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Nickel in PDB 3qys: Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8

Enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8

All present enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8:
5.3.1.5;

Protein crystallography data

The structure of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8, PDB code: 3qys 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) 10.00 / 1.85
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.900, 99.630, 102.840, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8 (pdb code 3qys). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8, PDB code: 3qys:

Nickel binding site 1 out of 1 in 3qys

Go back to Nickel Binding Sites List in 3qys
Nickel binding site 1 out of 1 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 0.6NI2+ Cation Bound in M2 Metal Binding Site at pH=5.8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:38.9
occ:0.60
 O A:HOH1073 2.1 33.0 1.0
OD2 A:ASP255 2.1 42.4 1.0
OE2 A:GLU217 2.3 34.7 1.0
OD1 A:ASP255 2.4 38.9 1.0
NE2 A:HIS220 2.5 24.3 1.0
CG A:ASP255 2.5 40.6 1.0
OD1 A:ASP257 2.6 28.5 1.0
CD2 A:HIS220 3.0 19.6 1.0
O A:HOH1059 3.4 37.0 1.0
CD A:GLU217 3.5 26.0 1.0
CG A:ASP257 3.5 25.0 1.0
OD2 A:ASP257 3.7 42.5 1.0
CE1 A:HIS220 3.7 21.5 1.0
CB A:ASP255 4.0 30.0 1.0
ND2 A:ASN247 4.1 21.5 1.0
OE1 A:GLU217 4.1 45.2 1.0
CG A:HIS220 4.3 17.6 1.0
O A:HOH1106 4.4 31.9 1.0
ND1 A:HIS220 4.6 22.4 1.0
CG A:GLU217 4.6 21.1 1.0
CE A:LYS183 4.6 25.2 1.0
NZ A:LYS183 4.6 27.5 1.0
CB A:ASP257 4.9 17.8 1.0

Reference:

A.Y.Kovalevsky, B.L.Hanson, S.A.Mason, T.Yoshida, S.Z.Fisher, M.Mustyakimov, V.T.Forsyth, M.P.Blakeley, D.A.Keen, P.Langan. Identification of the Elusive Hydronium Ion Exchanging Roles with A Proton in An Enzyme at Lower pH Values. Angew.Chem.Int.Ed.Engl. V. 50 7520 2011.
ISSN: ISSN 1433-7851
PubMed: 21604345
DOI: 10.1002/ANIE.201101753
Page generated: Wed Oct 9 17:45:45 2024

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