117 3.7 30.0 1.0 HA A:TYR120 3.8 25.3 1.0 HG2 A:GLN244 3.8 29.1 1.0 HB2 A:PHE31 3.9 28.1 1.0 HA3 A:GLY113 3.9 26.1 1.0 CD A:GLU32 3.9 42.1 1.0 H A:ASN119 4.0 30.0 1.0 CA A:SER30 4.0 31.1 1.0 HD2 A:PHE31 4.0 26.6 1.0 H A:GLN244 4.1 26.3 1.0 HB3 A:TYR120 4.1 24.3 1.0 CG2 A:THR117 4.1 30.2 1.0 HB2 A:ASN119 4.2 31.0 1.0 HG2 A:GLU32 4.3 40.2 1.0 CB A:SER30 4.3 32.0 1.0 N A:ASN119 4.3 29.4 1.0 H A:ALA114 4.3 26.2 1.0 CG A:GLN244 4.3 29.8 1.0 CA A:ASN119 4.4 29.6 1.0 CB A:ASP243 4.4 23.6 1.0 N A:TYR120 4.4 24.7 1.0 CA A:TYR120 4.5 25.7 1.0 HG22 A:THR117 4.6 30.1 1.0 CA A:THR117 4.6 29.1 1.0 O A:ALA114 4.6 27.6 1.0 N A:PHE31 4.7 29.0 1.0 C A:THR117 4.7 29.0 1.0 NE2 A:GLN244 4.7 33.1 1.0 CG A:GLU32 4.7 40.2 1.0 N A:GLN244 4.7 26.0 1.0 CB A:ASN119 4.8 29.7 1.0 HB3 A:ASP243 4.8 24.1 1.0 HB2 A:ASP243 4.8 23.2 1.0 CB A:TYR120 4.8 23.3 1.0 HE21 A:GLN244 4.8 33.8 1.0 OE2 A:GLU32 4.8 38.4 1.0 CB A:PHE31 4.8 28.4 1.0 CA A:GLY113 4.8 25.7 1.0 N A:ALA114 4.9 26.4 1.0 HG23 A:THR117 4.9 31.1 1.0 HA A:ASP243 4.9 23.7 1.0 HG3 A:GLN244 4.9 30.4 1.0 CD2 A:PHE31 4.9 27.1 1.0 HB3 A:SER30 4.9 33.0 1.0 N A:THR118 4.9 27.6 1.0 H A:THR118 5.0 28.9 1.0 O A:THR117 5.0 28.5 1.0 HB3 A:ASN119 5.0 29.9 1.0

Calcium binding site 2 out of 3 in the DUF4465 Domain Containing Protein in Complex with Vitamin B12.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DUF4465 Domain Containing Protein in Complex with Vitamin B12. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:30.8 occ:1.00 O B:ASN119 2.3 22.8 1.0 OG1 B:THR117 2.4 26.1 1.0 O B:SER30 2.4 23.5 1.0 OD1 B:ASP243 2.5 24.5 1.0 OE1 B:GLN244 2.6 29.8 1.0 OD2 B:ASP243 2.6 24.1 1.0 OE1 B:GLU32 2.6 44.6 1.0 CG B:ASP243 2.9 22.9 1.0 HB B:THR117 3.1 30.1 1.0 CB B:THR117 3.3 30.2 1.0 C B:SER30 3.5 24.8 1.0 C B:ASN119 3.5 24.3 1.0 HA B:SER30 3.6 25.3 1.0 HB2 B:SER30 3.6 27.5 1.0 HG21 B:THR117 3.6 32.4 1.0 CD B:GLN244 3.6 29.2 1.0 HA B:TYR120 3.8 21.9 1.0 HG2 B:GLN244 3.8 27.2 1.0 CD B:GLU32 3.9 44.1 1.0 HB2 B:PHE31 3.9 24.4 1.0 CA B:SER30 3.9 25.0 1.0 H B:ASN119 4.0 25.8 1.0 CG2 B:THR117 4.0 33.0 1.0 HA3 B:GLY113 4.0 25.3 1.0 HD2 B:PHE31 4.1 24.8 1.0 H B:GLN244 4.1 23.5 1.0 HB3 B:TYR120 4.2 22.6 1.0 HB2 B:ASN119 4.2 25.7 1.0 HG2 B:GLU32 4.2 41.1 1.0 CB B:SER30 4.2 27.8 1.0 H B:ALA114 4.3 24.7 1.0 N B:ASN119 4.3 25.0 1.0 CG B:GLN244 4.3 28.3 1.0 CB B:ASP243 4.4 21.4 1.0 CA B:ASN119 4.4 23.8 1.0 N B:TYR120 4.4 21.1 1.0 HG22 B:THR117 4.5 32.5 1.0 CA B:TYR120 4.5 21.5 1.0 CA B:THR117 4.5 30.1 1.0 O B:ALA114 4.6 25.9 1.0 N B:PHE31 4.6 25.0 1.0 C B:THR117 4.7 28.3 1.0 NE2 B:GLN244 4.7 30.4 1.0 CG B:GLU32 4.7 41.9 1.0 HE21 B:GLN244 4.7 31.0 1.0 N B:GLN244 4.8 22.6 1.0 OE2 B:GLU32 4.8 41.0 1.0 HG23 B:THR117 4.8 33.4 1.0 CB B:ASN119 4.8 25.1 1.0 CB B:PHE31 4.8 24.4 1.0 HB3 B:ASP243 4.8 21.9 1.0 HB2 B:ASP243 4.8 21.1 1.0 CB B:TYR120 4.9 22.0 1.0 N B:ALA114 4.9 25.4 1.0 HB3 B:SER30 4.9 28.3 1.0 HG3 B:GLN244 4.9 28.5 1.0 H B:THR118 4.9 29.0 1.0 N B:THR118 4.9 28.4 1.0 CA B:GLY113 4.9 25.0 1.0 HA B:ASP243 4.9 21.8 1.0 CD2 B:PHE31 5.0 24.6 1.0 O B:THR117 5.0 28.2 1.0

Calcium binding site 3 out of 3 in the DUF4465 Domain Containing Protein in Complex with Vitamin B12.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DUF4465 Domain Containing Protein in Complex with Vitamin B12. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:29.4 occ:1.00 O C:ASN119 2.4 25.2 1.0 OG1 C:THR117 2.4 24.6 1.0 OD1 C:ASP243 2.4 23.3 1.0 O C:SER30 2.4 28.0 1.0 OD2 C:ASP243 2.5 23.1 1.0 OE1 C:GLN244 2.5 26.2 1.0 OE1 C:GLU32 2.7 37.8 1.0 CG C:ASP243 2.8 23.2 1.0 HB C:THR117 3.3 26.5 1.0 CB C:THR117 3.4 25.9 1.0 C C:SER30 3.5 27.4 1.0 C C:ASN119 3.5 24.5 1.0 CD C:GLN244 3.6 25.9 1.0 HA C:SER30 3.6 26.4 1.0 HB2 C:SER30 3.6 27.2 1.0 HG21 C:THR117 3.7 27.5 1.0 HG2 C:GLN244 3.7 24.1 1.0 HA C:TYR120 3.8 22.1 1.0 CD C:GLU32 3.9 39.1 1.0 HA3 C:GLY113 4.0 23.2 1.0 H C:ASN119 4.0 25.8 1.0 HB2 C:PHE31 4.0 24.5 1.0 CA C:SER30 4.0 26.1 1.0 H C:GLN244 4.0 23.5 1.0 HD2 C:PHE31 4.1 24.7 1.0 CG2 C:THR117 4.1 27.8 1.0 HB3 C:TYR120 4.2 21.5 1.0 HG2 C:GLU32 4.2 37.0 1.0 HB2 C:ASN119 4.2 26.6 1.0 H C:ALA114 4.2 22.2 1.0 CG C:GLN244 4.2 25.0 1.0 CB C:SER30 4.3 27.6 1.0 N C:ASN119 4.3 25.1 1.0 CB C:ASP243 4.3 23.0 1.0 CA C:ASN119 4.4 24.7 1.0 N C:TYR120 4.5 22.8 1.0 CA C:TYR120 4.5 21.7 1.0 O C:ALA114 4.5 25.5 1.0 HG22 C:THR117 4.6 27.6 1.0 NE2 C:GLN244 4.6 27.7 1.0 CA C:THR117 4.6 27.8 1.0 CG C:GLU32 4.7 37.5 1.0 HE21 C:GLN244 4.7 28.1 1.0 N C:GLN244 4.7 23.2 1.0 N C:PHE31 4.7 26.4 1.0 C C:THR117 4.7 25.6 1.0 HB3 C:ASP243 4.7 23.0 1.0 HB2 C:ASP243 4.7 22.2 1.0 HG3 C:GLN244 4.8 25.3 1.0 OE2 C:GLU32 4.8 39.5 1.0 CB C:ASN119 4.8 25.7 1.0 N C:ALA114 4.8 22.3 1.0 CA C:GLY113 4.9 22.9 1.0 CB C:TYR120 4.9 20.9 1.0 CB C:PHE31 4.9 24.6 1.0 HA C:ASP243 4.9 22.5 1.0 HG23 C:THR117 4.9 28.5 1.0 HB3 C:SER30 5.0 27.9 1.0 CD2 C:PHE31 5.0 24.4 1.0

C.Clarke, M.Banasik, R.W.Pickersgill. DUF4465 Domains Bind Vitamin B12. To Be Published.