Magnesium in PDB 7cj5: Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose

The structure of Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose, PDB code: 7cj5 was solved by H.Yoshida, A.Yoshihara, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.42, 70.54, 140.22, 90, 90, 90
R / Rfree (%)	12.6 / 15.9

The structure of Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose (pdb code 7cj5). 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 Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose, PDB code: 7cj5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose


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 Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:37.2 occ:1.00 O A:HOH459 2.0 28.7 1.0 O A:HOH549 2.1 38.0 1.0 O A:HOH402 2.2 38.0 1.0 OD1 A:ASP273 2.4 17.5 0.5 CG A:ASP273 3.2 17.3 0.5 OD2 A:ASP273 3.4 17.1 0.5 OD2 A:ASP270 3.9 27.3 1.0 CB A:ASP273 4.5 20.3 0.5 CB A:ASP273 4.6 17.2 0.5 CG A:ASP270 4.6 25.9 1.0 OD1 A:ASP273 4.8 25.8 0.5 N A:ASP273 4.8 17.0 1.0 CA A:ASP273 4.9 18.2 0.5 CA A:ASP273 4.9 17.2 0.5

Magnesium binding site 2 out of 2 in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose


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 Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:29.9 occ:1.00 O B:ASN224 2.1 18.7 1.0 O A:HOH536 2.2 31.9 1.0 O B:HOH495 2.2 30.2 1.0 O A:HOH437 2.4 17.8 1.0 O A:HOH410 2.5 35.5 1.0 C B:ASN224 3.3 18.0 1.0 O A:ASN224 3.7 17.5 1.0 CA B:ASN224 3.9 17.3 1.0 N B:ASP226 4.0 19.2 1.0 CB B:ASN224 4.1 16.8 1.0 O B:HOH429 4.2 17.6 1.0 C B:VAL225 4.3 18.8 1.0 N B:VAL225 4.3 16.7 1.0 O A:HOH430 4.4 17.2 1.0 CB B:ASP226 4.4 21.8 1.0 CA B:VAL225 4.6 17.9 1.0 OD1 B:ASN190 4.6 16.1 1.0 CA B:ASP226 4.7 21.5 1.0 C A:ASN224 4.9 15.6 1.0 O B:VAL225 4.9 19.3 1.0 CB A:ASP226 4.9 17.7 1.0

H.Yoshida, A.Yoshihara, S.Kato, S.Mochizuki, K.Akimitsu, K.Izumori, S.Kamitori. Crystal Structure of A Novel Homodimeric L-Ribulose 3-Epimerase From Methylomonus Sp. Febs Open Bio 2021.
ISSN: ESSN 2211-5463
PubMed: 33838083
DOI: 10.1002/2211-5463.13159