Manganese in PDB 4pxc: The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine

All present enzymatic activity of The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine:
3.5.3.19;

The structure of The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine, PDB code: 4pxc was solved by I.Shin, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.504, 89.741, 164.081, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.5

The binding sites of Manganese atom in the The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine (pdb code 4pxc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine, PDB code: 4pxc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:13.9 occ:1.00 OD1 A:ASP149 2.2 12.4 1.0 NE2 A:HIS254 2.3 12.8 1.0 O A:HOH613 2.3 13.6 1.0 NE2 A:HIS138 2.3 12.1 1.0 O A:HOH732 2.6 20.8 1.0 O A:HOH787 2.7 22.9 1.0 CE1 A:HIS254 3.2 12.3 1.0 CD2 A:HIS138 3.2 13.5 1.0 CG A:ASP149 3.3 15.0 1.0 CD2 A:HIS254 3.4 12.5 1.0 CE1 A:HIS138 3.4 14.2 1.0 MN A:MN502 3.7 22.6 1.0 O A:HOH689 3.7 24.6 1.0 N A:GLY150 3.8 9.0 1.0 OD2 A:ASP149 3.8 14.8 1.0 CA A:GLY150 4.1 11.1 1.0 ND1 A:HIS424 4.1 10.7 1.0 C A:ASP149 4.3 12.1 1.0 ND1 A:HIS254 4.3 11.2 1.0 N A:HGY503 4.4 22.0 1.0 CG A:HIS138 4.4 13.7 1.0 CE1 A:HIS424 4.4 14.4 1.0 CG A:HIS254 4.4 10.8 1.0 NE2 A:GLN257 4.5 12.3 1.0 ND1 A:HIS138 4.5 13.4 1.0 O A:HOH602 4.5 10.3 1.0 CB A:ASP149 4.5 10.4 1.0 CA A:ASP149 4.7 10.1 1.0 OE2 A:GLU184 4.7 16.7 1.0 OE1 A:GLN257 4.7 13.6 1.0 CA A:HGY503 4.8 22.8 1.0 CD A:GLN257 4.9 13.7 1.0 OG A:SER137 5.0 11.6 1.0 O A:ASP149 5.0 11.5 1.0

Manganese binding site 2 out of 4 in the The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:22.6 occ:1.00 OD2 A:ASP149 2.3 14.8 1.0 OE2 A:GLU184 2.3 16.7 1.0 NE2 A:HIS448 2.4 17.4 1.0 O A:HOH689 2.4 24.6 1.0 O A:HOH732 2.4 20.8 1.0 OB A:HGY503 2.4 17.7 1.0 CA A:HGY503 3.0 22.8 1.0 CG A:ASP149 3.2 15.0 1.0 CD A:GLU184 3.2 18.0 1.0 CD2 A:HIS448 3.3 16.4 1.0 CE1 A:HIS448 3.4 16.4 1.0 OD1 A:ASP149 3.4 12.4 1.0 OE1 A:GLU184 3.4 14.3 1.0 O A:HOH787 3.7 22.9 1.0 N A:HGY503 3.7 22.0 1.0 MN A:MN501 3.7 13.9 1.0 O A:HOH646 3.8 15.3 1.0 NE2 A:GLN257 4.0 12.3 1.0 C A:HGY503 4.2 20.5 1.0 NE2 B:HIS290 4.3 15.7 1.0 ND1 A:HIS448 4.5 15.7 1.0 CG A:HIS448 4.5 14.7 1.0 NE2 A:HIS138 4.5 12.1 1.0 CE1 A:HIS138 4.5 14.2 1.0 CB A:ASP149 4.5 10.4 1.0 CG A:GLU184 4.6 16.3 1.0 CD2 B:HIS290 4.6 17.0 1.0 OXT A:HGY503 4.6 18.4 1.0 ND2 B:ASN340 4.8 12.9 1.0

Manganese binding site 3 out of 4 in the The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:15.4 occ:1.00 O B:HOH621 2.2 12.7 1.0 OD1 B:ASP149 2.2 11.3 1.0 NE2 B:HIS138 2.4 12.8 1.0 NE2 B:HIS254 2.4 13.3 1.0 O B:HOH760 2.5 25.7 1.0 O B:HOH1080 2.8 29.3 1.0 CD2 B:HIS138 3.2 13.7 1.0 CE1 B:HIS254 3.3 14.7 1.0 CG B:ASP149 3.4 16.0 1.0 CE1 B:HIS138 3.4 15.3 1.0 CD2 B:HIS254 3.4 13.6 1.0 MN B:MN502 3.7 27.0 1.0 N B:GLY150 3.7 11.8 1.0 OD2 B:ASP149 3.9 14.9 1.0 CA B:GLY150 4.1 12.6 1.0 ND1 B:HIS424 4.1 12.9 1.0 N B:HGY503 4.3 23.7 1.0 C B:ASP149 4.3 13.3 1.0 CG B:HIS138 4.4 15.6 1.0 ND1 B:HIS254 4.4 12.2 1.0 ND1 B:HIS138 4.5 16.9 1.0 O B:HOH622 4.5 12.2 1.0 CG B:HIS254 4.5 11.3 1.0 NE2 B:GLN257 4.5 14.6 1.0 CB B:ASP149 4.6 13.7 1.0 OE2 B:GLU184 4.6 18.4 1.0 CE1 B:HIS424 4.6 13.8 1.0 CA B:ASP149 4.7 13.5 1.0 OE1 B:GLN257 4.7 14.8 1.0 CA B:HGY503 4.8 25.9 1.0 CD B:GLN257 4.9 15.1 1.0 OG B:SER137 5.0 12.5 1.0 O B:TYR423 5.0 16.4 1.0

Manganese binding site 4 out of 4 in the The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of Atuah in Complex with (S)-Hydroxyglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:27.0 occ:1.00 OE2 B:GLU184 2.2 18.4 1.0 O B:HOH760 2.3 25.7 1.0 OD2 B:ASP149 2.3 14.9 1.0 NE2 B:HIS448 2.4 19.0 1.0 OB B:HGY503 2.5 21.9 1.0 CA B:HGY503 3.1 25.9 1.0 CD B:GLU184 3.2 17.7 1.0 CG B:ASP149 3.2 16.0 1.0 CD2 B:HIS448 3.3 17.6 1.0 OD1 B:ASP149 3.4 11.3 1.0 OE1 B:GLU184 3.4 16.2 1.0 CE1 B:HIS448 3.5 20.0 1.0 N B:HGY503 3.7 23.7 1.0 MN B:MN501 3.7 15.4 1.0 O B:HOH677 3.8 14.7 1.0 O B:HOH1080 3.8 29.3 1.0 NE2 B:GLN257 4.0 14.6 1.0 NE2 A:HIS290 4.4 19.2 1.0 C B:HGY503 4.4 21.6 1.0 NE2 B:HIS138 4.5 12.8 1.0 CE1 B:HIS138 4.5 15.3 1.0 CG B:HIS448 4.5 18.0 1.0 CG B:GLU184 4.5 15.7 1.0 ND1 B:HIS448 4.6 19.2 1.0 CB B:ASP149 4.6 13.7 1.0 CD2 A:HIS290 4.6 17.4 1.0 ND2 A:ASN340 4.8 18.5 1.0 OXT B:HGY503 4.9 22.4 1.0

I.Shin, K.Han, S.Rhee. Structural Insights Into the Substrate Specificity of (S)-Ureidoglycolate Amidohydrolase and Its Comparison with Allantoate Amidohydrolase J.Mol.Biol. 2014.
ISSN: ESSN 1089-8638
PubMed: 25020232
DOI: 10.1016/J.JMB.2014.06.017