Manganese in PDB 6q37: Complex of Arginase 2 with Example 23

All present enzymatic activity of Complex of Arginase 2 with Example 23:
3.5.3.1;

The structure of Complex of Arginase 2 with Example 23, PDB code: 6q37 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)	26.50 / 2.21
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.162, 128.162, 158.985, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 18.9

The binding sites of Manganese atom in the Complex of Arginase 2 with Example 23 (pdb code 6q37). 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 23, PDB code: 6q37:
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 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:20.4 occ:1.00 OD2 A:ASP143 2.1 21.7 1.0 OD2 A:ASP147 2.1 19.7 1.0 ND1 A:HIS120 2.2 18.4 1.0 O16 A:HE8405 2.2 16.0 1.0 O8 A:HE8405 2.3 20.0 1.0 OD2 A:ASP251 2.3 17.6 1.0 B6 A:HE8405 2.7 20.9 1.0 CG A:ASP147 3.1 21.7 1.0 CG A:ASP143 3.1 20.0 1.0 CE1 A:HIS120 3.1 21.7 1.0 CG A:HIS120 3.2 19.3 1.0 MN A:MN402 3.3 21.3 1.0 CG A:ASP251 3.3 18.4 1.0 OD1 A:ASP147 3.4 21.6 1.0 OD1 A:ASP143 3.4 20.2 1.0 CB A:HIS120 3.5 19.0 1.0 O7 A:HE8405 3.5 19.1 1.0 CB A:ASP251 3.6 17.8 1.0 C5 A:HE8405 4.2 18.8 1.0 NE2 A:HIS120 4.2 23.0 1.0 CD2 A:HIS120 4.3 15.7 1.0 NE1 A:TRP141 4.3 27.6 1.0 OD1 A:ASP251 4.4 18.5 1.0 CB A:ASP147 4.5 17.8 1.0 CB A:ASP143 4.5 17.2 1.0 O A:HIS160 4.5 22.6 1.0 CZ2 A:TRP141 4.6 17.6 1.0 CG A:GLU296 4.7 20.6 1.0 CE2 A:TRP141 4.8 18.3 1.0 OE2 A:GLU296 4.9 22.9 1.0 CA A:ASP251 4.9 20.7 1.0 CG2 A:VAL295 5.0 18.1 1.0 OD2 A:ASP253 5.0 21.8 1.0 CA A:HIS120 5.0 18.8 1.0

Manganese binding site 2 out of 6 in the Complex of Arginase 2 with Example 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:21.3 occ:1.00 OD2 A:ASP253 2.2 21.8 1.0 O16 A:HE8405 2.2 16.0 1.0 OD1 A:ASP143 2.2 20.2 1.0 ND1 A:HIS145 2.2 19.4 1.0 OD2 A:ASP251 2.3 17.6 1.0 OD1 A:ASP253 2.6 16.3 1.0 CG A:ASP253 2.7 24.2 1.0 O7 A:HE8405 2.8 19.1 1.0 CE1 A:HIS145 3.1 19.8 1.0 CG A:ASP251 3.1 18.4 1.0 B6 A:HE8405 3.1 20.9 1.0 CG A:ASP143 3.2 20.0 1.0 MN A:MN401 3.3 20.4 1.0 CG A:HIS145 3.3 21.1 1.0 OD2 A:ASP143 3.4 21.7 1.0 OD1 A:ASP251 3.7 18.5 1.0 CB A:HIS145 3.7 19.6 1.0 O8 A:HE8405 4.0 20.0 1.0 N A:HIS145 4.0 18.4 1.0 CB A:ASP251 4.0 17.8 1.0 NE2 A:HIS145 4.2 20.8 1.0 CB A:ASP253 4.3 16.6 1.0 N A:ALA144 4.3 20.6 1.0 OG1 A:THR265 4.3 21.3 0.3 C5 A:HE8405 4.3 18.8 1.0 C4 A:HE8405 4.4 22.5 1.0 CD2 A:HIS145 4.4 16.8 1.0 OD1 A:ASP147 4.5 21.6 1.0 CA A:HIS145 4.5 17.3 1.0 CB A:ASP143 4.5 17.2 1.0 CB A:ALA144 4.7 17.1 1.0 OD2 A:ASP147 4.8 19.7 1.0 O A:HOH544 4.8 20.6 1.0 C A:ALA144 4.8 21.2 1.0 CA A:ALA144 4.8 18.4 1.0 CA A:ASP143 4.9 18.4 1.0

Manganese binding site 3 out of 6 in the Complex of Arginase 2 with Example 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:21.9 occ:1.00 OD2 B:ASP147 2.1 22.0 1.0 OD2 B:ASP143 2.1 17.0 1.0 OD2 B:ASP251 2.2 17.7 1.0 O16 B:HE8405 2.3 19.6 1.0 O8 B:HE8405 2.3 20.9 1.0 ND1 B:HIS120 2.3 18.3 1.0 B6 B:HE8405 2.7 21.4 1.0 CG B:ASP147 3.0 25.7 1.0 CG B:ASP143 3.1 18.8 1.0 CG B:HIS120 3.3 22.7 1.0 OD1 B:ASP147 3.3 19.2 1.0 CG B:ASP251 3.3 21.9 1.0 MN B:MN402 3.3 22.4 1.0 CE1 B:HIS120 3.3 18.6 1.0 OD1 B:ASP143 3.4 15.8 1.0 CB B:HIS120 3.5 18.3 1.0 O7 B:HE8405 3.5 18.9 1.0 CB B:ASP251 3.6 18.5 1.0 C5 B:HE8405 4.2 23.1 1.0 NE1 B:TRP141 4.3 20.5 1.0 CB B:ASP147 4.4 20.9 1.0 NE2 B:HIS120 4.4 19.6 1.0 CD2 B:HIS120 4.4 18.2 1.0 OD1 B:ASP251 4.4 17.9 1.0 CB B:ASP143 4.5 18.7 1.0 O B:HIS160 4.5 21.3 1.0 CZ2 B:TRP141 4.6 19.9 1.0 CG B:GLU296 4.8 19.8 1.0 CE2 B:TRP141 4.8 19.4 1.0 CA B:ASP251 5.0 16.9 1.0

Manganese binding site 4 out of 6 in the Complex of Arginase 2 with Example 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:22.4 occ:1.00 O16 B:HE8405 2.1 19.6 1.0 OD1 B:ASP143 2.1 15.8 1.0 OD2 B:ASP253 2.2 20.2 1.0 ND1 B:HIS145 2.3 19.3 1.0 OD2 B:ASP251 2.4 17.7 1.0 OD1 B:ASP253 2.5 20.2 1.0 CG B:ASP253 2.7 20.1 1.0 O7 B:HE8405 2.8 18.9 1.0 CE1 B:HIS145 3.1 19.2 1.0 B6 B:HE8405 3.1 21.4 1.0 CG B:ASP143 3.1 18.8 1.0 CG B:ASP251 3.2 21.9 1.0 MN B:MN401 3.3 21.9 1.0 CG B:HIS145 3.4 22.1 1.0 OD2 B:ASP143 3.4 17.0 1.0 OD1 B:ASP251 3.7 17.9 1.0 CB B:HIS145 3.8 20.5 1.0 O8 B:HE8405 4.0 20.9 1.0 N B:HIS145 4.0 23.2 1.0 OG1 B:THR265 4.1 22.8 0.3 CB B:ASP251 4.1 18.5 1.0 N B:ALA144 4.2 19.8 1.0 NE2 B:HIS145 4.2 22.6 1.0 CB B:ASP253 4.3 17.8 1.0 C5 B:HE8405 4.3 23.1 1.0 C4 B:HE8405 4.4 19.1 1.0 CD2 B:HIS145 4.4 19.1 1.0 OD1 B:ASP147 4.4 19.2 1.0 CB B:ASP143 4.5 18.7 1.0 CA B:HIS145 4.5 19.5 1.0 CB B:ALA144 4.7 20.4 1.0 O B:HOH513 4.7 25.6 1.0 OD2 B:ASP147 4.8 22.0 1.0 CA B:ALA144 4.8 22.6 1.0 C B:ALA144 4.8 29.5 1.0 CA B:ASP143 4.9 18.5 1.0

Manganese binding site 5 out of 6 in the Complex of Arginase 2 with Example 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:23.0 occ:1.00 OD2 C:ASP253 2.2 20.4 1.0 O16 C:HE8406 2.2 19.6 1.0 OD2 C:ASP251 2.2 19.5 1.0 OD1 C:ASP143 2.3 21.1 1.0 ND1 C:HIS145 2.3 18.4 1.0 OD1 C:ASP253 2.6 17.8 1.0 CG C:ASP253 2.7 23.0 1.0 O7 C:HE8406 2.8 20.9 1.0 CG C:ASP251 3.1 22.2 1.0 B6 C:HE8406 3.2 23.3 1.0 CE1 C:HIS145 3.2 24.1 1.0 CG C:ASP143 3.2 20.6 1.0 MN C:MN402 3.3 21.3 1.0 CG C:HIS145 3.4 26.0 1.0 OD2 C:ASP143 3.4 20.7 1.0 CB C:HIS145 3.7 22.7 1.0 OD1 C:ASP251 3.8 19.7 1.0 O8 C:HE8406 4.0 22.5 1.0 N C:HIS145 4.0 20.4 1.0 CB C:ASP251 4.1 18.3 1.0 CB C:ASP253 4.2 21.9 1.0 N C:ALA144 4.3 18.2 1.0 NE2 C:HIS145 4.3 21.8 1.0 C5 C:HE8406 4.4 21.7 1.0 C4 C:HE8406 4.4 19.0 1.0 OG1 C:THR265 4.4 20.3 0.4 OD1 C:ASP147 4.4 22.4 1.0 CD2 C:HIS145 4.4 19.4 1.0 CA C:HIS145 4.5 22.3 1.0 CB C:ASP143 4.6 19.3 1.0 CB C:ALA144 4.7 19.7 1.0 O C:HOH550 4.8 21.3 1.0 C C:ALA144 4.8 19.9 1.0 CA C:ALA144 4.9 22.4 1.0 OD2 C:ASP147 4.9 24.8 1.0 CA C:ASP143 5.0 22.8 1.0

Manganese binding site 6 out of 6 in the Complex of Arginase 2 with Example 23


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 23 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:21.3 occ:1.00 OD2 C:ASP147 2.1 24.8 1.0 OD2 C:ASP143 2.2 20.7 1.0 ND1 C:HIS120 2.2 18.8 1.0 O16 C:HE8406 2.2 19.6 1.0 O8 C:HE8406 2.3 22.5 1.0 OD2 C:ASP251 2.4 19.5 1.0 B6 C:HE8406 2.7 23.3 1.0 CG C:ASP147 3.0 22.0 1.0 CG C:HIS120 3.1 23.5 1.0 CE1 C:HIS120 3.1 21.4 1.0 OD1 C:ASP147 3.2 22.4 1.0 CG C:ASP143 3.2 20.6 1.0 CG C:ASP251 3.3 22.2 1.0 MN C:MN401 3.3 23.0 1.0 CB C:HIS120 3.4 22.2 1.0 O7 C:HE8406 3.6 20.9 1.0 CB C:ASP251 3.6 18.3 1.0 OD1 C:ASP143 3.6 21.1 1.0 C5 C:HE8406 4.2 21.7 1.0 NE2 C:HIS120 4.2 19.8 1.0 CD2 C:HIS120 4.3 20.7 1.0 NE1 C:TRP141 4.4 21.0 1.0 CB C:ASP147 4.4 23.1 1.0 OD1 C:ASP251 4.5 19.7 1.0 O C:HIS160 4.5 21.6 1.0 CB C:ASP143 4.5 19.3 1.0 CZ2 C:TRP141 4.6 20.5 1.0 CG C:GLU296 4.8 23.9 1.0 CE2 C:TRP141 4.9 23.0 1.0 OE2 C:GLU296 4.9 22.7 1.0 CA C:HIS120 4.9 23.1 1.0 CA C:ASP251 4.9 19.1 1.0 CG2 C:VAL295 5.0 20.1 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