Zinc in PDB 7nut: Crystal Structure of Human AMDHD2 in Complex with Zn and GLCN6P

All present enzymatic activity of Crystal Structure of Human AMDHD2 in Complex with Zn and GLCN6P:
3.5.1.25;

The structure of Crystal Structure of Human AMDHD2 in Complex with Zn and GLCN6P, PDB code: 7nut was solved by S.Ruegenberg, V.Kroef, U.Baumann, M.S.Denzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.71 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.261, 161.449, 86.621, 90, 90, 90
R / Rfree (%)	18.5 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Human AMDHD2 in Complex with Zn and GLCN6P (pdb code 7nut). 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 Human AMDHD2 in Complex with Zn and GLCN6P, PDB code: 7nut:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human AMDHD2 in Complex with Zn and GLCN6P


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 Human AMDHD2 in Complex with Zn and GLCN6P within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:32.4 occ:1.00 O A:HOH602 1.8 38.2 1.0 OE1 A:GLU143 1.9 36.1 1.0 NE2 A:HIS211 2.0 30.0 1.0 NE2 A:HIS232 2.2 30.6 1.0 O A:HOH684 2.3 45.1 1.0 CD A:GLU143 2.7 35.7 1.0 HE2 A:HIS155 2.8 43.1 1.0 HN21 A:GLP501 2.9 41.7 1.0 CE1 A:HIS211 2.9 30.8 1.0 OE2 A:GLU143 3.0 38.1 1.0 HE1 A:HIS211 3.1 36.5 1.0 CD2 A:HIS211 3.1 28.7 1.0 CE1 A:HIS232 3.1 30.2 1.0 CD2 A:HIS232 3.1 29.0 1.0 H2 A:GLP501 3.3 37.7 1.0 HE1 A:HIS232 3.3 34.6 1.0 HD2 A:HIS232 3.3 30.5 1.0 HD2 A:HIS211 3.4 32.0 1.0 HE22 A:GLN71 3.5 49.4 1.0 N2 A:GLP501 3.6 34.7 1.0 HN22 A:GLP501 3.6 41.7 1.0 NE2 A:HIS155 3.6 34.0 1.0 HG22 A:THR231 3.7 36.5 1.0 C2 A:GLP501 3.9 31.3 1.0 HO3 A:GLP501 3.9 36.5 1.0 HG21 A:THR231 3.9 36.5 1.0 HE21 A:GLN71 3.9 49.4 1.0 O3 A:GLP501 4.0 30.3 1.0 NE2 A:GLN71 4.1 38.6 1.0 ND1 A:HIS211 4.1 30.2 1.0 CG A:GLU143 4.1 35.2 1.0 CG A:HIS211 4.2 29.8 1.0 ND1 A:HIS232 4.3 29.8 1.0 CG2 A:THR231 4.3 30.9 1.0 HD2 A:HIS155 4.3 41.1 1.0 CG A:HIS232 4.3 29.5 1.0 HG2 A:GLU143 4.3 42.2 1.0 HG3 A:GLU143 4.4 42.2 1.0 CD2 A:HIS155 4.4 34.0 1.0 O A:HOH614 4.5 43.1 1.0 HG23 A:THR231 4.6 36.5 1.0 C3 A:GLP501 4.6 30.4 1.0 CE1 A:HIS155 4.7 33.9 1.0 HE1 A:HIS155 4.8 41.9 1.0 HB3 A:ALA236 4.8 35.5 1.0 HD1 A:HIS211 4.9 33.9 1.0 OD2 A:ASP294 4.9 40.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human AMDHD2 in Complex with Zn and GLCN6P


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 Human AMDHD2 in Complex with Zn and GLCN6P within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:35.1 occ:1.00 OE2 B:GLU143 1.9 35.4 1.0 O B:HOH610 2.0 45.6 1.0 NE2 B:HIS211 2.0 32.0 1.0 O B:HOH601 2.1 45.8 1.0 NE2 B:HIS232 2.2 31.0 1.0 CD B:GLU143 2.7 35.6 1.0 OE1 B:GLU143 2.9 37.1 1.0 CE1 B:HIS211 3.0 33.6 1.0 HE2 B:HIS155 3.0 48.5 1.0 CD2 B:HIS211 3.1 30.8 1.0 HE1 B:HIS211 3.1 46.9 1.0 H2 B:GLP501 3.2 64.1 1.0 CE1 B:HIS232 3.2 31.1 1.0 CD2 B:HIS232 3.2 30.1 1.0 HD2 B:HIS211 3.3 40.9 1.0 N2 B:GLP501 3.3 54.3 1.0 HE1 B:HIS232 3.3 38.1 1.0 HD2 B:HIS232 3.3 36.2 1.0 HE22 B:GLN71 3.4 46.0 1.0 HN21 B:GLP501 3.5 65.2 1.0 HO3 B:GLP501 3.6 62.0 1.0 C2 B:GLP501 3.7 53.4 1.0 HG22 B:THR231 3.8 37.8 1.0 NE2 B:HIS155 3.8 38.1 1.0 HE21 B:GLN71 3.8 46.0 1.0 O3 B:GLP501 3.9 51.5 1.0 NE2 B:GLN71 4.0 36.4 1.0 HN22 B:GLP501 4.0 65.2 1.0 HG21 B:THR231 4.0 37.8 1.0 CG B:GLU143 4.1 33.9 1.0 ND1 B:HIS211 4.1 32.6 1.0 CG B:HIS211 4.2 31.2 1.0 ND1 B:HIS232 4.3 29.9 1.0 O B:HOH615 4.3 38.0 1.0 CG B:HIS232 4.3 29.3 1.0 HG2 B:GLU143 4.3 41.5 1.0 CG2 B:THR231 4.4 31.8 1.0 HG3 B:GLU143 4.4 41.5 1.0 C3 B:GLP501 4.4 58.1 1.0 OD2 B:ASP294 4.5 42.8 1.0 HD2 B:HIS155 4.6 56.4 1.0 CD2 B:HIS155 4.6 41.2 1.0 HG23 B:THR231 4.7 37.8 1.0 HB3 B:ALA236 4.7 40.2 1.0 CE1 B:HIS155 4.8 38.8 1.0 H1 B:GLP501 4.8 67.9 1.0 HE1 B:HIS155 4.9 49.5 1.0 HD1 B:HIS211 4.9 42.1 1.0 C1 B:GLP501 4.9 56.5 1.0

V.Kroef, S.Ruegenberg, M.Horn, K.Allmeroth, L.Ebert, S.Bozkus, S.Miethe, B.Schermer, U.Baumann, M.S.Denzel. GFAT2 and AMDHD2 Act in Tandem to Control the Hexosamine Biosynthetic Pathway To Be Published.