Manganese in PDB 7lol: The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine

All present enzymatic activity of The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine:
3.5.3.11;

The structure of The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine, PDB code: 7lol was solved by P.Maturana, M.Figueroa, F.Gonzalez-Ordenes, P.Villalobos, J.Martinez-Oyanedel, E.A.Uribe, V.Castro-Fernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.79 / 1.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	81.746, 81.746, 207.436, 90, 90, 120
R / Rfree (%)	17 / 19.5

The binding sites of Manganese atom in the The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine (pdb code 7lol). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine, PDB code: 7lol:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:27.9 occ:0.81 OD2 A:ASP149 2.1 24.7 1.0 O A:HOH501 2.2 29.5 1.0 ND1 A:HIS126 2.2 25.1 1.0 O A:URE405 2.3 33.2 1.0 OD2 A:ASP153 2.3 29.9 1.0 OD2 A:ASP230 2.4 25.9 1.0 C A:URE405 2.9 19.4 1.0 CG A:ASP149 3.0 25.1 1.0 CE1 A:HIS126 3.1 26.0 1.0 CG A:HIS126 3.2 26.4 1.0 OD1 A:ASP149 3.3 23.1 1.0 MN A:MN403 3.3 26.5 1.0 CG A:ASP230 3.4 26.3 1.0 CG A:ASP153 3.4 29.8 1.0 CB A:HIS126 3.5 25.6 1.0 N1 A:URE405 3.6 30.7 1.0 N2 A:URE405 3.6 27.0 1.0 CB A:ASP230 3.7 23.9 1.0 OD1 A:ASP153 3.9 30.2 1.0 NE2 A:HIS126 4.2 26.9 1.0 CD2 A:HIS126 4.3 28.6 1.0 NE2 A:HIS147 4.3 25.2 1.0 CB A:ASP149 4.4 24.7 1.0 OD1 A:ASP230 4.5 25.5 1.0 OE2 A:GLU274 4.7 32.8 1.0 O A:HIS151 4.7 25.5 1.0 CB A:ASP153 4.7 27.4 1.0 CG A:GLU274 4.8 30.9 1.0 CE A:MET166 4.9 29.5 1.0 CB A:HIS151 4.9 25.3 1.0 O A:HOH593 4.9 34.6 1.0 CA A:HIS126 5.0 26.0 1.0

Manganese binding site 2 out of 3 in the The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:26.5 occ:1.00 OD1 A:ASP149 2.1 23.1 1.0 OD2 A:ASP232 2.2 23.8 1.0 O A:HOH501 2.2 29.5 1.0 OD2 A:ASP230 2.3 25.9 1.0 ND1 A:HIS151 2.3 25.1 1.0 OD1 A:ASP232 2.5 24.1 1.0 CG A:ASP232 2.7 24.9 1.0 N2 A:URE405 2.9 27.0 1.0 CG A:ASP149 3.1 25.1 1.0 CG A:ASP230 3.2 26.3 1.0 CE1 A:HIS151 3.2 24.5 1.0 MN A:MN402 3.3 27.9 0.8 CG A:HIS151 3.4 27.0 1.0 C A:URE405 3.4 19.4 1.0 OD2 A:ASP149 3.5 24.7 1.0 O A:URE405 3.6 33.2 1.0 OD1 A:ASP230 3.7 25.5 1.0 CB A:HIS151 3.7 25.3 1.0 N A:HIS151 4.0 24.1 1.0 N A:ALA150 4.2 21.1 1.0 CB A:ASP232 4.2 22.1 1.0 CB A:ASP230 4.2 23.9 1.0 N1 A:URE405 4.2 30.7 1.0 NE2 A:HIS151 4.3 27.4 1.0 O A:HOH530 4.4 30.9 1.0 CB A:ASP149 4.4 24.7 1.0 CD2 A:HIS151 4.4 25.8 1.0 CA A:HIS151 4.5 25.5 1.0 C A:ALA150 4.8 23.2 1.0 CA A:ASP149 4.8 22.5 1.0 CA A:ALA150 4.8 22.1 1.0 CB A:ALA150 4.8 24.6 1.0 OD2 A:ASP153 4.9 29.9 1.0 O A:HIS151 4.9 25.5 1.0 C A:ASP149 5.0 22.2 1.0

Manganese binding site 3 out of 3 in the The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Agmatinase From E. Coli at 1.8 A Displaying Urea and Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:32.3 occ:0.33 OE1 A:GLN281 2.2 31.1 1.0 O A:HOH614 2.4 34.3 1.0 CD A:GLN281 3.1 29.3 1.0 NE2 A:GLN281 3.5 30.1 1.0 O A:HOH602 4.2 44.1 1.0 CG A:GLN281 4.4 26.6 1.0 CB A:GLN281 4.7 26.1 1.0

P.Maturana, M.S.Orellana, S.M.Herrera, I.Martinez, M.Figueroa, J.Martinez-Oyanedel, V.Castro-Fernandez, E.Uribe. Crystal Structure of Escherichia Coli Agmatinase: Catalytic Mechanism and Residues Relevant For Substrate Specificity Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22094769