Zinc in PDB 3w0t: Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor

All present enzymatic activity of Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor:
4.4.1.5;

The structure of Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor, PDB code: 3w0t was solved by T.A.Fukami, M.Irie, T.Matsuura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.570, 81.030, 68.620, 90.00, 90.13, 90.00
R / Rfree (%)	17.5 / 19.7

The binding sites of Zinc atom in the Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor (pdb code 3w0t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor, PDB code: 3w0t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:17.6 occ:1.00 OE1 A:GLN33 2.0 18.1 1.0 OE1 A:GLU99 2.0 19.4 1.0 O19 B:HPU204 2.1 17.2 1.0 O16 B:HPU204 2.1 28.2 1.0 NE2 B:HIS126 2.2 14.2 1.0 OE2 B:GLU172 2.2 24.7 1.0 CD A:GLU99 2.8 21.3 1.0 C18 B:HPU204 2.9 18.1 1.0 N15 B:HPU204 2.9 19.1 1.0 OE2 A:GLU99 3.0 24.4 1.0 CD A:GLN33 3.0 17.6 1.0 CE1 B:HIS126 3.1 14.7 1.0 CD2 B:HIS126 3.2 14.5 1.0 CD B:GLU172 3.3 35.3 1.0 NE2 A:GLN33 3.4 14.3 1.0 OE1 B:GLU172 3.6 36.6 1.0 C20 B:HPU204 4.3 16.5 1.0 CG A:GLU99 4.3 16.1 1.0 C13 B:HPU204 4.3 19.3 1.0 ND1 B:HIS126 4.3 14.2 1.0 CG B:HIS126 4.3 13.0 1.0 CG A:GLN33 4.3 14.5 1.0 O A:HOH337 4.4 21.7 1.0 CG B:GLU172 4.5 16.7 1.0 CB A:MET35 4.6 11.5 1.0 C8 B:HPU204 4.6 24.9 1.0 CB B:GLU172 4.6 14.4 1.0 CB A:GLU99 4.8 13.1 1.0 CG A:MET35 4.8 14.3 1.0 C12 B:HPU204 4.8 23.1 1.0

Zinc binding site 2 out of 4 in the Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:17.6 occ:1.00 OE1 B:GLN33 2.0 15.5 1.0 OE1 B:GLU99 2.0 21.2 1.0 NE2 A:HIS126 2.1 12.7 1.0 O19 A:HPU202 2.2 15.2 1.0 O16 A:HPU202 2.2 27.2 1.0 OE1 A:GLU172 2.3 24.6 1.0 CD B:GLU99 2.9 21.7 1.0 C18 A:HPU202 3.0 17.4 1.0 CD B:GLN33 3.0 15.2 1.0 N15 A:HPU202 3.0 20.3 1.0 OE2 B:GLU99 3.1 23.7 1.0 CE1 A:HIS126 3.1 13.6 1.0 CD2 A:HIS126 3.2 13.5 1.0 CD A:GLU172 3.2 30.8 1.0 NE2 B:GLN33 3.4 12.6 1.0 OE2 A:GLU172 3.6 28.0 1.0 ND1 A:HIS126 4.2 14.0 1.0 CG A:HIS126 4.3 12.3 1.0 CG B:GLU99 4.3 15.5 1.0 C20 A:HPU202 4.3 15.9 1.0 CG B:GLN33 4.3 12.8 1.0 C13 A:HPU202 4.4 23.7 1.0 CG A:GLU172 4.5 16.1 1.0 CB B:MET35 4.6 12.2 1.0 CB A:GLU172 4.6 11.7 1.0 CB B:GLU99 4.7 12.4 1.0 O B:HOH1024 4.7 19.5 1.0 CG B:MET35 4.8 13.3 1.0 C8 A:HPU202 4.9 34.4 1.0

Zinc binding site 3 out of 4 in the Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:17.9 occ:1.00 OE1 C:GLU99 2.0 22.6 1.0 O16 D:HPU203 2.0 26.8 1.0 OE1 C:GLN33 2.0 18.2 1.0 NE2 D:HIS126 2.1 14.0 1.0 O19 D:HPU203 2.1 15.7 1.0 OE1 D:GLU172 2.4 25.9 1.0 CD C:GLU99 2.7 21.3 1.0 OE2 C:GLU99 2.8 23.1 1.0 C18 D:HPU203 2.9 15.9 1.0 N15 D:HPU203 2.9 17.2 1.0 CD C:GLN33 3.0 17.7 1.0 CE1 D:HIS126 3.1 14.5 1.0 CD2 D:HIS126 3.1 15.3 1.0 CD D:GLU172 3.3 36.5 1.0 NE2 C:GLN33 3.4 15.3 1.0 OE2 D:GLU172 3.6 33.4 1.0 CG C:GLU99 4.2 17.3 1.0 C20 D:HPU203 4.2 14.8 1.0 C13 D:HPU203 4.2 18.3 1.0 CG D:HIS126 4.2 13.5 1.0 ND1 D:HIS126 4.3 14.4 1.0 CG C:GLN33 4.3 14.7 1.0 O C:HOH327 4.5 19.2 1.0 CG D:GLU172 4.6 17.8 1.0 C8 D:HPU203 4.6 21.7 1.0 CB C:MET35 4.6 11.8 1.0 CB D:GLU172 4.6 13.7 1.0 CB C:GLU99 4.7 14.2 1.0 C12 D:HPU203 4.8 21.2 1.0 CG C:MET35 4.9 13.6 1.0

Zinc binding site 4 out of 4 in the Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Glyoxalase I with An N-Hydroxypyridone Derivative Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:17.8 occ:1.00 OE1 D:GLU99 2.0 20.8 1.0 OE1 D:GLN33 2.0 15.1 1.0 NE2 C:HIS126 2.1 12.4 1.0 O19 C:HPU202 2.2 17.2 1.0 O16 C:HPU202 2.2 27.2 1.0 OE2 C:GLU172 2.3 23.2 1.0 CD D:GLU99 2.9 21.1 1.0 C18 C:HPU202 3.0 16.6 1.0 CD D:GLN33 3.0 15.5 1.0 N15 C:HPU202 3.0 20.2 1.0 CE1 C:HIS126 3.0 13.1 1.0 OE2 D:GLU99 3.1 21.1 1.0 CD2 C:HIS126 3.2 12.4 1.0 CD C:GLU172 3.3 30.5 1.0 NE2 D:GLN33 3.4 14.1 1.0 OE1 C:GLU172 3.6 28.2 1.0 ND1 C:HIS126 4.2 13.4 1.0 CG C:HIS126 4.3 11.9 1.0 CG D:GLU99 4.3 15.5 1.0 CG D:GLN33 4.3 13.1 1.0 C20 C:HPU202 4.3 16.1 1.0 C13 C:HPU202 4.4 22.4 1.0 CG C:GLU172 4.6 14.6 1.0 CB D:MET35 4.6 12.0 1.0 O D:HOH325 4.7 20.2 1.0 CB C:GLU172 4.7 11.6 1.0 CB D:GLU99 4.7 13.1 1.0 CG D:MET35 4.8 13.3 1.0 C8 C:HPU202 4.9 35.6 1.0 C12 C:HPU202 5.0 32.5 1.0

H.Koyano, T.Aoki, S.Yamamoto, T.Kobayashi, T.Miura, K.Ohara, T.A.Fukami, M.Irie, H.Sakamoto. N-Hydroxypyridone-Based Glyoxalase I Inhibitors Mimicking Binding Interactions of the Substrate To Be Published.