Magnesium in PDB 6a1m: Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid

Enzymatic activity of Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid

All present enzymatic activity of Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid:
1.1.3.46;

Protein crystallography data

The structure of Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid, PDB code: 6a1m was solved by T.L.Li, K.H.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.55
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 137.913, 137.913, 111.182, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid (pdb code 6a1m). 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 Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid, PDB code: 6a1m:

Magnesium binding site 1 out of 1 in 6a1m

Go back to Magnesium Binding Sites List in 6a1m
Magnesium binding site 1 out of 1 in the Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mandelate Oxidase Mutant-Y128F with 5-Deazariboflavin Mononucleotide and Benzoylformic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.1
occ:1.00
OBE A:9O9401 2.6 10.0 1.0
O A:LEU304 2.8 10.2 1.0
N A:GLY284 2.9 8.2 1.0
N A:ILE286 3.1 8.3 1.0
N A:GLY285 3.4 8.8 1.0
CG1 A:ILE286 3.5 11.2 1.0
CB A:ILE286 3.5 10.5 1.0
C A:GLY284 3.6 10.2 1.0
PBB A:9O9401 3.6 10.6 1.0
CA A:GLY284 3.6 8.4 1.0
OAX A:9O9401 3.9 19.4 1.0
C A:ASP283 3.9 8.6 1.0
OBC A:9O9401 3.9 10.9 1.0
CA A:ILE286 3.9 8.8 1.0
C A:LEU304 3.9 9.1 1.0
CA A:ASP283 3.9 7.0 1.0
CB A:ASP283 4.0 6.7 1.0
CA A:VAL305 4.0 9.0 1.0
NH1 A:ARG287 4.1 11.8 1.0
C A:GLY285 4.1 9.8 1.0
CAW A:9O9401 4.2 14.3 1.0
O A:GLY284 4.2 12.1 1.0
O A:ILE286 4.3 12.4 1.0
CA A:GLY285 4.3 11.0 1.0
N A:VAL305 4.4 8.3 1.0
N A:GLY306 4.4 8.8 1.0
C A:ILE286 4.6 11.1 1.0
C A:VAL305 4.8 7.8 1.0
CD1 A:ILE286 4.9 14.0 1.0
CG2 A:VAL305 4.9 10.1 1.0
CG2 A:ILE286 4.9 12.9 1.0
CB A:VAL305 4.9 8.3 1.0
CG A:ASP283 4.9 11.0 1.0
OBD A:9O9401 5.0 12.5 1.0
O A:ASP283 5.0 8.5 1.0

Reference:

S.Y.Lyu, K.H.Lin, H.W.Yeh, Y.S.Li, C.M.Huang, Y.L.Wang, H.W.Shih, N.S.Hsu, C.J.Wu, T.L.Li. The Flavin Mononucleotide Cofactor in Alpha-Hydroxyacid Oxidases Exerts Its Electrophilic/Nucleophilic Duality in Control of the Substrate-Oxidation Level. Acta Crystallogr D Struct V. 75 918 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31588923
DOI: 10.1107/S2059798319011938
Page generated: Mon Dec 14 22:18:40 2020

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