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Zinc in PDB 2dkc: Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex

Enzymatic activity of Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex

All present enzymatic activity of Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex:
5.4.2.3;

Protein crystallography data

The structure of Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex, PDB code: 2dkc was solved by Y.Nishitani, D.Maruyama, T.Nonaka, A.Kita, T.A.Fukami, T.Mio, H.Yamada-Okabe, T.Yamada-Okabe, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.48 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.348, 129.629, 80.487, 90.00, 108.56, 90.00
R / Rfree (%) 18.9 / 24

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex (pdb code 2dkc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex, PDB code: 2dkc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2dkc

Go back to Zinc Binding Sites List in 2dkc
Zinc binding site 1 out of 2 in the Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:37.2
occ:0.50
 OD2 A:ASP294 1.8 36.3 1.0
OG A:SER66 2.0 42.7 1.0
OD2 A:ASP290 2.2 35.5 1.0
CG A:ASP294 2.4 27.5 1.0
O2 A:PO4802 2.5 37.0 0.5
OD1 A:ASP294 2.5 37.3 1.0
OD1 A:ASP292 2.5 33.3 1.0
CG A:ASP290 3.3 28.3 1.0
CB A:SER66 3.3 38.1 1.0
CG A:ASP292 3.4 31.7 1.0
OD2 A:ASP292 3.5 34.3 1.0
OD1 A:ASP290 3.7 30.0 1.0
CB A:ASP294 3.8 28.0 1.0
P A:PO4802 3.8 39.5 0.5
CG A:ARG295 4.0 37.6 1.0
CA A:SER66 4.3 36.6 1.0
CE1 A:HIS391 4.3 42.4 1.0
N A:ASP294 4.3 19.9 1.0
O3 A:PO4802 4.3 36.8 0.5
O1 A:PO4802 4.4 36.3 0.5
CA A:ASP294 4.4 26.2 1.0
CD A:ARG295 4.5 42.5 1.0
CB A:ASP290 4.5 22.5 1.0
C A:ASP294 4.6 27.3 1.0
NE2 A:HIS391 4.7 40.7 1.0
N A:ARG295 4.7 25.1 1.0
C A:SER66 4.8 38.3 1.0
CB A:ASP292 4.8 26.8 1.0
NE A:ARG295 4.8 47.7 1.0
N A:HIS67 4.8 37.7 1.0
O4 A:PO4802 4.9 41.7 0.5
CB A:ARG295 4.9 27.2 1.0
N A:ASP292 5.0 22.5 1.0

Zinc binding site 2 out of 2 in 2dkc

Go back to Zinc Binding Sites List in 2dkc
Zinc binding site 2 out of 2 in the Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:37.3
occ:0.50
 OD1 B:ASP294 1.7 36.2 1.0
OG B:SER66 2.0 42.3 1.0
OD2 B:ASP290 2.1 28.7 1.0
OD2 B:ASP292 2.2 39.4 1.0
CG B:ASP294 2.3 34.5 1.0
OD2 B:ASP294 2.5 44.1 1.0
O2 B:PO4801 2.6 29.9 0.5
CG B:ASP292 3.0 34.6 1.0
OD1 B:ASP292 3.1 39.0 1.0
CG B:ASP290 3.2 26.6 1.0
CB B:SER66 3.3 35.8 1.0
OD1 B:ASP290 3.6 21.0 1.0
CB B:ASP294 3.7 29.6 1.0
O B:HOH1171 3.8 46.8 1.0
P B:PO4801 3.8 31.0 0.5
N B:ASP294 4.0 25.8 1.0
CA B:SER66 4.0 36.7 1.0
CE1 B:HIS391 4.1 49.1 1.0
O3 B:PO4801 4.1 28.4 0.5
CA B:ASP294 4.3 28.9 1.0
O4 B:PO4801 4.3 33.3 0.5
C B:SER66 4.4 36.4 1.0
CB B:ASP292 4.4 29.9 1.0
CD B:ARG295 4.4 37.2 1.0
N B:HIS67 4.5 35.8 1.0
CB B:ASP290 4.5 23.6 1.0
C B:ASP294 4.5 29.4 1.0
NE2 B:HIS391 4.5 46.8 1.0
N B:ASP292 4.6 23.2 1.0
N B:ARG295 4.6 26.6 1.0
CA B:ASP292 4.9 28.6 1.0
C B:ASP292 4.9 27.2 1.0
CB B:ARG295 4.9 29.0 1.0
CG B:ARG295 5.0 34.2 1.0

Reference:

Y.Nishitani, D.Maruyama, T.Nonaka, A.Kita, T.A.Fukami, T.Mio, H.Yamada-Okabe, T.Yamada-Okabe, K.Miki. Crystal Structures of N-Acetylglucosamine-Phosphate Mutase, A Member of the {Alpha}-D-Phosphohexomutase Superfamily, and Its Substrate and Product Complexes. J.Biol.Chem. V. 281 19740 2006.
ISSN: ISSN 0021-9258
PubMed: 16651269
DOI: 10.1074/JBC.M600801200
Page generated: Wed Oct 16 22:45:50 2024

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