Magnesium in PDB 8i5j: Crystal Structure of Chitin Oligosaccharide Binding Protein From Vibrio Cholera.

The structure of Crystal Structure of Chitin Oligosaccharide Binding Protein From Vibrio Cholera., PDB code: 8i5j was solved by T.Ohnuma, D.Takeshita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.12, 81.643, 87.273, 90, 104.15, 90
R / Rfree (%)	16.2 / 19.1

The binding sites of Magnesium atom in the Crystal Structure of Chitin Oligosaccharide Binding Protein From Vibrio Cholera. (pdb code 8i5j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Chitin Oligosaccharide Binding Protein From Vibrio Cholera., PDB code: 8i5j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Chitin Oligosaccharide Binding Protein From Vibrio Cholera.


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 Chitin Oligosaccharide Binding Protein From Vibrio Cholera. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:20.3 occ:1.00 O A:PHE343 2.3 19.2 1.0 OD1 A:ASP337 2.3 23.9 1.0 OD1 A:ASN339 2.3 30.5 1.0 OD1 A:ASP341 2.4 24.2 1.0 OE1 A:GLU345 2.4 37.4 1.0 OE2 A:GLU345 2.6 27.1 1.0 CD A:GLU345 2.8 37.1 1.0 CG A:ASP341 3.1 28.8 1.0 CG A:ASN339 3.2 32.0 1.0 CG A:ASP337 3.3 26.6 1.0 C A:PHE343 3.4 18.7 1.0 OD2 A:ASP341 3.5 25.4 1.0 ND2 A:ASN339 3.6 28.3 1.0 N A:PHE343 3.8 19.3 1.0 CA A:ASP337 3.9 19.2 1.0 N A:ASP341 3.9 25.6 1.0 CB A:ASP337 4.0 20.2 1.0 CA A:PHE343 4.1 17.5 1.0 N A:ASN339 4.1 28.7 1.0 OD2 A:ASP337 4.1 28.8 1.0 N A:VAL338 4.2 22.6 1.0 CB A:ASP341 4.3 30.7 1.0 C A:ASP337 4.3 23.4 1.0 N A:GLY340 4.3 31.8 1.0 CG A:GLU345 4.4 27.0 1.0 CB A:PHE343 4.4 16.3 1.0 CB A:ASN339 4.5 30.1 1.0 CA A:ASP341 4.5 22.6 1.0 N A:VAL344 4.5 17.2 1.0 N A:GLY342 4.5 22.3 1.0 C A:VAL344 4.6 18.5 1.0 N A:GLU345 4.6 15.4 1.0 CA A:ASN339 4.6 28.3 1.0 CA A:VAL344 4.7 18.0 1.0 C A:ASP341 4.7 29.7 1.0 C A:ASN339 4.7 34.1 1.0 O A:HOH886 4.7 26.6 1.0 C A:GLY340 4.9 33.1 1.0 C A:GLY342 4.9 22.1 1.0 O A:VAL344 5.0 19.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Chitin Oligosaccharide Binding Protein From Vibrio Cholera.


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 Chitin Oligosaccharide Binding Protein From Vibrio Cholera. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:30.7 occ:1.00 OD1 B:ASP337 2.1 24.4 1.0 OD1 B:ASP341 2.2 34.9 1.0 O B:PHE343 2.2 24.7 1.0 OD1 B:ASN339 2.3 34.8 1.0 OE1 B:GLU345 2.5 41.2 1.0 OE2 B:GLU345 2.5 28.0 1.0 CD B:GLU345 2.8 36.7 1.0 CG B:ASP341 3.1 39.9 1.0 CG B:ASN339 3.2 39.5 1.0 CG B:ASP337 3.3 30.0 1.0 C B:PHE343 3.3 26.6 1.0 OD2 B:ASP341 3.7 37.5 1.0 ND2 B:ASN339 3.7 51.0 1.0 N B:PHE343 3.7 23.6 1.0 N B:ASP341 3.9 40.5 1.0 CA B:PHE343 4.0 24.2 1.0 CA B:ASP337 4.1 19.8 1.0 N B:ASN339 4.1 31.1 1.0 CB B:ASP337 4.1 29.7 1.0 OD2 B:ASP337 4.1 36.9 1.0 N B:GLY340 4.2 38.1 1.0 CB B:PHE343 4.3 27.4 1.0 CB B:ASP341 4.3 31.9 1.0 CB B:ASN339 4.3 31.9 1.0 CG B:GLU345 4.3 31.4 1.0 CA B:ASP341 4.4 31.9 1.0 N B:GLY342 4.4 32.8 1.0 N B:VAL344 4.4 20.3 1.0 N B:VAL338 4.4 24.5 1.0 C B:VAL344 4.4 18.9 1.0 O B:HOH818 4.4 29.5 1.0 N B:GLU345 4.5 18.9 1.0 CA B:ASN339 4.5 28.1 1.0 C B:ASP341 4.5 42.3 1.0 C B:ASP337 4.6 23.5 1.0 C B:ASN339 4.6 41.2 1.0 CA B:VAL344 4.7 19.4 1.0 C B:GLY340 4.7 42.2 1.0 O B:VAL344 4.8 20.4 1.0 C B:GLY342 4.8 26.1 1.0 OG B:SER351 5.0 39.2 1.0 CA B:GLY340 5.0 40.0 1.0

T.Ohnuma, J.Tsujii, C.Kataoka, T.Yoshimoto, D.Takeshita, O.Lampela, A.H.Juffer, W.Suginta, T.Fukamizo. Periplasmic Chitooligosaccharide-Binding Protein Requires A Three-Domain Organization For Substrate Translocation. Sci Rep V. 13 20558 2023.
ISSN: ESSN 2045-2322
PubMed: 37996461
DOI: 10.1038/S41598-023-47253-Y