Sodium in PDB 5b5h: Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus

The structure of Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus, PDB code: 5b5h was solved by J.Cheng, Y.Hanada, A.Miura, S.Tsuda, H.Kondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.40 / 1.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.388, 104.849, 35.626, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 13.6

The binding sites of Sodium atom in the Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus (pdb code 5b5h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus, PDB code: 5b5h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:6.5 occ:1.00 O A:HOH1323 3.0 25.7 1.0 OG A:SER129 3.1 11.2 0.5 O A:HOH1231 3.1 18.1 1.0 N A:GLY111 3.1 7.5 1.0 N A:SER129 3.2 6.4 1.0 CA A:GLY111 3.6 7.8 1.0 CA A:ALA128 3.7 7.0 1.0 N A:LEU110 3.8 7.0 1.0 CB A:ALA109 3.9 10.7 1.0 C A:ALA109 3.9 8.2 1.0 CB A:SER129 3.9 8.8 1.0 O A:GLY127 4.0 8.3 1.0 C A:ALA128 4.0 6.5 1.0 CA A:ALA109 4.0 8.1 1.0 CA A:SER129 4.1 6.8 1.0 OG A:SER129 4.3 8.4 0.5 C A:LEU110 4.3 7.0 1.0 N A:ALA128 4.5 6.9 1.0 C A:GLY127 4.6 6.9 1.0 O A:ALA109 4.6 10.2 1.0 C A:GLY111 4.6 8.2 1.0 CA A:LEU110 4.7 6.7 1.0 O A:GLY111 4.7 8.9 1.0 N A:ALA130 4.7 6.9 1.0 CB A:ALA128 4.7 8.8 1.0 C A:SER129 4.8 6.9 1.0

Sodium binding site 2 out of 2 in the Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hydrophobic Ice-Binding Site Confer Hyperactivity on Antifreeze Protein From A Snow Mold Fungus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:29.7 occ:1.00 O A:HOH1132 1.8 24.4 1.0 O A:HOH1138 2.0 30.4 1.0 OG A:SER52 3.3 7.3 0.5 O A:HOH1375 3.3 23.8 1.0 OG A:SER53 3.6 21.0 1.0 N A:SER53 3.6 12.3 1.0 O A:HOH1297 3.7 28.6 1.0 CB A:SER52 4.0 9.6 1.0 CA A:SER52 4.1 9.1 1.0 CB A:SER53 4.4 17.5 1.0 C A:SER52 4.4 9.1 1.0 CA A:SER53 4.5 14.3 1.0 CZ A:PHE57 4.6 9.1 1.0 N A:THR54 4.9 11.2 1.0 OG A:SER52 5.0 12.4 0.5

J.Cheng, Y.Hanada, A.Miura, S.Tsuda, H.Kondo. Hydrophobic Ice-Binding Sites Confer Hyperactivity of An Antifreeze Protein From A Snow Mold Fungus. Biochem.J. V. 473 4011 2016.
ISSN: ESSN 1470-8728
PubMed: 27613857
DOI: 10.1042/BCJ20160543