Manganese in PDB 1xib: 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: 1xib 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)	9.00 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.880, 99.680, 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 1xib). 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: 1xib:
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:9.7 occ:1.00 OE2 A:GLU217 2.2 7.7 1.0 OD1 A:ASP257 2.3 8.4 1.0 O A:HOH409 2.3 10.9 1.0 OD2 A:ASP255 2.3 9.4 1.0 NE2 A:HIS220 2.3 9.1 1.0 OD1 A:ASP255 2.4 7.5 1.0 CG A:ASP255 2.7 9.7 1.0 CD A:GLU217 3.0 11.0 1.0 CD2 A:HIS220 3.0 7.1 1.0 OE1 A:GLU217 3.1 9.2 1.0 CG A:ASP257 3.2 13.7 1.0 OD2 A:ASP257 3.3 15.3 1.0 CE1 A:HIS220 3.4 11.0 1.0 O A:HOH565 3.8 16.6 1.0 ND2 A:ASN247 4.0 5.0 1.0 O A:HOH412 4.1 7.2 1.0 CB A:ASP255 4.2 6.6 1.0 CG A:HIS220 4.2 9.3 1.0 ND1 A:HIS220 4.4 9.1 1.0 CG A:GLU217 4.4 7.0 1.0 O A:HOH507 4.5 27.5 1.0 CB A:ASP257 4.5 6.6 1.0 O A:HOH615 4.6 24.9 1.0 OD2 A:ASP287 4.7 15.5 1.0 MN A:MN391 4.8 14.1 1.0 NZ A:LYS183 4.8 10.1 1.0 CE A:LYS183 4.8 8.3 1.0 CA A:ASP257 4.9 6.7 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:14.1 occ:1.00 OD2 A:ASP287 2.2 15.5 1.0 OD2 A:ASP245 2.2 11.4 1.0 OE1 A:GLU217 2.2 9.2 1.0 OE2 A:GLU181 2.3 15.8 1.0 O A:HOH609 2.6 44.5 1.0 O A:HOH507 2.7 27.5 1.0 CD A:GLU181 3.0 16.0 1.0 CG A:ASP287 3.2 16.1 1.0 OE1 A:GLU181 3.2 17.5 1.0 CG A:ASP245 3.3 13.2 1.0 CD A:GLU217 3.4 11.0 1.0 CB A:ASP287 3.5 11.2 1.0 CB A:ASP245 3.9 8.5 1.0 O A:HOH408 3.9 31.3 1.0 O A:HOH409 3.9 10.9 1.0 O A:HOH631 3.9 44.5 1.0 CG A:GLU217 4.0 7.0 1.0 CE1 A:HIS220 4.1 11.0 1.0 CB A:GLU217 4.2 5.7 1.0 OD1 A:ASP287 4.2 12.5 1.0 OE2 A:GLU217 4.2 7.7 1.0 OD1 A:ASP245 4.3 12.4 1.0 CG A:GLU181 4.3 11.0 1.0 NE2 A:HIS220 4.8 9.1 1.0 O A:HOH633 4.8 55.8 1.0 ND1 A:HIS220 4.8 9.1 1.0 MN A:MN390 4.8 9.7 1.0 ND2 A:ASN215 4.9 12.4 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