Manganese in PDB 6q39: Complex of Arginase 2 with Example 49

All present enzymatic activity of Complex of Arginase 2 with Example 49:
3.5.3.1;

The structure of Complex of Arginase 2 with Example 49, PDB code: 6q39 was solved by A.D.Podjarny, M.C.Van Zandt, A.Cousido-Siah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.91 / 2.21
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.303, 128.303, 159.155, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 21

The binding sites of Manganese atom in the Complex of Arginase 2 with Example 49 (pdb code 6q39). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Complex of Arginase 2 with Example 49, PDB code: 6q39:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Complex of Arginase 2 with Example 49


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Complex of Arginase 2 with Example 49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:22.9 occ:1.00 OD2 A:ASP143 2.1 24.9 1.0 OD2 A:ASP147 2.1 22.4 1.0 ND1 A:HIS120 2.2 21.5 1.0 O23 A:HDQ405 2.2 26.1 1.0 O7 A:HDQ405 2.2 20.0 1.0 OD2 A:ASP251 2.3 23.2 1.0 B6 A:HDQ405 2.9 25.1 1.0 CE1 A:HIS120 3.1 25.4 1.0 CG A:ASP143 3.1 21.6 1.0 CG A:ASP147 3.1 22.9 1.0 CG A:HIS120 3.1 20.8 1.0 CG A:ASP251 3.3 23.4 1.0 MN A:MN402 3.3 25.0 1.0 OD1 A:ASP143 3.4 22.5 1.0 OD1 A:ASP147 3.4 24.6 1.0 CB A:HIS120 3.5 22.1 1.0 CB A:ASP251 3.6 20.2 1.0 O8 A:HDQ405 3.8 23.3 1.0 C5 A:HDQ405 4.2 21.6 1.0 NE2 A:HIS120 4.2 28.1 1.0 CD2 A:HIS120 4.2 21.6 1.0 NE1 A:TRP141 4.3 26.9 1.0 OD1 A:ASP251 4.4 19.1 1.0 CB A:ASP143 4.5 22.1 1.0 CB A:ASP147 4.5 20.6 1.0 O A:HIS160 4.6 22.0 1.0 CZ2 A:TRP141 4.6 22.1 1.0 CE2 A:TRP141 4.8 20.6 1.0 CG A:GLU296 4.8 22.1 1.0 CA A:ASP251 4.9 21.9 1.0 CG2 A:VAL295 4.9 19.2 1.0 OE1 A:GLU296 4.9 26.1 1.0 CA A:HIS120 5.0 22.2 1.0

Manganese binding site 2 out of 6 in the Complex of Arginase 2 with Example 49


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Complex of Arginase 2 with Example 49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:25.0 occ:1.00 ND1 A:HIS145 2.2 23.9 1.0 OD1 A:ASP143 2.2 22.5 1.0 OD2 A:ASP253 2.2 23.4 1.0 O7 A:HDQ405 2.2 20.0 1.0 OD2 A:ASP251 2.3 23.2 1.0 OD1 A:ASP253 2.6 21.4 1.0 CG A:ASP253 2.8 30.0 1.0 O8 A:HDQ405 2.9 23.3 1.0 CE1 A:HIS145 3.0 24.7 1.0 CG A:ASP143 3.1 21.6 1.0 CG A:ASP251 3.2 23.4 1.0 B6 A:HDQ405 3.2 25.1 1.0 CG A:HIS145 3.3 22.9 1.0 MN A:MN401 3.3 22.9 1.0 OD2 A:ASP143 3.4 24.9 1.0 CB A:HIS145 3.7 22.9 1.0 OD1 A:ASP251 3.8 19.1 1.0 O23 A:HDQ405 3.9 26.1 1.0 N A:HIS145 4.0 19.8 1.0 CB A:ASP251 4.1 20.2 1.0 NE2 A:HIS145 4.2 25.0 1.0 N A:ALA144 4.2 21.7 1.0 CB A:ASP253 4.3 19.7 1.0 CD2 A:HIS145 4.3 18.6 1.0 C4 A:HDQ405 4.3 22.2 1.0 OG1 A:THR265 4.3 27.4 0.4 C5 A:HDQ405 4.3 21.6 1.0 CA A:HIS145 4.4 21.3 1.0 OD1 A:ASP147 4.5 24.6 1.0 CB A:ASP143 4.5 22.1 1.0 OD2 A:ASP147 4.7 22.4 1.0 CB A:ALA144 4.8 22.1 1.0 C A:ALA144 4.8 25.7 1.0 O A:HOH562 4.8 25.4 1.0 CA A:ALA144 4.8 24.5 1.0 CA A:ASP143 4.9 20.0 1.0

Manganese binding site 3 out of 6 in the Complex of Arginase 2 with Example 49


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Complex of Arginase 2 with Example 49 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:25.7 occ:1.00 OD2 B:ASP147 2.1 25.8 1.0 OD2 B:ASP143 2.1 22.4 1.0 O23 B:HDQ405 2.3 21.8 1.0 O7 B:HDQ405 2.3 24.0 1.0 OD2 B:ASP251 2.3 23.6 1.0 ND1 B:HIS120 2.3 23.9 1.0 B6 B:HDQ405 2.9 26.4 1.0 CG B:ASP147 3.1 28.2 1.0 CG B:ASP143 3.2 22.2 1.0 CG B:HIS120 3.2 25.4 1.0 MN B:MN402 3.3 27.0 1.0 CE1 B:HIS120 3.3 20.8 1.0 CG B:ASP251 3.3 23.6 1.0 OD1 B:ASP147 3.4 22.9 1.0 CB B:HIS120 3.4 19.4 1.0 OD1 B:ASP143 3.5 22.8 1.0 O8 B:HDQ405 3.6 24.5 1.0 CB B:ASP251 3.6 20.4 1.0 C5 B:HDQ405 4.2 24.9 1.0 NE1 B:TRP141 4.3 23.4 1.0 CD2 B:HIS120 4.4 24.8 1.0 NE2 B:HIS120 4.4 25.3 1.0 CB B:ASP147 4.5 21.3 1.0 OD1 B:ASP251 4.5 21.3 1.0 CB B:ASP143 4.5 19.7 1.0 O B:HIS160 4.6 22.9 1.0 CZ2 B:TRP141 4.7 22.7 1.0 CG B:GLU296 4.8 21.0 1.0 CE2 B:TRP141 4.9 19.6 1.0 CA B:HIS120 5.0 20.4 1.0 CA B:ASP251 5.0 17.6 1.0 OE2 B:GLU296 5.0 26.4 1.0

Manganese binding site 4 out of 6 in the Complex of Arginase 2 with Example 49


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Complex of Arginase 2 with Example 49 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:27.0 occ:1.00 OD1 B:ASP143 2.2 22.8 1.0 OD2 B:ASP253 2.2 23.1 1.0 ND1 B:HIS145 2.3 25.2 1.0 O7 B:HDQ405 2.3 24.0 1.0 OD2 B:ASP251 2.5 23.6 1.0 OD1 B:ASP253 2.6 24.5 1.0 O8 B:HDQ405 2.7 24.5 1.0 CG B:ASP253 2.7 23.0 1.0 CE1 B:HIS145 3.0 22.2 1.0 CG B:ASP143 3.1 22.2 1.0 B6 B:HDQ405 3.2 26.4 1.0 CG B:ASP251 3.3 23.6 1.0 MN B:MN401 3.3 25.7 1.0 CG B:HIS145 3.4 25.7 1.0 OD2 B:ASP143 3.4 22.4 1.0 CB B:HIS145 3.8 22.6 1.0 OD1 B:ASP251 3.8 21.3 1.0 N B:HIS145 4.0 23.3 1.0 O23 B:HDQ405 4.0 21.8 1.0 CB B:ASP251 4.2 20.4 1.0 N B:ALA144 4.2 23.4 1.0 NE2 B:HIS145 4.2 26.5 1.0 OG1 B:THR265 4.3 24.8 0.5 CB B:ASP253 4.3 21.3 1.0 C5 B:HDQ405 4.3 24.9 1.0 C4 B:HDQ405 4.3 19.6 1.0 CD2 B:HIS145 4.4 25.1 1.0 OD1 B:ASP147 4.4 22.9 1.0 CA B:HIS145 4.5 23.8 1.0 CB B:ASP143 4.5 19.7 1.0 CB B:ALA144 4.7 25.7 1.0 O B:HOH538 4.7 30.3 1.0 OD2 B:ASP147 4.7 25.8 1.0 C B:ALA144 4.8 31.7 1.0 CA B:ALA144 4.8 24.3 1.0 CA B:ASP143 4.9 18.4 1.0 C B:ASP143 5.0 23.1 1.0

Manganese binding site 5 out of 6 in the Complex of Arginase 2 with Example 49


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Complex of Arginase 2 with Example 49 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:27.6 occ:1.00 OD2 C:ASP253 2.2 26.1 1.0 OD2 C:ASP251 2.2 24.1 1.0 OD1 C:ASP143 2.2 24.6 1.0 O7 C:HDQ405 2.3 23.9 1.0 ND1 C:HIS145 2.3 22.7 1.0 OD1 C:ASP253 2.6 22.6 1.0 CG C:ASP253 2.7 30.1 1.0 O8 C:HDQ405 2.8 28.0 1.0 CG C:ASP251 3.2 25.1 1.0 CE1 C:HIS145 3.2 28.8 1.0 B6 C:HDQ405 3.2 32.3 1.0 CG C:ASP143 3.2 21.3 1.0 CG C:HIS145 3.4 29.5 1.0 MN C:MN402 3.4 26.0 1.0 OD2 C:ASP143 3.5 24.8 1.0 CB C:HIS145 3.7 27.1 1.0 OD1 C:ASP251 3.8 24.1 1.0 O23 C:HDQ405 4.0 25.8 1.0 N C:HIS145 4.0 22.4 1.0 CB C:ASP251 4.1 19.8 1.0 CB C:ASP253 4.2 23.9 1.0 N C:ALA144 4.3 22.1 1.0 C4 C:HDQ405 4.3 20.4 1.0 C5 C:HDQ405 4.3 28.2 1.0 NE2 C:HIS145 4.3 24.7 1.0 OG1 C:THR265 4.3 28.6 0.5 OD2 C:ASP147 4.4 26.1 1.0 CD2 C:HIS145 4.4 26.1 1.0 CA C:HIS145 4.5 24.1 1.0 CB C:ASP143 4.6 23.3 1.0 CB C:ALA144 4.7 21.1 1.0 C C:ALA144 4.8 23.3 1.0 O C:HOH559 4.8 28.1 1.0 CA C:ALA144 4.8 22.8 1.0 CA C:ASP143 4.9 23.8 1.0

Manganese binding site 6 out of 6 in the Complex of Arginase 2 with Example 49


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Complex of Arginase 2 with Example 49 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:26.0 occ:1.00 OD1 C:ASP147 2.1 29.8 1.0 OD2 C:ASP143 2.2 24.8 1.0 O23 C:HDQ405 2.2 25.8 1.0 ND1 C:HIS120 2.3 24.4 1.0 O7 C:HDQ405 2.3 23.9 1.0 OD2 C:ASP251 2.4 24.1 1.0 B6 C:HDQ405 2.9 32.3 1.0 CG C:ASP147 3.0 24.7 1.0 OD2 C:ASP147 3.1 26.1 1.0 CG C:HIS120 3.2 27.4 1.0 CG C:ASP143 3.2 21.3 1.0 CE1 C:HIS120 3.2 34.3 1.0 CG C:ASP251 3.4 25.1 1.0 MN C:MN401 3.4 27.6 1.0 CB C:HIS120 3.4 23.9 1.0 OD1 C:ASP143 3.5 24.6 1.0 CB C:ASP251 3.7 19.8 1.0 O8 C:HDQ405 3.7 28.0 1.0 C5 C:HDQ405 4.1 28.2 1.0 NE1 C:TRP141 4.3 25.6 1.0 CD2 C:HIS120 4.3 26.1 1.0 NE2 C:HIS120 4.3 36.0 1.0 CB C:ASP147 4.4 25.8 1.0 O C:HIS160 4.4 26.0 1.0 OD1 C:ASP251 4.5 24.1 1.0 CB C:ASP143 4.6 23.3 1.0 CZ2 C:TRP141 4.6 21.3 1.0 CE2 C:TRP141 4.8 30.0 1.0 CG C:GLU296 4.9 29.1 1.0 OE2 C:GLU296 4.9 28.7 1.0 CA C:HIS120 4.9 25.3 1.0

M.C.Van Zandt, G.E.Jagdmann, D.L.Whitehouse, M.Ji, J.Savoy, O.Potapova, A.Cousido-Siah, A.Mitschler, E.I.Howard, A.M.Pyle, A.D.Podjarny. Discovery Ofn-Substituted 3-Amino-4-(3-Boronopropyl)Pyrrolidine-3-Carboxylic Acids As Highly Potent Third-Generation Inhibitors of Human Arginase I and II. J.Med.Chem. V. 62 8164 2019.
ISSN: ISSN 0022-2623
PubMed: 31408339
DOI: 10.1021/ACS.JMEDCHEM.9B00931