Manganese in PDB 3gnx: Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus

All present enzymatic activity of Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus:
5.3.1.5;

The structure of Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus, PDB code: 3gnx was solved by F.Gramiccia, M.Schiltz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.35 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.853, 87.650, 94.531, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.6

The binding sites of Manganese atom in the Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus (pdb code 3gnx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus, PDB code: 3gnx:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn390 b:49.6 occ:0.80 OE2 A:GLU217 2.7 10.6 1.0 OD1 A:ASP257 2.8 18.7 1.0 O2 A:XYL389 3.0 7.2 1.0 OD1 A:ASP287 3.3 7.8 1.0 CG A:ASP257 3.3 16.4 1.0 CG A:ASP287 3.3 7.6 1.0 OE1 A:GLU217 3.4 9.9 1.0 CD A:GLU217 3.4 10.0 1.0 OD2 A:ASP287 3.4 7.7 1.0 OD2 A:ASP257 3.4 17.8 1.0 O A:ASP287 3.7 9.1 1.0 C1 A:XYL389 3.8 12.2 1.0 O1 A:XYL389 3.8 10.6 1.0 ND2 A:ASN247 4.0 6.5 1.0 O A:HOH542 4.0 19.9 1.0 C2 A:XYL389 4.0 12.2 1.0 MN A:MN391 4.1 12.7 1.0 CB A:ASP287 4.2 8.8 1.0 C3 A:XYL389 4.2 16.8 1.0 C A:ASP287 4.3 8.4 1.0 NE2 A:HIS220 4.4 7.8 1.0 OD1 A:ASP255 4.6 27.0 1.0 O4 A:XYL389 4.6 23.3 1.0 CB A:ASP257 4.6 14.2 1.0 NZ A:LYS289 4.7 19.6 1.0 O A:HOH559 4.7 31.9 1.0 CA A:ASP287 4.8 9.5 1.0 OD2 A:ASP255 4.9 25.0 1.0 CG A:GLU217 4.9 8.7 1.0 C4 A:XYL389 4.9 18.4 1.0 N A:PHE288 5.0 7.4 1.0

Manganese binding site 2 out of 4 in the Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn391 b:12.7 occ:1.00 OE2 A:GLU181 2.1 7.7 1.0 OD2 A:ASP245 2.2 7.8 1.0 OE1 A:GLU217 2.2 9.9 1.0 OD2 A:ASP287 2.2 7.7 1.0 O2 A:XYL389 2.3 7.2 1.0 O3 A:XYL389 2.5 11.0 1.0 C3 A:XYL389 2.6 16.8 1.0 CD A:GLU181 3.0 6.6 1.0 C2 A:XYL389 3.2 12.2 1.0 CG A:ASP287 3.2 7.6 1.0 CG A:ASP245 3.3 9.2 1.0 CD A:GLU217 3.3 10.0 1.0 OE1 A:GLU181 3.3 6.2 1.0 CB A:ASP287 3.7 8.8 1.0 O A:HOH471 3.8 13.7 1.0 CB A:ASP245 3.8 7.6 1.0 C4 A:XYL389 3.8 18.4 1.0 OE2 A:GLU217 4.0 10.6 1.0 MN A:MN390 4.1 49.6 0.8 CE1 A:HIS220 4.2 8.4 1.0 CB A:GLU217 4.2 6.3 1.0 OD1 A:ASP287 4.3 7.8 1.0 CG A:GLU217 4.3 8.7 1.0 OD1 A:ASP245 4.3 8.8 1.0 C5 A:XYL389 4.4 16.9 1.0 CG A:GLU181 4.4 6.9 1.0 NE2 A:HIS220 4.4 7.8 1.0 C1 A:XYL389 4.5 12.2 1.0 O4 A:XYL389 4.6 23.3 1.0 ND2 A:ASN215 4.7 8.4 1.0

Manganese binding site 3 out of 4 in the Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn390 b:41.1 occ:0.80 O1 E:XYL389 1.6 23.9 1.0 C1 E:XYL389 2.6 22.2 1.0 O2 E:XYL389 2.7 17.2 1.0 O E:HOH539 2.8 21.7 1.0 NZ E:LYS183 3.0 7.0 1.0 C2 E:XYL389 3.0 20.5 1.0 NE2 E:HIS220 3.0 7.7 1.0 CE E:LYS183 3.5 4.6 1.0 CE1 E:HIS220 3.6 7.6 1.0 OD2 E:ASP255 3.6 27.4 1.0 CD E:LYS183 3.7 5.4 1.0 CZ2 E:TRP137 3.7 8.6 1.0 O E:HOH429 3.9 10.0 1.0 CE2 E:TRP137 4.0 9.5 1.0 CH2 E:TRP137 4.1 9.3 1.0 CD2 E:HIS220 4.1 6.8 1.0 O4 E:XYL389 4.3 8.9 1.0 NE1 E:TRP137 4.4 9.2 1.0 CG E:ASP255 4.5 25.1 1.0 CD2 E:TRP137 4.5 8.8 1.0 C3 E:XYL389 4.6 19.3 1.0 CZ3 E:TRP137 4.6 8.7 1.0 OE2 E:GLU217 4.7 10.7 1.0 ND1 E:HIS220 4.8 7.9 1.0 CE3 E:TRP137 4.8 7.8 1.0 OD1 E:ASP255 4.8 27.4 1.0 O E:HOH505 4.9 31.6 1.0 CG E:LYS183 4.9 6.1 1.0 OE1 E:GLU217 5.0 10.6 1.0

Manganese binding site 4 out of 4 in the Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Dehydrated D-Xylose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn391 b:12.0 occ:1.00 OE2 E:GLU181 2.1 8.2 1.0 OE1 E:GLU217 2.2 10.6 1.0 OD2 E:ASP245 2.2 6.2 1.0 OD2 E:ASP287 2.2 8.5 1.0 O2 E:XYL389 2.4 17.2 1.0 C3 E:XYL389 2.5 19.3 1.0 C2 E:XYL389 2.9 20.5 1.0 CD E:GLU181 3.1 8.0 1.0 CG E:ASP245 3.2 6.0 1.0 OE1 E:GLU181 3.3 8.3 1.0 CG E:ASP287 3.3 7.6 1.0 C4 E:XYL389 3.3 19.1 1.0 CD E:GLU217 3.4 9.9 1.0 O3 E:XYL389 3.7 23.8 1.0 CB E:ASP245 3.8 6.0 1.0 CB E:ASP287 3.8 7.9 1.0 O4 E:XYL389 3.8 8.9 1.0 O E:HOH474 3.9 16.3 1.0 O E:HOH429 4.0 10.0 1.0 C1 E:XYL389 4.1 22.2 1.0 CE1 E:HIS220 4.1 7.6 1.0 OE2 E:GLU217 4.2 10.7 1.0 CB E:GLU217 4.2 6.7 1.0 OD1 E:ASP245 4.3 6.9 1.0 OD1 E:ASP287 4.3 7.0 1.0 CG E:GLU217 4.3 7.3 1.0 NE2 E:HIS220 4.3 7.7 1.0 CG E:GLU181 4.4 7.2 1.0 C5 E:XYL389 4.5 14.6 1.0 O1 E:XYL389 4.7 23.9 1.0 ND2 E:ASN215 4.8 7.6 1.0

F.Gramiccia, C.Besnard, M.Schiltz. Dehydration-Induced Structural Phase Transition in Crystals of D-Xylose Isomerase From Streptomyces Rubiginosus To Be Published.