Manganese in PDB 4pxe: The Crystal Structure of Atuah in Complex with Glyoxylate

All present enzymatic activity of The Crystal Structure of Atuah in Complex with Glyoxylate:
3.5.3.19;

The structure of The Crystal Structure of Atuah in Complex with Glyoxylate, PDB code: 4pxe 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)	46.67 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.983, 89.758, 163.932, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 17.6

The binding sites of Manganese atom in the The Crystal Structure of Atuah in Complex with Glyoxylate (pdb code 4pxe). 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 Glyoxylate, PDB code: 4pxe:
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 Glyoxylate


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 Glyoxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:11.6 occ:1.00 OD1 A:ASP149 2.2 12.8 1.0 O A:HOH621 2.2 17.5 1.0 O A:HOH608 2.2 14.2 1.0 NE2 A:HIS138 2.3 13.4 1.0 NE2 A:HIS254 2.3 11.2 1.0 O A:HOH648 2.5 16.2 1.0 CE1 A:HIS254 3.2 10.9 1.0 CE1 A:HIS138 3.3 12.9 1.0 CG A:ASP149 3.3 13.4 1.0 CD2 A:HIS138 3.3 12.2 1.0 CD2 A:HIS254 3.4 11.2 1.0 OD2 A:ASP149 3.7 18.3 1.0 N A:GLY150 3.8 10.2 1.0 MN A:MN502 3.8 26.4 1.0 O B:HOH615 3.8 17.6 1.0 OE1 A:GLU183 4.0 17.0 1.0 ND1 A:HIS424 4.1 13.5 1.0 CA A:GLY150 4.2 11.8 1.0 O1 A:GLV503 4.3 16.8 1.0 C A:ASP149 4.3 11.8 1.0 ND1 A:HIS254 4.3 10.6 1.0 ND1 A:HIS138 4.4 11.6 1.0 CG A:HIS138 4.4 12.2 1.0 CD A:GLU183 4.4 15.4 1.0 CG A:HIS254 4.5 10.9 1.0 CB A:ASP149 4.5 11.7 1.0 CE1 A:HIS424 4.5 14.0 1.0 NE2 A:GLN257 4.6 12.2 1.0 OE1 A:GLN257 4.6 12.8 1.0 O A:HOH604 4.6 13.0 1.0 OE2 A:GLU183 4.6 19.2 1.0 CA A:ASP149 4.7 10.6 1.0 OE2 A:GLU184 4.8 15.9 1.0 CD A:GLN257 4.9 11.2 1.0 O A:TYR423 4.9 13.8 1.0

Manganese binding site 2 out of 4 in the The Crystal Structure of Atuah in Complex with Glyoxylate


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 Glyoxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:26.4 occ:1.00 O B:HOH615 1.8 17.6 1.0 O A:HOH621 2.1 17.5 1.0 OE2 A:GLU184 2.2 15.9 1.0 OD2 A:ASP149 2.2 18.3 1.0 NE2 A:HIS448 2.3 17.7 1.0 CD A:GLU184 3.1 15.6 1.0 CG A:ASP149 3.2 13.4 1.0 CD2 A:HIS448 3.3 16.4 1.0 CE1 A:HIS448 3.3 16.0 1.0 OE1 A:GLU184 3.4 14.6 1.0 OD1 A:ASP149 3.4 12.8 1.0 C1 A:GLV503 3.4 15.8 1.0 O1 A:GLV503 3.7 16.8 1.0 O A:HOH623 3.8 15.3 1.0 MN A:MN501 3.8 11.6 1.0 O A:HOH648 3.8 16.2 1.0 NE2 A:GLN257 4.1 12.2 1.0 OE1 A:GLU183 4.2 17.0 1.0 NE2 B:HIS290 4.2 15.3 1.0 C2 A:GLV503 4.3 13.9 1.0 ND1 A:HIS448 4.4 14.1 1.0 CG A:GLU184 4.4 14.0 1.0 CG A:HIS448 4.4 14.5 1.0 CE1 A:HIS138 4.5 12.9 1.0 CB A:ASP149 4.5 11.7 1.0 NE2 A:HIS138 4.6 13.4 1.0 CD2 B:HIS290 4.7 13.4 1.0 O3 A:GLV503 4.8 14.6 1.0 ND2 B:ASN340 4.8 13.3 1.0

Manganese binding site 3 out of 4 in the The Crystal Structure of Atuah in Complex with Glyoxylate


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 Glyoxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:10.8 occ:1.00 O B:HOH638 2.2 16.1 1.0 OD1 B:ASP149 2.2 11.7 1.0 O B:HOH621 2.2 12.6 1.0 NE2 B:HIS138 2.3 11.1 1.0 NE2 B:HIS254 2.4 8.8 1.0 O B:HOH672 2.4 13.9 1.0 CE1 B:HIS254 3.2 9.1 1.0 CE1 B:HIS138 3.2 10.2 1.0 CG B:ASP149 3.2 11.4 1.0 CD2 B:HIS138 3.3 11.0 1.0 CD2 B:HIS254 3.4 9.9 1.0 OD2 B:ASP149 3.7 17.5 1.0 MN B:MN502 3.8 24.8 1.0 N B:GLY150 3.8 9.7 1.0 O A:HOH1238 3.9 18.0 1.0 OE1 B:GLU183 4.0 15.6 1.0 ND1 B:HIS424 4.1 10.1 1.0 O1 B:GLV503 4.2 15.5 1.0 CA B:GLY150 4.2 10.8 1.0 C B:ASP149 4.3 9.6 1.0 ND1 B:HIS254 4.3 9.4 1.0 ND1 B:HIS138 4.4 11.4 1.0 CG B:HIS138 4.4 10.1 1.0 CD B:GLU183 4.4 15.5 1.0 CB B:ASP149 4.5 11.4 1.0 CG B:HIS254 4.5 8.3 1.0 O B:HOH622 4.5 12.4 1.0 NE2 B:GLN257 4.5 11.2 1.0 CE1 B:HIS424 4.5 10.1 1.0 OE1 B:GLN257 4.6 11.0 1.0 OE2 B:GLU183 4.6 16.6 1.0 CA B:ASP149 4.6 9.4 1.0 OE2 B:GLU184 4.7 15.7 1.0 CD B:GLN257 4.9 10.3 1.0 O B:TYR423 4.9 11.2 1.0

Manganese binding site 4 out of 4 in the The Crystal Structure of Atuah in Complex with Glyoxylate


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 Glyoxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:24.8 occ:1.00 O A:HOH1238 2.0 18.0 1.0 OE2 B:GLU184 2.1 15.7 1.0 O B:HOH638 2.1 16.1 1.0 OD2 B:ASP149 2.2 17.5 1.0 NE2 B:HIS448 2.3 14.9 1.0 CD B:GLU184 3.1 15.8 1.0 CG B:ASP149 3.1 11.4 1.0 CD2 B:HIS448 3.3 14.1 1.0 CE1 B:HIS448 3.3 14.6 1.0 OE1 B:GLU184 3.4 14.8 1.0 OD1 B:ASP149 3.4 11.7 1.0 C1 B:GLV503 3.4 14.5 1.0 O1 B:GLV503 3.6 15.5 1.0 MN B:MN501 3.8 10.8 1.0 O B:HOH658 3.8 14.8 1.0 O B:HOH672 3.9 13.9 1.0 NE2 B:GLN257 4.0 11.2 1.0 OE1 B:GLU183 4.3 15.6 1.0 NE2 A:HIS290 4.3 13.4 1.0 C2 B:GLV503 4.3 13.9 1.0 CG B:GLU184 4.4 14.2 1.0 ND1 B:HIS448 4.4 14.4 1.0 CG B:HIS448 4.4 12.9 1.0 CE1 B:HIS138 4.5 10.2 1.0 CB B:ASP149 4.5 11.4 1.0 NE2 B:HIS138 4.6 11.1 1.0 CD2 A:HIS290 4.7 12.9 1.0 O2 B:GLV503 4.7 14.2 1.0 ND2 A:ASN340 4.8 12.9 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