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Nickel in PDB 3kbw: Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors

Enzymatic activity of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors

All present enzymatic activity of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors:
5.3.1.5;

Protein crystallography data

The structure of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors, PDB code: 3kbw 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 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.972, 99.701, 102.855, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 16.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors (pdb code 3kbw). 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 Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors, PDB code: 3kbw:

Nickel binding site 1 out of 1 in 3kbw

Go back to Nickel Binding Sites List in 3kbw
Nickel binding site 1 out of 1 in the Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(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 X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni391

b:14.0
occ:1.00
O A:HOH1001 2.0 18.1 1.0
OE2 A:GLU217 2.0 15.4 1.0
OD2 A:ASP255 2.0 15.3 1.0
OD1 A:ASP257 2.2 12.9 1.0
NE2 A:HIS220 2.2 12.7 1.0
OD1 A:ASP255 2.3 15.4 1.0
CG A:ASP255 2.5 13.4 1.0
CD2 A:HIS220 2.9 9.7 1.0
CD A:GLU217 3.0 9.2 1.0
CG A:ASP257 3.1 13.6 1.0
CE1 A:HIS220 3.2 12.2 1.0
OE1 A:GLU217 3.2 16.6 1.0
OD2 A:ASP257 3.3 17.8 1.0
O A:HOH1055 3.6 20.1 1.0
ND2 A:ASN247 4.0 12.5 1.0
O A:HOH1017 4.0 12.8 1.0
CB A:ASP255 4.0 13.4 1.0
CG A:HIS220 4.1 11.1 1.0
ND1 A:HIS220 4.2 9.9 1.0
CG A:GLU217 4.4 11.7 1.0
O A:HOH1085 4.5 36.3 1.0
CB A:ASP257 4.5 11.8 1.0
CE A:LYS183 4.7 14.7 1.0
NZ A:LYS183 4.8 15.4 1.0
CA A:ASP257 4.9 11.6 1.0
N A:ASP257 4.9 10.7 1.0
CA A:ASP255 4.9 11.1 1.0

Reference:

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
Page generated: Fri Sep 25 08:26:12 2020
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