Magnesium in PDB 7ddb: Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity

The structure of Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity, PDB code: 7ddb was solved by N.M.M.U.Khan, T.Arai, S.Tsuda, H.Kondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.68 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.79, 63.143, 102.086, 90, 90, 90
R / Rfree (%)	20.8 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity (pdb code 7ddb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity, PDB code: 7ddb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:9.9 occ:1.00 OG A:SER129 3.0 17.7 1.0 N A:GLY111 3.2 11.2 1.0 N A:SER129 3.3 12.2 1.0 CA A:GLY111 3.7 11.6 1.0 C A:ALA109 3.7 11.0 1.0 N A:LEU110 3.8 10.4 1.0 CB A:ALA109 3.8 11.2 1.0 CA A:ALA109 3.9 11.4 1.0 CB A:SER129 4.0 14.2 1.0 CA A:ALA128 4.0 11.8 1.0 C A:ALA128 4.1 11.8 1.0 O A:ALA109 4.2 12.3 1.0 CA A:SER129 4.2 12.2 1.0 C A:LEU110 4.3 10.3 1.0 O A:GLY127 4.4 11.4 1.0 CA A:LEU110 4.7 10.4 1.0 N A:ALA128 4.7 11.6 1.0 O A:GLY111 4.8 13.3 1.0 C A:GLY111 4.8 12.6 1.0 C A:GLY127 4.8 11.4 1.0 N A:ALA130 4.8 10.3 1.0 C A:SER129 4.9 11.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:11.9 occ:1.00 OG B:SER129 2.9 17.0 1.0 N B:GLY111 3.3 12.3 1.0 N B:SER129 3.3 13.2 1.0 CB B:ALA109 3.6 11.6 1.0 CA B:GLY111 3.7 11.2 1.0 O B:HOH616 3.7 32.4 1.0 C B:ALA109 3.8 12.3 1.0 N B:LEU110 3.8 13.2 1.0 CB B:SER129 3.8 15.7 1.0 CA B:ALA109 3.8 12.0 1.0 CA B:ALA128 4.0 13.3 1.0 C B:ALA128 4.1 13.7 1.0 CA B:SER129 4.2 14.5 1.0 O B:HOH509 4.3 29.4 1.0 O B:GLY127 4.3 13.1 1.0 C B:LEU110 4.4 11.8 1.0 O B:ALA109 4.5 14.5 1.0 N B:ALA128 4.6 13.3 1.0 C B:GLY127 4.7 12.8 1.0 CA B:LEU110 4.8 12.1 1.0 C B:GLY111 4.8 11.4 1.0 O B:GLY111 4.9 10.7 1.0 N B:ALA130 4.9 12.8 1.0 C B:SER129 4.9 13.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Fungal Antifreeze Protein with Intermediate Activity within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:26.5 occ:1.00 O B:HOH645 2.0 27.0 1.0 O B:HOH607 2.0 23.1 1.0 O B:HOH562 2.2 24.8 1.0 O B:HOH552 3.9 20.6 1.0 O B:HOH540 4.3 15.9 1.0 O B:ASP71 4.3 11.7 1.0 O B:HOH620 4.4 23.2 1.0 O B:TYR72 5.0 9.8 1.0

N.M.U.Khan, T.Arai, S.Tsuda, H.Kondo. Characterization of Microbial Antifreeze Protein with Intermediate Activity Suggests That A Bound-Water Network Is Essential For Hyperactivity. Sci Rep V. 11 5971 2021.
ISSN: ESSN 2045-2322
PubMed: 33727595
DOI: 10.1038/S41598-021-85559-X