Manganese in PDB 4e2s: Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine

The structure of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine, PDB code: 4e2s 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)	50.00 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.098, 174.894, 154.300, 90.00, 99.26, 90.00
R / Rfree (%)	20.9 / 27.1

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine (pdb code 4e2s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine, PDB code: 4e2s:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:36.3 occ:1.00 NE2 A:HIS237 2.2 31.9 1.0 O A:UGY302 2.2 46.4 1.0 OE1 A:GLU235 2.3 36.4 1.0 NB A:UGY302 2.3 47.8 1.0 NE2 A:HIS241 2.3 37.3 1.0 OE1 A:GLN275 2.5 27.9 1.0 CE1 A:HIS237 3.0 32.6 1.0 C A:UGY302 3.0 46.1 1.0 CD2 A:HIS241 3.0 35.1 1.0 CA A:UGY302 3.2 46.9 1.0 CG A:UGY302 3.2 50.4 1.0 CD2 A:HIS237 3.3 33.0 1.0 NE A:UGY302 3.3 49.9 1.0 CD A:GLN275 3.4 29.9 1.0 CD A:GLU235 3.4 36.1 1.0 CE1 A:HIS241 3.4 36.0 1.0 OE2 A:GLU235 4.0 37.7 1.0 NE2 A:GLN275 4.0 27.2 1.0 N A:UGY302 4.2 45.3 1.0 OXT A:UGY302 4.2 45.8 1.0 ND1 A:HIS237 4.2 31.9 1.0 CG A:HIS241 4.3 33.7 1.0 OE A:UGY302 4.3 52.2 1.0 CG A:HIS237 4.4 33.1 1.0 CG A:GLN275 4.4 29.6 1.0 ND1 A:HIS241 4.4 34.4 1.0 CB A:GLU235 4.5 30.7 1.0 CG A:GLU235 4.6 33.0 1.0

Manganese binding site 2 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:32.2 occ:1.00 OE1 B:GLU235 2.1 35.4 1.0 O B:UGY302 2.1 47.5 1.0 OE1 B:GLN275 2.2 30.0 1.0 NE2 B:HIS241 2.3 30.1 1.0 NE2 B:HIS237 2.4 24.1 1.0 NB B:UGY302 2.5 47.7 1.0 CD2 B:HIS241 3.0 28.3 1.0 C B:UGY302 3.0 47.5 1.0 CD B:GLU235 3.1 35.5 1.0 CA B:UGY302 3.2 47.0 1.0 CE1 B:HIS237 3.3 22.8 1.0 CD B:GLN275 3.3 27.5 1.0 CD2 B:HIS237 3.4 23.9 1.0 CE1 B:HIS241 3.4 29.4 1.0 CG B:UGY302 3.5 49.2 1.0 NE B:UGY302 3.6 48.8 1.0 OE2 B:GLU235 3.6 38.5 1.0 N B:UGY302 4.0 46.4 1.0 NE2 B:GLN275 4.1 28.8 1.0 OXT B:UGY302 4.1 47.5 1.0 CG B:HIS241 4.2 28.8 1.0 CG B:GLU235 4.3 33.4 1.0 ND1 B:HIS241 4.3 29.0 1.0 CG B:GLN275 4.3 27.0 1.0 CB B:GLU235 4.4 30.4 1.0 ND1 B:HIS237 4.4 25.4 1.0 CG B:HIS237 4.5 24.7 1.0 OE B:UGY302 4.6 50.4 1.0

Manganese binding site 3 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:29.5 occ:1.00 O C:UGY302 2.2 44.0 1.0 OE2 C:GLU235 2.2 34.4 1.0 NB C:UGY302 2.3 45.0 1.0 NE2 C:HIS241 2.4 36.4 1.0 NE2 C:HIS237 2.4 27.1 1.0 OE1 C:GLN275 2.5 29.0 1.0 C C:UGY302 3.0 42.5 1.0 CE1 C:HIS241 3.1 36.6 1.0 CG C:UGY302 3.2 47.2 1.0 CA C:UGY302 3.2 42.7 1.0 NE C:UGY302 3.3 45.5 1.0 CD2 C:HIS237 3.3 28.4 1.0 CD2 C:HIS241 3.4 36.0 1.0 CE1 C:HIS237 3.4 30.2 1.0 CD C:GLN275 3.4 29.0 1.0 CD C:GLU235 3.5 34.6 1.0 OE1 C:GLU235 4.1 37.0 1.0 OXT C:UGY302 4.2 40.6 1.0 NE2 C:GLN275 4.2 30.3 1.0 ND1 C:HIS241 4.2 36.5 1.0 OE C:UGY302 4.2 49.1 1.0 N C:UGY302 4.3 43.0 1.0 CG C:GLN275 4.3 28.1 1.0 CG C:HIS241 4.4 35.7 1.0 CB C:GLU235 4.4 32.0 1.0 ND1 C:HIS237 4.5 29.5 1.0 CG C:HIS237 4.5 29.2 1.0 CG C:GLU235 4.6 33.8 1.0 CE C:MET269 4.7 31.2 1.0

Manganese binding site 4 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:31.7 occ:1.00 OE1 D:GLN275 2.1 29.8 1.0 OE1 D:GLU235 2.1 32.0 1.0 O D:UGY302 2.1 41.9 1.0 NE2 D:HIS241 2.4 31.0 1.0 NB D:UGY302 2.5 45.1 1.0 NE2 D:HIS237 2.5 29.6 1.0 CD2 D:HIS241 3.0 31.4 1.0 C D:UGY302 3.0 43.7 1.0 CG D:UGY302 3.1 47.1 1.0 CA D:UGY302 3.3 42.9 1.0 NE D:UGY302 3.3 47.1 1.0 CD D:GLN275 3.3 30.7 1.0 CD D:GLU235 3.3 33.7 1.0 CE1 D:HIS237 3.4 26.9 1.0 CE1 D:HIS241 3.5 32.3 1.0 CD2 D:HIS237 3.5 30.2 1.0 OE2 D:GLU235 3.9 34.5 1.0 OE D:UGY302 4.1 49.4 1.0 OXT D:UGY302 4.2 44.0 1.0 NE2 D:GLN275 4.2 32.0 1.0 CG D:GLN275 4.2 29.1 1.0 CG D:HIS241 4.2 32.6 1.0 N D:UGY302 4.3 42.6 1.0 ND1 D:HIS241 4.5 33.5 1.0 CG D:GLU235 4.5 32.7 1.0 CB D:GLU235 4.5 31.7 1.0 ND1 D:HIS237 4.6 28.7 1.0 CG D:HIS237 4.6 29.5 1.0 CD2 D:LEU289 5.0 32.3 1.0

Manganese binding site 5 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:31.8 occ:1.00 OE1 E:GLU235 2.1 28.3 1.0 OXT E:UGY302 2.1 38.9 1.0 NB E:UGY302 2.3 42.2 1.0 NE2 E:HIS241 2.3 31.9 1.0 NE2 E:HIS237 2.4 29.5 1.0 OE1 E:GLN275 2.5 31.5 1.0 C E:UGY302 3.0 41.8 1.0 CD2 E:HIS241 3.1 31.8 1.0 CA E:UGY302 3.1 42.1 1.0 CG E:UGY302 3.2 42.9 1.0 CD E:GLU235 3.3 30.1 1.0 CD2 E:HIS237 3.3 30.1 1.0 NE E:UGY302 3.4 41.4 1.0 CE1 E:HIS237 3.4 30.4 1.0 CE1 E:HIS241 3.5 30.5 1.0 CD E:GLN275 3.6 31.5 1.0 N E:UGY302 3.9 42.1 1.0 OE2 E:GLU235 4.0 29.3 1.0 O E:UGY302 4.1 41.4 1.0 NE2 E:GLN275 4.2 29.9 1.0 OE E:UGY302 4.3 43.0 1.0 CG E:HIS241 4.3 32.2 1.0 CG E:GLU235 4.4 30.1 1.0 CB E:GLU235 4.4 30.0 1.0 ND1 E:HIS241 4.5 31.4 1.0 CG E:HIS237 4.5 31.4 1.0 ND1 E:HIS237 4.5 31.0 1.0 CG E:GLN275 4.6 29.7 1.0

Manganese binding site 6 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn301 b:36.8 occ:1.00 O F:UGY302 2.2 46.4 1.0 NE2 F:HIS241 2.2 32.4 1.0 OE1 F:GLU235 2.3 38.5 1.0 NE2 F:HIS237 2.4 32.3 1.0 OE1 F:GLN275 2.4 34.1 1.0 NB F:UGY302 2.4 43.8 1.0 C F:UGY302 3.0 46.4 1.0 CD2 F:HIS241 3.1 31.4 1.0 CE1 F:HIS241 3.2 33.2 1.0 CA F:UGY302 3.3 45.6 1.0 CG F:UGY302 3.3 46.0 1.0 CD2 F:HIS237 3.3 33.9 1.0 CD F:GLU235 3.3 38.1 1.0 CE1 F:HIS237 3.4 33.7 1.0 NE F:UGY302 3.4 46.4 1.0 CD F:GLN275 3.4 32.6 1.0 OE2 F:GLU235 3.8 40.1 1.0 NE2 F:GLN275 4.0 33.3 1.0 N F:UGY302 4.1 44.7 1.0 OXT F:UGY302 4.2 47.5 1.0 CG F:HIS241 4.3 32.8 1.0 ND1 F:HIS241 4.3 34.0 1.0 OE F:UGY302 4.4 47.2 1.0 ND1 F:HIS237 4.5 34.2 1.0 CG F:HIS237 4.5 34.1 1.0 CG F:GLN275 4.5 33.2 1.0 CG F:GLU235 4.5 36.6 1.0 CB F:GLU235 4.6 35.5 1.0

Manganese binding site 7 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn301 b:31.2 occ:1.00 OE1 G:GLU235 2.2 40.5 1.0 NE2 G:HIS241 2.2 36.1 1.0 OXT G:UGY302 2.3 55.0 1.0 NE2 G:HIS237 2.3 39.2 1.0 NB G:UGY302 2.4 56.4 1.0 OE1 G:GLN275 2.5 37.5 1.0 C G:UGY302 3.1 55.1 1.0 CD G:GLN275 3.1 38.0 1.0 CD2 G:HIS241 3.1 34.9 1.0 CA G:UGY302 3.2 54.6 1.0 CE1 G:HIS241 3.2 36.4 1.0 CD2 G:HIS237 3.3 38.0 1.0 CE1 G:HIS237 3.3 37.7 1.0 CG G:UGY302 3.3 59.0 1.0 CD G:GLU235 3.4 38.7 1.0 NE G:UGY302 3.5 59.9 1.0 NE2 G:GLN275 3.5 37.7 1.0 N G:UGY302 3.9 53.1 1.0 OE2 G:GLU235 4.1 40.2 1.0 CG G:GLN275 4.1 37.9 1.0 O G:UGY302 4.2 54.9 1.0 CG G:HIS241 4.3 33.7 1.0 ND1 G:HIS241 4.3 33.8 1.0 CB G:GLU235 4.4 33.4 1.0 ND1 G:HIS237 4.4 37.6 1.0 CG G:GLU235 4.4 34.7 1.0 CG G:HIS237 4.4 37.2 1.0 OE G:UGY302 4.5 61.1 1.0

Manganese binding site 8 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn301 b:33.4 occ:1.00 OXT H:UGY302 2.1 43.7 1.0 OE1 H:GLU235 2.1 30.3 1.0 NE2 H:HIS241 2.4 33.4 1.0 NE2 H:HIS237 2.4 31.6 1.0 NB H:UGY302 2.5 46.5 1.0 OE1 H:GLN275 2.5 31.2 1.0 C H:UGY302 3.0 45.5 1.0 CD2 H:HIS241 3.1 32.3 1.0 CG H:UGY302 3.1 49.5 1.0 CA H:UGY302 3.2 45.4 1.0 CD H:GLN275 3.3 30.9 1.0 CD H:GLU235 3.3 30.9 1.0 CD2 H:HIS237 3.3 32.5 1.0 NE H:UGY302 3.3 49.2 1.0 CE1 H:HIS237 3.3 31.3 1.0 CE1 H:HIS241 3.4 32.0 1.0 NE2 H:GLN275 3.7 33.0 1.0 OE2 H:GLU235 3.8 29.3 1.0 OE H:UGY302 4.1 51.0 1.0 N H:UGY302 4.2 45.6 1.0 O H:UGY302 4.2 45.2 1.0 CG H:HIS241 4.3 32.2 1.0 ND1 H:HIS241 4.4 32.0 1.0 CG H:GLN275 4.4 31.6 1.0 ND1 H:HIS237 4.5 33.8 1.0 CG H:HIS237 4.5 32.0 1.0 CG H:GLU235 4.5 30.0 1.0 CB H:GLU235 4.6 30.6 1.0

Manganese binding site 9 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn301 b:35.9 occ:1.00 OE2 I:GLU235 2.1 40.5 1.0 OE1 I:GLN275 2.2 36.8 1.0 NE2 I:HIS241 2.3 33.7 1.0 NB I:UGY302 2.3 50.9 1.0 OXT I:UGY302 2.3 50.0 1.0 NE2 I:HIS237 2.4 35.0 1.0 CD2 I:HIS241 3.1 34.5 1.0 C I:UGY302 3.1 50.0 1.0 CA I:UGY302 3.1 49.3 1.0 CE1 I:HIS237 3.2 34.1 1.0 CG I:UGY302 3.2 53.0 1.0 CD I:GLU235 3.3 41.7 1.0 CD I:GLN275 3.3 36.4 1.0 NE I:UGY302 3.4 51.8 1.0 CE1 I:HIS241 3.4 35.0 1.0 CD2 I:HIS237 3.5 35.4 1.0 N I:UGY302 3.9 46.0 1.0 OE1 I:GLU235 4.0 44.4 1.0 NE2 I:GLN275 4.2 35.4 1.0 CG I:GLN275 4.2 34.1 1.0 CB I:GLU235 4.2 38.5 1.0 O I:UGY302 4.2 49.8 1.0 CG I:HIS241 4.3 34.6 1.0 CG I:GLU235 4.3 40.4 1.0 ND1 I:HIS237 4.4 35.2 1.0 OE I:UGY302 4.4 54.4 1.0 ND1 I:HIS241 4.4 35.3 1.0 CG I:HIS237 4.6 34.6 1.0

Manganese binding site 10 out of 16 in the Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of (S)-Ureidoglycine Aminohydrolase From Arabidopsis Thaliana in Complex with Its Substrate, (S)-Ureidoglycine within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn301 b:47.2 occ:1.00 OE2 J:GLU235 2.1 35.6 1.0 NE2 J:HIS241 2.2 46.4 1.0 NB J:UGY302 2.3 56.7 1.0 OXT J:UGY302 2.3 58.4 1.0 NE2 J:HIS237 2.6 44.3 1.0 OE1 J:GLN275 2.8 40.4 1.0 CD2 J:HIS241 3.0 47.1 1.0 C J:UGY302 3.1 57.7 1.0 CA J:UGY302 3.2 57.4 1.0 CD J:GLU235 3.2 37.5 1.0 CG J:UGY302 3.2 57.8 1.0 CE1 J:HIS241 3.2 48.0 1.0 NE J:UGY302 3.3 56.6 1.0 CE1 J:HIS237 3.4 42.6 1.0 CD J:GLN275 3.5 39.8 1.0 OE1 J:GLU235 3.7 37.9 1.0 CD2 J:HIS237 3.8 42.6 1.0 N J:UGY302 3.9 56.2 1.0 CG J:HIS241 4.2 45.4 1.0 NE2 J:GLN275 4.2 40.0 1.0 CG J:GLN275 4.2 38.6 1.0 ND1 J:HIS241 4.2 46.0 1.0 O J:UGY302 4.3 56.6 1.0 OE J:UGY302 4.4 58.4 1.0 CG J:GLU235 4.4 37.3 1.0 CB J:GLU235 4.4 38.8 1.0 ND1 J:HIS237 4.6 42.1 1.0 CG J:HIS237 4.8 41.6 1.0

I.Shin, R.Percudani, S.Rhee. Structural and Functional Insights Into (S)-Ureidoglycine Aminohydrolase, Key Enzyme of Purine Catabolism in Arabidopsis Thaliana J.Biol.Chem. V. 287 18796 2012.
ISSN: ISSN 0021-9258
PubMed: 22493446
DOI: 10.1074/JBC.M111.331819