Manganese in PDB 1t5f: Arginase I-Aoh Complex

All present enzymatic activity of Arginase I-Aoh Complex:
3.5.3.1;

The structure of Arginase I-Aoh Complex, PDB code: 1t5f was solved by H.Shin, E.Cama, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.59 / 2.20
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	87.900, 87.900, 105.200, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 24.1

The binding sites of Manganese atom in the Arginase I-Aoh Complex (pdb code 1t5f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Arginase I-Aoh Complex, PDB code: 1t5f:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Arginase I-Aoh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase I-Aoh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn320 b:25.6 occ:1.00 O1 A:DHH1000 2.0 30.3 1.0 OD2 A:ASP124 2.1 16.6 1.0 ND1 A:HIS101 2.1 25.6 1.0 OD2 A:ASP232 2.2 19.0 1.0 OD2 A:ASP128 2.3 19.9 1.0 O A:HOH843 2.6 46.1 1.0 CG A:HIS101 3.1 24.2 1.0 CG A:ASP232 3.1 19.1 1.0 CE1 A:HIS101 3.1 24.4 1.0 CG A:ASP124 3.1 17.4 1.0 O2 A:DHH1000 3.2 30.3 1.0 C10 A:DHH1000 3.2 57.6 1.0 CB A:ASP232 3.3 18.6 1.0 MN A:MN1 3.3 20.7 1.0 CB A:HIS101 3.4 22.8 1.0 CG A:ASP128 3.4 23.7 1.0 OD1 A:ASP124 3.5 16.3 1.0 OD1 A:ASP128 3.8 23.9 1.0 C09 A:DHH1000 4.2 57.8 1.0 NE2 A:HIS101 4.2 23.7 1.0 CD2 A:HIS101 4.2 24.0 1.0 OD1 A:ASP232 4.3 19.1 1.0 CB A:ASP124 4.3 18.5 1.0 NE1 A:TRP122 4.3 21.1 1.0 CG A:GLU277 4.6 24.6 1.0 CZ2 A:TRP122 4.6 20.3 1.0 CA A:ASP232 4.6 17.3 1.0 OE2 A:GLU277 4.6 27.3 1.0 CB A:ASP128 4.7 22.8 1.0 CE2 A:TRP122 4.8 19.3 1.0 O A:ALA141 4.8 23.5 1.0 CA A:HIS101 4.9 22.4 1.0 OD2 A:ASP234 4.9 21.0 1.0

Manganese binding site 2 out of 6 in the Arginase I-Aoh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase I-Aoh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:20.7 occ:1.00 OD1 A:ASP124 2.2 16.3 1.0 OD2 A:ASP234 2.2 21.0 1.0 O A:HOH843 2.3 46.1 1.0 ND1 A:HIS126 2.3 19.4 1.0 OD2 A:ASP232 2.3 19.0 1.0 OD1 A:ASP234 2.4 17.9 1.0 O1 A:DHH1000 2.4 30.3 1.0 CG A:ASP234 2.6 16.7 1.0 CE1 A:HIS126 3.0 20.4 1.0 CG A:ASP124 3.1 17.4 1.0 CG A:ASP232 3.1 19.1 1.0 C10 A:DHH1000 3.2 57.6 1.0 OD2 A:ASP124 3.3 16.6 1.0 MN A:MN320 3.3 25.6 1.0 CG A:HIS126 3.4 18.3 1.0 OD1 A:ASP232 3.7 19.1 1.0 CB A:HIS126 3.9 17.5 1.0 C09 A:DHH1000 4.0 57.8 1.0 CB A:ASP232 4.0 18.6 1.0 N A:HIS126 4.1 16.2 1.0 CB A:ASP234 4.1 17.6 1.0 N A:ALA125 4.2 17.9 1.0 O2 A:DHH1000 4.2 30.3 1.0 NE2 A:HIS126 4.2 18.9 1.0 CB A:ASP124 4.4 18.5 1.0 CD2 A:HIS126 4.4 17.2 1.0 OD1 A:ASP128 4.6 23.9 1.0 C08 A:DHH1000 4.6 57.0 1.0 CA A:HIS126 4.6 17.5 1.0 OD2 A:ASP128 4.7 19.9 1.0 O A:HOH731 4.8 16.7 1.0 CB A:ALA125 4.8 14.9 1.0 CA A:ASP124 4.8 18.5 1.0 C A:ALA125 4.9 17.3 1.0 CA A:ALA125 4.9 16.2 1.0 C A:ASP124 5.0 19.5 1.0

Manganese binding site 3 out of 6 in the Arginase I-Aoh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase I-Aoh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn5 b:24.8 occ:1.00 O1 B:DHH1001 2.0 30.3 1.0 OD2 B:ASP124 2.0 19.6 1.0 ND1 B:HIS101 2.2 22.2 1.0 OD2 B:ASP128 2.2 20.8 1.0 OD2 B:ASP232 2.3 12.2 1.0 O B:HOH844 2.5 35.4 1.0 CG B:ASP124 3.1 16.8 1.0 CE1 B:HIS101 3.1 21.4 1.0 CG B:HIS101 3.1 21.9 1.0 C10 B:DHH1001 3.2 55.1 1.0 CG B:ASP232 3.2 14.7 1.0 O2 B:DHH1001 3.2 30.3 1.0 CG B:ASP128 3.3 21.9 1.0 MN B:MN3 3.3 19.6 1.0 CB B:ASP232 3.4 15.4 1.0 CB B:HIS101 3.4 21.9 1.0 OD1 B:ASP124 3.5 18.9 1.0 OD1 B:ASP128 3.6 22.6 1.0 C09 B:DHH1001 4.1 55.4 1.0 NE2 B:HIS101 4.2 21.0 1.0 NE1 B:TRP122 4.3 20.2 1.0 CD2 B:HIS101 4.3 20.9 1.0 CB B:ASP124 4.3 16.8 1.0 OD1 B:ASP232 4.4 15.3 1.0 CZ2 B:TRP122 4.6 20.5 1.0 CB B:ASP128 4.6 20.2 1.0 CG B:GLU277 4.7 23.8 1.0 OE2 B:GLU277 4.7 27.0 1.0 O B:ALA141 4.7 23.4 1.0 CA B:ASP232 4.7 15.7 1.0 CE2 B:TRP122 4.7 20.1 1.0 OD2 B:ASP234 4.9 21.2 1.0 CA B:HIS101 4.9 22.1 1.0 ND1 B:HIS126 5.0 19.1 1.0

Manganese binding site 4 out of 6 in the Arginase I-Aoh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase I-Aoh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn3 b:19.6 occ:1.00 OD2 B:ASP234 2.1 21.2 1.0 OD1 B:ASP124 2.2 18.9 1.0 OD2 B:ASP232 2.2 12.2 1.0 ND1 B:HIS126 2.3 19.1 1.0 O B:HOH844 2.3 35.4 1.0 OD1 B:ASP234 2.4 18.9 1.0 O1 B:DHH1001 2.4 30.3 1.0 CG B:ASP234 2.6 17.7 1.0 CE1 B:HIS126 3.0 18.0 1.0 CG B:ASP232 3.0 14.7 1.0 CG B:ASP124 3.1 16.8 1.0 C10 B:DHH1001 3.2 55.1 1.0 MN B:MN5 3.3 24.8 1.0 OD2 B:ASP124 3.3 19.6 1.0 CG B:HIS126 3.5 19.2 1.0 OD1 B:ASP232 3.6 15.3 1.0 CB B:HIS126 3.9 16.6 1.0 C09 B:DHH1001 4.0 55.4 1.0 CB B:ASP232 4.0 15.4 1.0 CB B:ASP234 4.1 15.9 1.0 N B:HIS126 4.2 16.3 1.0 O2 B:DHH1001 4.2 30.3 1.0 N B:ALA125 4.2 15.6 1.0 NE2 B:HIS126 4.2 18.8 1.0 O B:HOH757 4.4 24.2 1.0 CB B:ASP124 4.4 16.8 1.0 CD2 B:HIS126 4.5 19.4 1.0 OD1 B:ASP128 4.6 22.6 1.0 C08 B:DHH1001 4.6 54.5 1.0 CA B:HIS126 4.7 17.2 1.0 OD2 B:ASP128 4.7 20.8 1.0 CA B:ASP124 4.8 17.4 1.0 CB B:ALA125 4.9 12.5 1.0 CA B:ALA125 5.0 15.1 1.0 C B:ALA125 5.0 15.2 1.0 C B:ASP124 5.0 17.3 1.0

Manganese binding site 5 out of 6 in the Arginase I-Aoh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase I-Aoh Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn2 b:18.4 occ:1.00 OD1 C:ASP124 2.1 21.1 1.0 OD2 C:ASP234 2.2 17.7 1.0 OD2 C:ASP232 2.2 13.1 1.0 ND1 C:HIS126 2.3 18.2 1.0 O C:HOH835 2.3 29.5 1.0 OD1 C:ASP234 2.4 15.0 1.0 O1 C:DHH1002 2.4 30.3 1.0 CG C:ASP234 2.6 16.6 1.0 CE1 C:HIS126 3.0 16.6 1.0 CG C:ASP124 3.0 20.9 1.0 CG C:ASP232 3.0 14.4 1.0 C10 C:DHH1002 3.2 36.1 1.0 MN C:MN4 3.3 20.4 1.0 OD2 C:ASP124 3.3 20.9 1.0 CG C:HIS126 3.4 18.5 1.0 OD1 C:ASP232 3.6 15.6 1.0 CB C:HIS126 3.9 17.6 1.0 C09 C:DHH1002 4.0 36.6 1.0 CB C:ASP232 4.0 14.5 1.0 N C:HIS126 4.1 16.9 1.0 N C:ALA125 4.1 17.3 1.0 CB C:ASP234 4.1 15.7 1.0 NE2 C:HIS126 4.2 15.7 1.0 O2 C:DHH1002 4.3 30.3 1.0 CB C:ASP124 4.4 18.4 1.0 CD2 C:HIS126 4.4 18.9 1.0 OD1 C:ASP128 4.5 20.0 1.0 CA C:HIS126 4.6 17.8 1.0 C08 C:DHH1002 4.7 35.8 1.0 OD2 C:ASP128 4.7 21.5 1.0 CB C:ALA125 4.7 18.1 1.0 CA C:ASP124 4.7 17.3 1.0 O C:HOH671 4.8 22.8 1.0 CA C:ALA125 4.9 17.9 1.0 C C:ALA125 4.9 17.1 1.0 C C:ASP124 4.9 17.3 1.0

Manganese binding site 6 out of 6 in the Arginase I-Aoh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase I-Aoh Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn4 b:20.4 occ:1.00 O1 C:DHH1002 1.9 30.3 1.0 OD2 C:ASP124 2.1 20.9 1.0 ND1 C:HIS101 2.2 23.6 1.0 OD2 C:ASP232 2.2 13.1 1.0 OD2 C:ASP128 2.3 21.5 1.0 O C:HOH835 2.4 29.5 1.0 CG C:ASP124 3.1 20.9 1.0 C10 C:DHH1002 3.1 36.1 1.0 CG C:ASP232 3.1 14.4 1.0 CG C:HIS101 3.1 22.8 1.0 O2 C:DHH1002 3.1 30.3 1.0 CE1 C:HIS101 3.2 22.2 1.0 MN C:MN2 3.3 18.4 1.0 CG C:ASP128 3.3 22.2 1.0 CB C:HIS101 3.4 21.1 1.0 CB C:ASP232 3.4 14.5 1.0 OD1 C:ASP124 3.5 21.1 1.0 OD1 C:ASP128 3.7 20.0 1.0 C09 C:DHH1002 4.0 36.6 1.0 OD1 C:ASP232 4.3 15.6 1.0 CD2 C:HIS101 4.3 22.8 1.0 NE2 C:HIS101 4.3 23.9 1.0 CB C:ASP124 4.4 18.4 1.0 NE1 C:TRP122 4.4 18.8 1.0 OE2 C:GLU277 4.6 26.3 1.0 CG C:GLU277 4.6 22.9 1.0 CB C:ASP128 4.6 21.4 1.0 CZ2 C:TRP122 4.6 17.3 1.0 CA C:ASP232 4.7 14.0 1.0 O C:ALA141 4.7 20.3 1.0 CE2 C:TRP122 4.9 19.5 1.0 CA C:HIS101 4.9 21.3 1.0 OD2 C:ASP234 4.9 17.7 1.0 ND1 C:HIS126 5.0 18.2 1.0

H.Shin, E.Cama, D.W.Christianson. Design of Amino Acid Aldehydes As Transition-State Analogue Inhibitors of Arginase J.Am.Chem.Soc. V. 126 10278 2004.
ISSN: ISSN 0002-7863
PubMed: 15315440
DOI: 10.1021/JA047788W