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Magnesium 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

Other elements in 3kbw:

The structure of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium 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:

Magnesium binding site 1 out of 1 in 3kbw

Go back to Magnesium Binding Sites List in 3kbw
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg392

b:15.1
occ:1.00
OD2 A:ASP287 2.3 21.6 1.0
OE2 A:GLU181 2.3 35.9 1.0
OE1 A:GLU217 2.4 16.6 1.0
OD2 A:ASP245 2.5 21.1 1.0
CD A:GLU181 3.0 22.7 1.0
OE1 A:GLU181 3.1 24.5 1.0
CG A:ASP287 3.3 14.1 1.0
O A:HOH1116 3.4 34.2 1.0
CG A:ASP245 3.5 15.3 1.0
O A:HOH1097 3.6 25.6 1.0
O A:HOH1115 3.6 37.2 1.0
CD A:GLU217 3.6 9.2 1.0
CB A:ASP287 3.6 13.7 1.0
O A:HOH1142 3.7 37.5 1.0
O A:HOH1001 3.9 18.1 1.0
CB A:ASP245 4.0 12.6 1.0
CB A:GLU217 4.1 11.3 1.0
CG A:GLU217 4.2 11.7 1.0
CE1 A:HIS220 4.3 12.2 1.0
CG A:GLU181 4.3 17.0 1.0
OD1 A:ASP287 4.4 16.5 1.0
OD1 A:ASP245 4.6 20.8 1.0
OE2 A:GLU217 4.6 15.4 1.0
ND2 A:ASN215 4.7 17.0 1.0
ND1 A:HIS220 4.9 9.9 1.0
NE2 A:HIS220 5.0 12.7 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: Wed Aug 14 18:01:48 2024

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