Magnesium in PDB 3cwh: D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose

All present enzymatic activity of D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose:
5.3.1.5;

The binding sites of Magnesium atom in the D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose (pdb code 3cwh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose, PDB code: 3cwh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg391 b:19.0 occ:1.00 OD1 A:ASP255 2.2 15.0 1.0 OE2 A:GLU217 2.2 9.8 1.0 O A:OH501 2.2 17.1 1.0 OD1 A:ASP257 2.2 8.5 1.0 DO A:OH501 2.3 17.9 1.0 OD2 A:ASP255 2.4 17.2 1.0 NE2 A:HIS220 2.5 4.0 1.0 CG A:ASP255 2.6 15.5 1.0 DO1 A:XUL401 2.9 31.1 1.0 CD2 A:HIS220 3.0 4.8 1.0 HD2 A:HIS220 3.1 5.5 1.0 O1 A:XUL401 3.2 30.2 1.0 CD A:GLU217 3.2 6.6 1.0 CG A:ASP257 3.2 9.2 1.0 OD2 A:ASP257 3.4 11.9 1.0 OE1 A:GLU217 3.5 6.3 1.0 CE1 A:HIS220 3.5 4.0 1.0 DD21 A:ASN247 3.5 10.7 0.9 D11 A:XUL401 3.8 30.2 1.0 DD22 A:ASN247 3.9 5.5 1.0 HE3 A:LYS183 3.9 6.8 1.0 HE1 A:HIS220 3.9 6.8 1.0 C1 A:XUL401 4.0 31.4 1.0 ND2 A:ASN247 4.0 8.7 1.0 CB A:ASP255 4.1 13.3 1.0 O2 A:XUL401 4.2 31.8 1.0 CG A:HIS220 4.2 5.2 1.0 DZ2 A:LYS183 4.3 6.0 0.1 ND1 A:HIS220 4.4 4.8 1.0 CG A:GLU217 4.4 5.5 1.0 HB2 A:ASP255 4.5 13.7 1.0 HG2 A:GLU217 4.5 6.7 1.0 C2 A:XUL401 4.5 32.1 1.0 HA A:ASP257 4.6 9.1 1.0 HB3 A:ASP255 4.6 13.7 1.0 CB A:ASP257 4.6 9.9 1.0 OD2 A:ASP287 4.7 9.4 1.0 D A:HIS220 4.7 4.9 1.0 DZ1 A:LYS183 4.8 5.2 1.0 D A:ASP257 4.8 10.2 0.4 CE A:LYS183 4.8 5.3 1.0 NZ A:LYS183 4.8 6.2 1.0 MG A:MG392 4.9 23.2 1.0 D12 A:XUL401 5.0 32.1 1.0 HA2 A:GLY219 5.0 8.7 1.0

Magnesium binding site 2 out of 2 in the D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D-Xylose Isomerase in Complex with Linear Product, Per-Deuterated Xylulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg392 b:23.2 occ:1.00 OE1 A:GLU217 2.0 6.3 1.0 OD2 A:ASP287 2.1 9.4 1.0 OE2 A:GLU181 2.2 14.4 1.0 OD2 A:ASP245 2.2 9.2 1.0 O2 A:XUL401 2.4 31.8 1.0 O4 A:XUL401 2.6 27.8 1.0 DO4 A:XUL401 2.8 28.9 1.0 CD A:GLU181 3.1 13.5 1.0 CD A:GLU217 3.2 6.6 1.0 CG A:ASP287 3.3 9.1 1.0 OE1 A:GLU181 3.3 13.1 1.0 C2 A:XUL401 3.4 32.1 1.0 CG A:ASP245 3.4 6.5 1.0 HB2 A:GLU217 3.4 5.9 1.0 C4 A:XUL401 3.5 29.8 1.0 HB3 A:ASP287 3.5 7.9 1.0 HE1 A:HIS220 3.6 6.8 1.0 D4 A:XUL401 3.6 30.4 1.0 HB2 A:ASP287 3.7 7.9 1.0 C3 A:XUL401 3.7 31.2 1.0 CB A:ASP287 3.7 9.1 1.0 HB3 A:ASP245 3.8 7.0 1.0 O A:OH501 3.8 17.1 1.0 O3 A:XUL401 3.9 31.6 1.0 HB2 A:ASP245 4.0 7.0 1.0 CB A:ASP245 4.0 6.7 1.0 OE2 A:GLU217 4.0 9.8 1.0 CE1 A:HIS220 4.1 4.0 1.0 CG A:GLU217 4.1 5.5 1.0 HG3 A:GLU217 4.2 5.5 1.0 D1 A:DOD1119 4.2 45.5 1.0 CB A:GLU217 4.2 6.8 1.0 OD1 A:ASP287 4.3 8.7 1.0 OD1 A:ASP245 4.3 7.0 1.0 DO1 A:XUL401 4.3 31.1 1.0 CG A:GLU181 4.4 12.2 1.0 DO A:OH501 4.5 17.9 1.0 HB3 A:GLU217 4.6 5.5 1.0 C1 A:XUL401 4.6 31.4 1.0 HZ2 A:TRP16 4.7 4.0 1.0 HG3 A:GLU181 4.7 13.8 1.0 NE2 A:HIS220 4.7 4.0 1.0 ND1 A:HIS220 4.7 4.8 1.0 HG2 A:GLU181 4.7 12.6 1.0 D3 A:XUL401 4.8 31.3 1.0 D2 A:DOD1119 4.8 46.8 1.0 DO3 A:XUL401 4.8 28.9 1.0 DD1 A:HIS220 4.8 4.0 1.0 C5 A:XUL401 4.8 29.5 1.0 MG A:MG391 4.9 19.0 1.0 D11 A:XUL401 4.9 30.2 1.0 O A:DOD1119 4.9 46.3 1.0 DD22 A:ASN215 4.9 5.9 1.0 O1 A:XUL401 5.0 30.2 1.0 D51 A:XUL401 5.0 29.0 1.0 DD21 A:ASN215 5.0 8.8 0.7

A.Y.Kovalevsky, A.K.Katz, H.L.Carrell, L.Hanson, M.Mustyakimov, S.Z.Fisher, L.Coates, B.P.Schoenborn, G.J.Bunick, J.P.Glusker, P.Langan. Hydrogen Location in Stages of An Enzyme-Catalyzed Reaction: Time-of-Flight Neutron Structure of D-Xylose Isomerase with Bound D-Xylulose Biochemistry V. 47 7595 2008.
ISSN: ISSN 0006-2960
PubMed: 18578508
DOI: 10.1021/BI8005434