Manganese in PDB 3e6k: X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh

All present enzymatic activity of X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh:
3.5.3.1;

The structure of X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh, PDB code: 3e6k was solved by L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.38 / 2.10
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.766, 90.766, 69.501, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 24.5

The binding sites of Manganese atom in the X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh (pdb code 3e6k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh, PDB code: 3e6k:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn323 b:22.5 occ:1.00 OD1 A:ASP124 2.1 19.9 1.0 OD2 A:ASP234 2.1 18.4 1.0 O1 A:ABH552 2.2 23.0 0.5 O3 A:ABH552 2.5 24.4 0.5 OD2 A:ASP232 2.5 18.6 1.0 OD1 A:ASP234 2.5 19.8 1.0 ND1 A:HIS126 2.6 17.1 1.0 CG A:ASP234 2.7 17.9 1.0 B A:ABH552 2.9 23.5 0.5 CG A:ASP124 3.0 21.8 1.0 OD2 A:ASP124 3.2 25.1 1.0 CE1 A:HIS126 3.4 13.1 1.0 MN A:MN324 3.5 17.6 1.0 CG A:ASP232 3.5 17.5 1.0 CG A:HIS126 3.6 15.2 1.0 O2 A:ABH552 3.9 22.2 0.5 CB A:HIS126 3.9 15.9 1.0 N A:HIS126 4.1 16.1 1.0 CE A:ABH552 4.1 22.0 0.5 OD1 A:ASP232 4.2 19.2 1.0 CB A:ASP234 4.2 15.4 1.0 N A:ALA125 4.2 17.6 1.0 CD A:ABH552 4.3 23.4 0.5 CB A:ASP124 4.4 20.6 1.0 OD2 A:ASP128 4.5 10.6 1.0 CB A:ASP232 4.5 18.0 1.0 NE2 A:HIS126 4.5 12.0 1.0 CA A:HIS126 4.6 16.1 1.0 O A:HOH626 4.6 21.2 1.0 CD2 A:HIS126 4.6 13.1 1.0 OD1 A:ASP128 4.6 14.5 1.0 CB A:ALA125 4.8 17.2 1.0 C A:ALA125 4.9 15.5 1.0 CA A:ALA125 4.9 16.9 1.0 O A:THR246 4.9 19.1 1.0 CA A:ASP124 4.9 18.7 1.0 O A:HOH625 5.0 25.6 1.0 CG A:ASP128 5.0 14.3 1.0

Manganese binding site 2 out of 4 in the X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn324 b:17.6 occ:1.00 O1 A:ABH552 2.1 23.0 0.5 OD1 A:ASP128 2.1 14.5 1.0 OD2 A:ASP124 2.1 25.1 1.0 ND1 A:HIS101 2.4 21.0 1.0 OD2 A:ASP232 2.4 18.6 1.0 O2 A:ABH552 2.6 22.2 0.5 B A:ABH552 2.9 23.5 0.5 CG A:ASP128 3.1 14.3 1.0 CG A:ASP124 3.2 21.8 1.0 CG A:HIS101 3.3 20.7 1.0 CG A:ASP232 3.4 17.5 1.0 CE1 A:HIS101 3.4 19.2 1.0 MN A:MN323 3.5 22.5 1.0 CB A:HIS101 3.5 21.5 1.0 OD2 A:ASP128 3.6 10.6 1.0 OD1 A:ASP124 3.7 19.9 1.0 O3 A:ABH552 3.7 24.4 0.5 CB A:ASP232 3.9 18.0 1.0 CE A:ABH552 4.0 22.0 0.5 O A:HIS141 4.3 14.6 1.0 OD1 A:ASP232 4.3 19.2 1.0 NE1 A:TRP122 4.4 17.8 1.0 CD2 A:HIS101 4.4 19.9 1.0 NE2 A:HIS101 4.4 18.8 1.0 CB A:ASP128 4.5 15.8 1.0 CB A:ASP124 4.5 20.6 1.0 CZ2 A:TRP122 4.7 13.2 1.0 CG A:GLU277 4.9 21.9 1.0 CE2 A:TRP122 4.9 14.5 1.0

Manganese binding site 3 out of 4 in the X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn323 b:26.4 occ:1.00 O1 B:ABH555 2.1 21.5 0.5 OD2 B:ASP234 2.2 28.9 1.0 ND1 B:HIS126 2.3 13.3 1.0 OD1 B:ASP124 2.3 17.5 1.0 OD1 B:ASP234 2.6 27.6 1.0 CG B:ASP234 2.7 28.6 1.0 OD2 B:ASP232 2.8 23.7 1.0 O3 B:ABH555 2.9 22.4 0.5 B B:ABH555 3.0 22.1 0.5 CE1 B:HIS126 3.1 16.8 1.0 CG B:ASP124 3.1 17.1 1.0 OD2 B:ASP124 3.2 20.5 1.0 CG B:ASP232 3.4 23.2 1.0 CG B:HIS126 3.5 16.9 1.0 MN B:MN324 3.5 25.6 1.0 OD1 B:ASP232 3.9 19.1 1.0 CB B:HIS126 3.9 16.2 1.0 O2 B:ABH555 4.0 20.9 0.5 N B:HIS126 4.1 15.4 1.0 CE B:ABH555 4.1 22.8 0.5 CD B:ABH555 4.1 24.9 0.5 N B:ALA125 4.2 16.3 1.0 CB B:ASP234 4.2 23.3 1.0 NE2 B:HIS126 4.3 16.7 1.0 CB B:ASP232 4.3 22.3 1.0 CD2 B:HIS126 4.5 16.2 1.0 OD1 B:ASP128 4.5 21.9 1.0 CB B:ASP124 4.5 17.8 1.0 OD2 B:ASP128 4.6 22.6 1.0 CA B:HIS126 4.6 16.8 1.0 CB B:ALA125 4.7 17.3 1.0 O B:HOH620 4.8 19.5 1.0 C B:ALA125 4.8 14.0 1.0 CA B:ALA125 4.8 15.5 1.0 O B:THR246 4.9 25.2 1.0

Manganese binding site 4 out of 4 in the X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of Human Arginase I: the Mutant D183A in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn324 b:25.6 occ:1.00 OD1 B:ASP128 2.1 21.9 1.0 O1 B:ABH555 2.1 21.5 0.5 OD2 B:ASP124 2.3 20.5 1.0 OD2 B:ASP232 2.3 23.7 1.0 O2 B:ABH555 2.3 20.9 0.5 ND1 B:HIS101 2.3 23.6 1.0 B B:ABH555 2.8 22.1 0.5 CG B:HIS101 3.2 24.0 1.0 CG B:ASP128 3.3 21.8 1.0 CE1 B:HIS101 3.3 22.3 1.0 CG B:ASP232 3.4 23.2 1.0 CG B:ASP124 3.5 17.1 1.0 CB B:HIS101 3.5 25.3 1.0 MN B:MN323 3.5 26.4 1.0 O3 B:ABH555 3.7 22.4 0.5 OD2 B:ASP128 3.8 22.6 1.0 CE B:ABH555 3.9 22.8 0.5 CB B:ASP232 3.9 22.3 1.0 OD1 B:ASP124 4.0 17.5 1.0 O B:HIS141 4.2 21.8 1.0 NE2 B:HIS101 4.3 23.4 1.0 CD2 B:HIS101 4.4 23.8 1.0 NE1 B:TRP122 4.4 15.4 1.0 CB B:ASP128 4.5 22.3 1.0 OD1 B:ASP232 4.5 19.1 1.0 CZ2 B:TRP122 4.6 14.9 1.0 CB B:ASP124 4.6 17.8 1.0 CG B:GLU277 4.8 25.0 1.0 CE2 B:TRP122 4.9 15.3 1.0 CD B:ABH555 5.0 24.9 0.5

E.Y.Shishova, L.Di Costanzo, F.A.Emig, D.E.Ash, D.W.Christianson. Probing the Specificity Determinants of Amino Acid Recognition By Arginase. Biochemistry V. 48 121 2009.
ISSN: ISSN 0006-2960
PubMed: 19093830
DOI: 10.1021/BI801911V