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

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

All present enzymatic activity of Crystal Structure of N-Acetylglucosamine-Phosphate Mutase, A Member of the Alpha-D-Phosphohexomutase Superfamily, in the Product 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 Product Complex, PDB code: 2dkd 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) 36.59 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.185, 129.519, 81.251, 90.00, 109.22, 90.00
R / Rfree (%) 18.1 / 22.5

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 Product Complex (pdb code 2dkd). 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 Product Complex, PDB code: 2dkd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2dkd

Go back to Zinc Binding Sites List in 2dkd
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 Product 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 Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn921

b:24.7
occ:1.00
 OD2 A:ASP294 2.0 15.1 1.0
OD2 A:ASP290 2.0 14.9 1.0
OD1 A:ASP292 2.1 19.9 1.0
O1 A:PO4911 2.3 30.8 0.5
OG A:SER66 2.3 42.7 1.0
CG A:ASP294 2.8 16.8 1.0
CG A:ASP292 2.9 16.4 1.0
CG A:ASP290 3.0 10.6 1.0
OD1 A:ASP294 3.2 17.5 1.0
OD2 A:ASP292 3.2 16.2 1.0
OD1 A:ASP290 3.3 8.4 1.0
P A:PO4911 3.4 32.7 0.5
CB A:SER66 3.5 41.2 1.0
O A:HOH1130 3.6 38.3 1.0
O3 A:PO4911 3.7 31.6 0.5
O4 A:PO4911 3.9 30.9 0.5
CA A:SER66 4.0 40.1 1.0
CB A:ASP294 4.1 14.7 1.0
N A:ASP294 4.2 11.4 1.0
O A:HOH1326 4.3 42.0 1.0
CB A:ASP290 4.3 9.4 1.0
CB A:ASP292 4.3 12.8 1.0
CG A:ARG295 4.4 18.9 1.0
N A:ASP292 4.5 12.8 1.0
CA A:ASP294 4.5 13.3 1.0
C A:ASP294 4.6 12.5 1.0
O2 A:PO4911 4.7 30.1 0.5
C A:SER66 4.7 41.9 1.0
CD A:ARG295 4.7 17.5 1.0
CA A:ASP292 4.8 14.7 1.0
NE A:ARG295 4.8 24.6 1.0
N A:ARG295 4.8 12.2 1.0
N A:ALA293 4.9 9.3 1.0
C A:ASP292 4.9 12.9 1.0
CB A:ARG295 5.0 14.2 1.0

Zinc binding site 2 out of 2 in 2dkd

Go back to Zinc Binding Sites List in 2dkd
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 Product 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 Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn922

b:26.8
occ:1.00
 OD2 B:ASP294 1.8 21.1 1.0
O2 B:PO4912 1.9 37.6 0.5
OD2 B:ASP290 2.0 15.1 1.0
OD1 B:ASP292 2.0 20.6 1.0
CG B:ASP294 2.7 20.2 1.0
CG B:ASP292 2.9 18.5 1.0
OD1 B:ASP294 2.9 26.3 1.0
CG B:ASP290 3.0 10.6 1.0
OD2 B:ASP292 3.1 21.9 1.0
CB B:SER66 3.2 37.0 1.0
OD1 B:ASP290 3.3 9.9 1.0
P B:PO4912 3.3 38.0 0.5
OG B:SER66 3.4 40.4 1.0
CA B:SER66 3.9 34.6 1.0
O1 B:PO4912 3.9 38.5 0.5
O3 B:PO4912 4.0 39.5 0.5
CB B:ASP294 4.0 18.6 1.0
N B:ASP294 4.1 14.2 1.0
O4 B:PO4912 4.3 37.5 0.5
CB B:ASP292 4.3 15.5 1.0
CB B:ASP290 4.3 10.8 1.0
CG B:ARG295 4.4 15.5 1.0
C B:SER66 4.4 36.0 1.0
N B:ASP292 4.4 13.1 1.0
CA B:ASP294 4.5 13.9 1.0
N B:HIS67 4.5 35.5 1.0
NE B:ARG295 4.6 22.2 1.0
CD2 B:HIS67 4.6 43.6 1.0
C B:ASP294 4.6 12.7 1.0
N B:ARG295 4.6 13.3 1.0
CD B:ARG295 4.7 16.3 1.0
CA B:ASP292 4.7 14.5 1.0
C B:ASP292 4.8 13.8 1.0
N B:ALA293 4.9 10.2 1.0
CB B:ARG295 4.9 12.5 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 Dec 16 03:21:40 2020

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