Manganese in PDB 3e6v: X-Ray Structure of Human Arginase I-D183N Mutant: the Complex with Abh

All present enzymatic activity of X-Ray Structure of Human Arginase I-D183N Mutant: the Complex with Abh:
3.5.3.1;

The structure of X-Ray Structure of Human Arginase I-D183N Mutant: the Complex with Abh, PDB code: 3e6v 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)	30.00 / 1.72
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	91.036, 91.036, 69.773, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 23.2

The binding sites of Manganese atom in the X-Ray Structure of Human Arginase I-D183N Mutant: the Complex with Abh (pdb code 3e6v). 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-D183N Mutant: the Complex with Abh, PDB code: 3e6v:
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-D183N Mutant: the 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-D183N Mutant: the Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn514 b:12.0 occ:1.00 O1 A:ABH552 2.1 13.7 1.0 OD1 A:ASP124 2.1 8.9 1.0 ND1 A:HIS126 2.3 12.7 1.0 OD2 A:ASP232 2.4 10.8 1.0 OD1 A:ASP234 2.4 6.9 1.0 OD2 A:ASP234 2.5 9.3 1.0 CG A:ASP234 2.8 6.8 1.0 CE1 A:HIS126 2.9 12.0 1.0 O3 A:ABH552 3.0 13.9 1.0 CG A:ASP124 3.1 12.3 1.0 B A:ABH552 3.1 10.9 1.0 CG A:ASP232 3.3 11.1 1.0 MN A:MN515 3.4 11.7 1.0 OD2 A:ASP124 3.4 12.2 1.0 CG A:HIS126 3.4 11.7 1.0 OD1 A:ASP232 3.9 10.3 1.0 CB A:HIS126 4.0 11.7 1.0 N A:HIS126 4.0 10.4 1.0 OG1 A:THR246 4.0 19.0 1.0 O2 A:ABH552 4.1 14.6 1.0 N A:ALA125 4.1 7.8 1.0 NE2 A:HIS126 4.1 13.4 1.0 CE A:ABH552 4.2 10.5 1.0 CB A:ASP232 4.2 12.6 1.0 CD A:ABH552 4.2 9.9 1.0 CB A:ASP234 4.3 7.7 1.0 CD2 A:HIS126 4.4 11.8 1.0 CB A:ASP124 4.5 9.7 1.0 OD1 A:ASP128 4.5 6.8 1.0 CB A:ALA125 4.6 10.1 1.0 CA A:HIS126 4.6 10.3 1.0 O A:HOH570 4.6 6.2 1.0 CA A:ALA125 4.8 8.3 1.0 OD2 A:ASP128 4.8 8.7 1.0 C A:ALA125 4.8 8.6 1.0 CA A:ASP124 4.9 8.5 1.0 C A:ASP124 5.0 6.5 1.0

Manganese binding site 2 out of 4 in the X-Ray Structure of Human Arginase I-D183N Mutant: the 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-D183N Mutant: the Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn515 b:11.7 occ:1.00 OD2 A:ASP124 2.1 12.2 1.0 O1 A:ABH552 2.1 13.7 1.0 OD2 A:ASP128 2.1 8.7 1.0 ND1 A:HIS101 2.3 8.6 1.0 O2 A:ABH552 2.3 14.6 1.0 OD2 A:ASP232 2.4 10.8 1.0 B A:ABH552 2.8 10.9 1.0 CG A:ASP128 3.1 7.6 1.0 CG A:ASP124 3.1 12.3 1.0 CG A:HIS101 3.2 9.6 1.0 CE1 A:HIS101 3.3 6.2 1.0 MN A:MN514 3.4 12.0 1.0 CG A:ASP232 3.4 11.1 1.0 OD1 A:ASP128 3.4 6.8 1.0 OD1 A:ASP124 3.4 8.9 1.0 CB A:HIS101 3.5 9.3 1.0 O3 A:ABH552 3.6 13.9 1.0 CB A:ASP232 3.7 12.6 1.0 CE A:ABH552 4.0 10.5 1.0 O A:HIS141 4.4 6.8 1.0 NE2 A:HIS101 4.4 6.3 1.0 CD2 A:HIS101 4.4 8.4 1.0 NE1 A:TRP122 4.4 12.3 1.0 CB A:ASP124 4.4 9.7 1.0 OD1 A:ASP232 4.5 10.3 1.0 CB A:ASP128 4.5 9.4 1.0 CZ2 A:TRP122 4.7 11.4 1.0 CG A:GLU277 4.7 11.2 1.0 CE2 A:TRP122 4.9 11.0 1.0 OE2 A:GLU277 5.0 11.0 1.0 CA A:HIS101 5.0 10.0 1.0

Manganese binding site 3 out of 4 in the X-Ray Structure of Human Arginase I-D183N Mutant: the 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-D183N Mutant: the Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn514 b:17.2 occ:1.00 OD1 B:ASP234 2.1 9.5 1.0 OD1 B:ASP124 2.2 8.0 1.0 O1 B:ABH555 2.2 20.0 1.0 ND1 B:HIS126 2.4 10.4 1.0 OD2 B:ASP234 2.5 9.8 1.0 O3 B:ABH555 2.6 20.2 1.0 OD2 B:ASP232 2.6 13.0 1.0 CG B:ASP234 2.6 13.1 1.0 B B:ABH555 2.9 21.1 1.0 CG B:ASP124 3.1 9.8 1.0 CG B:ASP232 3.2 12.0 1.0 CE1 B:HIS126 3.3 11.8 1.0 MN B:MN515 3.3 17.5 1.0 OD2 B:ASP124 3.3 9.5 1.0 CG B:HIS126 3.4 12.7 1.0 OD1 B:ASP232 3.6 10.3 1.0 CB B:HIS126 3.8 11.0 1.0 O2 B:ABH555 3.9 20.9 1.0 N B:HIS126 4.1 10.3 1.0 CE B:ABH555 4.1 20.3 1.0 CB B:ASP234 4.1 11.1 1.0 CB B:ASP232 4.2 13.0 1.0 CD B:ABH555 4.3 20.4 1.0 N B:ALA125 4.3 9.3 1.0 NE2 B:HIS126 4.4 11.0 1.0 OD1 B:ASP128 4.5 9.8 1.0 CB B:ASP124 4.5 8.2 1.0 CD2 B:HIS126 4.5 10.1 1.0 CA B:HIS126 4.5 11.1 1.0 O B:HOH698 4.6 17.9 1.0 CB B:ALA125 4.8 8.4 1.0 OD2 B:ASP128 4.8 7.7 1.0 C B:ALA125 4.9 8.6 1.0 CA B:ALA125 5.0 8.3 1.0 O B:THR246 5.0 18.0 1.0

Manganese binding site 4 out of 4 in the X-Ray Structure of Human Arginase I-D183N Mutant: the 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-D183N Mutant: the Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn515 b:17.5 occ:1.00 OD2 B:ASP124 2.1 9.5 1.0 O1 B:ABH555 2.1 20.0 1.0 OD2 B:ASP128 2.2 7.7 1.0 OD2 B:ASP232 2.3 13.0 1.0 ND1 B:HIS101 2.4 22.8 1.0 O2 B:ABH555 2.5 20.9 1.0 B B:ABH555 2.9 21.1 1.0 CG B:ASP128 3.1 8.3 1.0 CG B:ASP124 3.1 9.8 1.0 MN B:MN514 3.3 17.2 1.0 CG B:HIS101 3.3 20.3 1.0 CG B:ASP232 3.3 12.0 1.0 CE1 B:HIS101 3.3 21.1 1.0 OD1 B:ASP128 3.4 9.8 1.0 OD1 B:ASP124 3.5 8.0 1.0 CB B:HIS101 3.5 20.1 1.0 CB B:ASP232 3.6 13.0 1.0 O3 B:ABH555 3.7 20.2 1.0 CE B:ABH555 4.1 20.3 1.0 NE1 B:TRP122 4.3 11.6 1.0 O B:HIS141 4.4 16.8 1.0 CB B:ASP124 4.4 8.2 1.0 NE2 B:HIS101 4.5 19.9 1.0 CZ2 B:TRP122 4.5 14.1 1.0 OD1 B:ASP232 4.5 10.3 1.0 CD2 B:HIS101 4.5 21.7 1.0 CB B:ASP128 4.5 11.1 1.0 CE2 B:TRP122 4.7 12.9 1.0 CG B:GLU277 4.7 15.8 1.0 CA B:ASP232 4.9 13.0 1.0

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