Nickel in PDB 3kbv: Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors

All present enzymatic activity of Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors:
5.3.1.5;

The structure of Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors, PDB code: 3kbv was solved by A.Y.Kovalevsky, L.Hanson, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.990, 99.470, 102.960, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.3

The binding sites of Nickel atom in the Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors (pdb code 3kbv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors, PDB code: 3kbv:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni391 b:18.6 occ:1.00 O A:HOH1002 2.0 18.8 1.0 OE2 A:GLU217 2.0 19.8 1.0 OD2 A:ASP255 2.1 18.0 1.0 OD1 A:ASP257 2.1 18.0 1.0 NE2 A:HIS220 2.2 20.2 1.0 OD1 A:ASP255 2.3 16.5 1.0 CG A:ASP255 2.5 16.5 1.0 CD2 A:HIS220 2.9 15.3 1.0 CD A:GLU217 3.0 16.8 1.0 CG A:ASP257 3.1 20.1 1.0 OE1 A:GLU217 3.2 19.6 1.0 OD2 A:ASP257 3.3 21.9 1.0 CE1 A:HIS220 3.3 18.4 1.0 O A:HOH1056 3.7 22.5 1.0 O A:HOH1017 4.0 18.0 1.0 ND2 A:ASN247 4.0 17.8 1.0 CB A:ASP255 4.0 15.3 1.0 CG A:HIS220 4.1 14.0 1.0 ND1 A:HIS220 4.2 15.3 1.0 CG A:GLU217 4.3 12.8 1.0 O A:HOH1151 4.4 33.8 1.0 CB A:ASP257 4.5 12.8 1.0 CE A:LYS183 4.8 15.0 1.0 O A:HOH1149 4.9 37.0 1.0 CA A:ASP257 4.9 11.0 1.0 N A:ASP257 4.9 15.2 1.0 CA A:ASP255 4.9 17.4 1.0 NZ A:LYS183 4.9 19.3 1.0

Nickel binding site 2 out of 2 in the Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Room Temperature Structure of D-Xylose Isomerase in Complex with 2NI(2+) Co-Factors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni392 b:33.0 occ:1.00 OE2 A:GLU181 2.1 40.2 1.0 OD2 A:ASP287 2.2 27.3 1.0 OE1 A:GLU217 2.3 19.6 1.0 OD2 A:ASP245 2.3 25.1 1.0 O A:HOH1149 2.6 37.0 1.0 CD A:GLU181 3.0 32.5 1.0 O A:HOH1179 3.0 48.3 1.0 OE1 A:GLU181 3.2 31.8 1.0 CG A:ASP287 3.2 30.1 1.0 CG A:ASP245 3.4 29.3 1.0 CD A:GLU217 3.5 16.8 1.0 CB A:ASP287 3.6 18.4 1.0 O A:HOH1166 3.6 44.7 1.0 O A:HOH1111 3.7 41.2 1.0 O A:HOH1002 3.9 18.8 1.0 CB A:ASP245 3.9 14.8 1.0 CB A:GLU217 4.1 15.7 1.0 CG A:GLU217 4.2 12.8 1.0 CE1 A:HIS220 4.2 18.4 1.0 OD1 A:ASP287 4.3 25.3 1.0 CG A:GLU181 4.3 19.6 1.0 OE2 A:GLU217 4.5 19.8 1.0 OD1 A:ASP245 4.5 24.2 1.0 ND1 A:HIS220 4.8 15.3 1.0 NE2 A:HIS220 4.8 20.2 1.0 ND2 A:ASN215 4.9 18.4 1.0

A.Y.Kovalevsky, L.Hanson, S.Z.Fisher, M.Mustyakimov, S.A.Mason, V.T.Forsyth, M.P.Blakeley, D.A.Keen, T.Wagner, H.L.Carrell, A.K.Katz, J.P.Glusker, P.Langan. Metal Ion Roles and the Movement of Hydrogen During Reaction Catalyzed By D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study. Structure V. 18 688 2010.
ISSN: ISSN 0969-2126
PubMed: 20541506
DOI: 10.1016/J.STR.2010.03.011