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

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

The structure of The Crystal Structure of Atuah in Complex with (S)-Ureidoglycolate, PDB code: 4pxb 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)	30.64 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.015, 89.520, 163.061, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.9

The binding sites of Manganese atom in the The Crystal Structure of Atuah in Complex with (S)-Ureidoglycolate (pdb code 4pxb). 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)-Ureidoglycolate, PDB code: 4pxb:
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)-Ureidoglycolate


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)-Ureidoglycolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:11.9 occ:1.00 OD1 A:ASP149 2.2 11.6 1.0 O A:HOH610 2.3 12.2 1.0 NE2 A:HIS138 2.3 9.8 1.0 NE2 A:HIS254 2.4 8.3 1.0 O A:HOH671 2.5 19.9 1.0 N1 A:UGC503 2.7 16.1 1.0 CD2 A:HIS138 3.2 9.7 1.0 CE1 A:HIS254 3.3 11.0 1.0 CG A:ASP149 3.3 11.0 1.0 C1 A:UGC503 3.3 17.6 1.0 CE1 A:HIS138 3.3 12.5 1.0 CD2 A:HIS254 3.4 9.0 1.0 MN A:MN502 3.7 14.4 1.0 N A:GLY150 3.8 7.9 1.0 OD2 A:ASP149 3.8 9.0 1.0 O1 A:UGC503 3.9 20.9 1.0 N2 A:UGC503 4.0 19.6 1.0 CA A:GLY150 4.1 8.0 1.0 ND1 A:HIS424 4.2 10.9 1.0 C A:ASP149 4.3 9.2 1.0 CG A:HIS138 4.4 10.8 1.0 ND1 A:HIS254 4.4 7.8 1.0 ND1 A:HIS138 4.4 10.6 1.0 NE2 A:GLN257 4.5 13.5 1.0 CG A:HIS254 4.5 9.3 1.0 CB A:ASP149 4.5 7.9 1.0 O A:HOH622 4.5 11.7 1.0 CE1 A:HIS424 4.6 12.1 1.0 CA A:ASP149 4.6 7.5 1.0 OE2 A:GLU184 4.7 12.8 1.0 OE1 A:GLN257 4.8 12.3 1.0 C2 A:UGC503 5.0 19.0 1.0 CD A:GLN257 5.0 14.2 1.0 O A:ASP149 5.0 9.4 1.0

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


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)-Ureidoglycolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:14.4 occ:1.00 OD2 A:ASP149 2.2 9.0 1.0 OE2 A:GLU184 2.3 12.8 1.0 NE2 A:HIS448 2.3 11.3 1.0 O A:HOH671 2.4 19.9 1.0 O1 A:UGC503 2.6 20.9 1.0 O2 A:UGC503 2.6 16.1 1.0 C2 A:UGC503 2.9 19.0 1.0 C1 A:UGC503 3.0 17.6 1.0 CG A:ASP149 3.1 11.0 1.0 CD A:GLU184 3.2 13.2 1.0 N2 A:UGC503 3.3 19.6 1.0 CE1 A:HIS448 3.3 11.8 1.0 CD2 A:HIS448 3.3 12.0 1.0 OD1 A:ASP149 3.4 11.6 1.0 OE1 A:GLU184 3.4 11.6 1.0 MN A:MN501 3.7 11.9 1.0 O A:HOH605 3.8 10.6 1.0 N1 A:UGC503 3.9 16.1 1.0 NE2 A:GLN257 4.0 13.5 1.0 C3 A:UGC503 4.3 16.8 1.0 ND1 A:HIS448 4.4 11.8 1.0 NE2 B:HIS290 4.4 12.9 1.0 CG A:HIS448 4.4 10.9 1.0 CE1 A:HIS138 4.5 12.5 1.0 CB A:ASP149 4.5 7.9 1.0 NE2 A:HIS138 4.5 9.8 1.0 CG A:GLU184 4.6 11.9 1.0 ND2 B:ASN340 4.8 11.4 1.0 CD2 B:HIS290 4.8 13.2 1.0 O3 A:UGC503 4.8 14.7 1.0

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


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)-Ureidoglycolate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:10.7 occ:1.00 OD1 B:ASP149 2.2 11.0 1.0 O B:HOH614 2.2 8.3 1.0 NE2 B:HIS138 2.3 9.0 1.0 NE2 B:HIS254 2.4 9.6 1.0 O B:HOH662 2.4 18.1 1.0 N1 B:UGC503 2.8 17.9 1.0 CE1 B:HIS254 3.2 8.8 1.0 CD2 B:HIS138 3.2 9.5 1.0 CE1 B:HIS138 3.3 9.6 1.0 CG B:ASP149 3.3 11.0 1.0 C1 B:UGC503 3.3 20.4 1.0 CD2 B:HIS254 3.4 8.4 1.0 MN B:MN502 3.7 16.0 1.0 N B:GLY150 3.7 8.9 1.0 OD2 B:ASP149 3.8 10.5 1.0 O1 B:UGC503 3.9 21.2 1.0 N2 B:UGC503 4.1 22.7 1.0 CA B:GLY150 4.1 7.1 1.0 ND1 B:HIS424 4.2 7.9 1.0 C B:ASP149 4.3 10.0 1.0 ND1 B:HIS254 4.4 7.3 1.0 ND1 B:HIS138 4.4 12.2 1.0 CG B:HIS138 4.4 10.0 1.0 NE2 B:GLN257 4.4 11.6 1.0 CG B:HIS254 4.5 7.8 1.0 CB B:ASP149 4.5 9.5 1.0 O B:HOH613 4.5 10.9 1.0 OE2 B:GLU184 4.6 13.5 1.0 CE1 B:HIS424 4.6 9.8 1.0 CA B:ASP149 4.6 7.8 1.0 OE1 B:GLN257 4.8 12.3 1.0 CD B:GLN257 4.9 10.2 1.0 OG B:SER137 5.0 10.2 1.0

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


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)-Ureidoglycolate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:16.0 occ:1.00 OE2 B:GLU184 2.2 13.5 1.0 OD2 B:ASP149 2.2 10.5 1.0 NE2 B:HIS448 2.3 11.7 1.0 O B:HOH662 2.4 18.1 1.0 O1 B:UGC503 2.5 21.2 1.0 O2 B:UGC503 2.7 20.1 1.0 C1 B:UGC503 3.0 20.4 1.0 C2 B:UGC503 3.0 23.4 1.0 CG B:ASP149 3.2 11.0 1.0 CD B:GLU184 3.2 15.2 1.0 CD2 B:HIS448 3.3 11.4 1.0 N2 B:UGC503 3.3 22.7 1.0 CE1 B:HIS448 3.4 12.8 1.0 OD1 B:ASP149 3.4 11.0 1.0 OE1 B:GLU184 3.5 13.4 1.0 MN B:MN501 3.7 10.7 1.0 O B:HOH642 3.8 10.1 1.0 NE2 B:GLN257 3.9 11.6 1.0 N1 B:UGC503 4.0 17.9 1.0 C3 B:UGC503 4.4 18.0 1.0 NE2 A:HIS290 4.4 14.2 1.0 CG B:HIS448 4.5 11.6 1.0 ND1 B:HIS448 4.5 12.9 1.0 CE1 B:HIS138 4.5 9.6 1.0 CG B:GLU184 4.5 14.2 1.0 CB B:ASP149 4.5 9.5 1.0 NE2 B:HIS138 4.6 9.0 1.0 CD2 A:HIS290 4.7 11.9 1.0 ND2 A:ASN340 4.8 12.9 1.0 O3 B:UGC503 4.9 16.5 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