Manganese in PDB 1xii: Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase

All present enzymatic activity of Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase:
5.3.1.5;

The structure of Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase, PDB code: 1xii was solved by H.L.Carrell, J.P.Glusker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.780, 99.540, 102.900, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Manganese atom in the Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase (pdb code 1xii). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase, PDB code: 1xii:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn390 b:7.4 occ:1.00 OE2 A:GLU217 2.2 5.4 1.0 OD1 A:ASP257 2.3 5.0 1.0 OD1 A:ASP255 2.3 5.0 1.0 O A:HOH409 2.3 5.0 1.0 OD2 A:ASP255 2.4 7.5 1.0 NE2 A:HIS220 2.4 5.8 1.0 CG A:ASP255 2.8 8.3 1.0 CD2 A:HIS220 3.0 5.0 1.0 CD A:GLU217 3.0 5.5 1.0 OE1 A:GLU217 3.1 5.0 1.0 CG A:ASP257 3.2 5.0 1.0 OD2 A:ASP257 3.4 5.0 1.0 CE1 A:HIS220 3.5 5.8 1.0 O1 A:XUL389 3.6 12.8 1.0 ND2 A:ASN247 3.9 5.0 1.0 O2 A:XUL389 4.0 8.8 1.0 O A:HOH412 4.0 5.0 1.0 CG A:HIS220 4.2 5.0 1.0 CB A:ASP255 4.2 5.0 1.0 ND1 A:HIS220 4.4 5.0 1.0 CG A:GLU217 4.4 5.0 1.0 CB A:ASP257 4.6 5.0 1.0 C2 A:XUL389 4.6 15.0 1.0 C1 A:XUL389 4.6 16.1 1.0 OD2 A:ASP287 4.6 8.2 1.0 MN A:MN391 4.7 6.3 1.0 O A:HOH615 4.7 18.9 1.0 NZ A:LYS183 4.8 5.0 1.0 CE A:LYS183 4.9 5.0 1.0 CA A:ASP257 5.0 5.0 1.0

Manganese binding site 2 out of 2 in the Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn391 b:6.3 occ:1.00 OD2 A:ASP287 2.2 8.2 1.0 OE2 A:GLU181 2.2 6.2 1.0 OD2 A:ASP245 2.2 7.7 1.0 OE1 A:GLU217 2.3 5.0 1.0 O4 A:XUL389 2.4 11.3 1.0 O2 A:XUL389 2.4 8.8 1.0 CD A:GLU181 3.1 6.7 1.0 CG A:ASP287 3.2 8.9 1.0 C2 A:XUL389 3.4 15.0 1.0 CG A:ASP245 3.4 8.7 1.0 OE1 A:GLU181 3.4 5.1 1.0 C4 A:XUL389 3.4 15.8 1.0 CD A:GLU217 3.4 5.5 1.0 CB A:ASP287 3.6 5.5 1.0 C3 A:XUL389 3.7 15.3 1.0 O3 A:XUL389 3.8 18.1 1.0 O A:HOH409 3.9 5.0 1.0 CB A:ASP245 3.9 5.0 1.0 CE1 A:HIS220 4.0 5.8 1.0 CG A:GLU217 4.1 5.0 1.0 O A:HOH408 4.1 13.2 1.0 CB A:GLU217 4.2 5.0 1.0 OD1 A:ASP287 4.3 5.7 1.0 OD1 A:ASP245 4.3 8.0 1.0 OE2 A:GLU217 4.3 5.4 1.0 CG A:GLU181 4.4 5.3 1.0 NE2 A:HIS220 4.6 5.8 1.0 C5 A:XUL389 4.7 17.2 1.0 MN A:MN390 4.7 7.4 1.0 ND1 A:HIS220 4.8 5.0 1.0 C1 A:XUL389 4.8 16.1 1.0 ND2 A:ASN215 5.0 5.2 1.0 O1 A:XUL389 5.0 12.8 1.0

H.L.Carrell, H.Hoier, J.P.Glusker. Modes of Binding Substrates and Their Analogues to the Enzyme D-Xylose Isomerase. Acta Crystallogr.,Sect.D V. 50 113 1994.
ISSN: ISSN 0907-4449
PubMed: 15299449
DOI: 10.1107/S0907444993009345