Manganese in PDB 4lnc: Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant

All present enzymatic activity of Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant:
5.3.1.5;

The structure of Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant, PDB code: 4lnc was solved by P.Munshi, F.Meilleur, D.Myles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.19
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.970, 99.520, 102.920, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 20.9

The structure of Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant (pdb code 4lnc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant, PDB code: 4lnc:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:25.9 occ:1.00 HE2 A:HIS220 1.9 20.8 0.1 DE2 A:HIS220 1.9 20.8 0.9 OD2 A:ASP255 2.2 22.7 1.0 OE2 A:GLU217 2.2 20.6 1.0 O A:DOD755 2.2 29.5 1.0 D1 A:DOD755 2.3 29.3 1.0 OD1 A:ASP257 2.3 20.5 1.0 OD1 A:ASP255 2.4 18.4 1.0 NE2 A:HIS220 2.6 16.9 1.0 CG A:ASP255 2.6 20.1 1.0 D2 A:DOD581 2.8 28.2 1.0 D2 A:DOD755 2.8 30.2 1.0 HD2 A:HIS220 3.1 19.6 1.0 CD2 A:HIS220 3.1 12.7 1.0 CD A:GLU217 3.2 17.5 1.0 CG A:ASP257 3.2 18.0 1.0 DD22 A:ASN247 3.4 17.1 0.6 HD22 A:ASN247 3.4 17.1 0.4 OD2 A:ASP257 3.4 20.5 1.0 OE1 A:GLU217 3.5 27.7 1.0 DD21 A:ASN247 3.6 15.2 1.0 HD21 A:ASN247 3.6 15.2 0.0 O A:DOD581 3.6 28.4 1.0 CE1 A:HIS220 3.7 14.7 1.0 D1 A:DOD533 3.8 27.9 1.0 ND2 A:ASN247 3.8 14.8 1.0 HE3 A:LYS183 3.9 16.4 1.0 HE1 A:HIS220 4.0 21.0 1.0 CB A:ASP255 4.1 19.3 1.0 HO2 A:GLC401 4.2 24.0 0.3 DO2 A:GLC401 4.2 24.0 0.7 O3 A:GLC401 4.2 32.2 1.0 D1 A:DOD581 4.3 28.2 1.0 CG A:HIS220 4.3 10.4 1.0 DO3 A:GLC401 4.4 23.9 0.3 HO3 A:GLC401 4.4 23.9 0.7 HG2 A:GLU217 4.4 15.7 1.0 CG A:GLU217 4.4 12.2 1.0 HB2 A:ASP255 4.4 15.0 1.0 OD2 A:ASP287 4.5 18.2 1.0 HB3 A:ASP255 4.5 18.1 1.0 HA A:ASP257 4.5 12.8 1.0 O A:DOD533 4.5 27.6 1.0 ND1 A:HIS220 4.5 14.2 1.0 DZ1 A:LYS183 4.6 21.2 1.0 CB A:ASP257 4.6 18.3 1.0 MG A:MG404 4.6 16.8 0.8 D2 A:DOD628 4.7 31.1 1.0 D A:ASP257 4.8 14.9 0.5 H A:ASP257 4.8 14.9 0.5 DZ3 A:LYS183 4.8 18.9 1.0 D1 A:DOD613 4.8 31.2 1.0 CE A:LYS183 4.8 16.5 1.0 MN A:MN403 4.9 18.4 0.2 HD2 A:LYS183 4.9 18.1 1.0 HA A:ASP255 4.9 16.2 1.0 CA A:ASP257 5.0 13.9 1.0 HG3 A:GLU217 5.0 15.2 1.0 NZ A:LYS183 5.0 17.7 1.0

Manganese binding site 2 out of 2 in the Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Neutron Structure of the Cyclic Glucose Bound Xylose Isomerase E186Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:18.4 occ:0.25 MG A:MG404 0.3 16.8 0.8 OE1 A:GLU217 2.0 27.7 1.0 O4 A:GLC401 2.1 26.6 1.0 OD2 A:ASP287 2.1 18.2 1.0 OE2 A:GLU181 2.2 29.2 1.0 OD2 A:ASP245 2.2 21.4 1.0 O3 A:GLC401 2.6 32.2 1.0 DO4 A:GLC401 2.7 26.6 1.0 CD A:GLU181 3.1 24.6 1.0 CD A:GLU217 3.1 17.5 1.0 CG A:ASP287 3.1 16.8 1.0 C4 A:GLC401 3.2 27.8 1.0 DO3 A:GLC401 3.2 23.9 0.3 HO3 A:GLC401 3.2 23.9 0.7 C3 A:GLC401 3.3 28.2 1.0 CG A:ASP245 3.3 24.1 1.0 OE1 A:GLU181 3.3 22.0 1.0 HB3 A:ASP287 3.3 19.6 1.0 H3 A:GLC401 3.5 29.2 1.0 HB2 A:GLU217 3.5 16.0 1.0 H4 A:GLC401 3.5 25.8 1.0 CB A:ASP287 3.6 13.3 1.0 HB3 A:ASP245 3.6 16.7 1.0 HB2 A:ASP287 3.6 20.7 1.0 HE1 A:HIS220 3.7 21.0 1.0 HG3 A:GLU217 3.8 15.2 1.0 O A:DOD755 3.8 29.5 1.0 CB A:ASP245 3.9 12.0 1.0 HB2 A:ASP245 3.9 17.8 1.0 CG A:GLU217 3.9 12.2 1.0 OE2 A:GLU217 4.0 20.6 1.0 D1 A:DOD755 4.1 29.3 1.0 CE1 A:HIS220 4.2 14.7 1.0 CB A:GLU217 4.2 14.7 1.0 OD1 A:ASP245 4.3 18.3 1.0 OD1 A:ASP287 4.3 15.3 1.0 CG A:GLU181 4.4 16.4 1.0 DD22 A:ASN215 4.5 17.0 1.0 C5 A:GLC401 4.5 32.1 1.0 O6 A:GLC401 4.5 36.0 1.0 H5 A:GLC401 4.5 24.1 1.0 D2 A:DOD755 4.5 30.2 1.0 HB3 A:GLU217 4.6 14.4 1.0 HG3 A:GLU181 4.6 18.4 1.0 NE2 A:HIS220 4.7 16.9 1.0 HG2 A:GLU181 4.7 18.9 1.0 HE2 A:HIS220 4.7 20.8 0.1 DE2 A:HIS220 4.7 20.8 0.9 HZ2 A:TRP16 4.7 16.6 1.0 HO2 A:GLC401 4.7 24.0 0.3 DO2 A:GLC401 4.7 24.0 0.7 C2 A:GLC401 4.7 36.5 1.0 HG2 A:GLU217 4.8 15.7 1.0 D2 A:DOD581 4.8 28.2 1.0 ND1 A:HIS220 4.8 14.2 1.0 MN A:MN402 4.9 25.9 1.0 H2 A:GLC401 4.9 26.2 1.0 DD21 A:ASN215 4.9 16.0 0.1 HD21 A:ASN215 4.9 16.0 0.9 DD21 A:ASN247 5.0 15.2 1.0 HD21 A:ASN247 5.0 15.2 0.0 HO6 A:GLC401 5.0 19.8 1.0 DD1 A:HIS220 5.0 18.1 0.7 HD1 A:HIS220 5.0 18.1 0.3

P.Munshi, E.H.Snell, M.J.Van Der Woerd, R.A.Judge, D.A.Myles, Z.Ren, F.Meilleur. Neutron Structure of the Cyclic Glucose-Bound Xylose Isomerase E186Q Mutant. Acta Crystallogr.,Sect.D V. 70 414 2014.
ISSN: ISSN 0907-4449
PubMed: 24531475
DOI: 10.1107/S1399004713029684