Manganese in PDB 1t4t: Arginase-Dinor-Noha Complex

All present enzymatic activity of Arginase-Dinor-Noha Complex:
3.5.3.1;

The structure of Arginase-Dinor-Noha Complex, PDB code: 1t4t was solved by E.Cama, S.Pethe, J.-L.Boucher, H.Shoufa, F.A.Emig, D.E.Ash, R.E.Viola, D.Mansuy, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.90 / 2.20
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	88.300, 88.300, 113.100, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 28.1

The binding sites of Manganese atom in the Arginase-Dinor-Noha Complex (pdb code 1t4t). 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-Dinor-Noha Complex, PDB code: 1t4t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Arginase-Dinor-Noha Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase-Dinor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:27.4 occ:1.00 OD2 A:ASP234 2.1 34.7 1.0 OD2 A:ASP232 2.1 29.9 1.0 ND1 A:HIS126 2.2 26.1 1.0 OD1 A:ASP124 2.4 23.1 1.0 OH1 A:DIR1000 2.4 52.5 1.0 OD1 A:ASP234 2.5 29.4 1.0 CG A:ASP234 2.6 32.5 1.0 CE1 A:HIS126 3.0 27.4 1.0 CG A:ASP232 3.1 30.0 1.0 CG A:ASP124 3.2 22.0 1.0 CG A:HIS126 3.3 26.2 1.0 NH1 A:DIR1000 3.3 52.8 1.0 MN A:MN501 3.4 29.9 1.0 OD2 A:ASP124 3.4 26.3 1.0 NH2 A:DIR1000 3.6 53.1 1.0 CB A:HIS126 3.7 26.3 1.0 OD1 A:ASP232 3.8 28.9 1.0 CD A:DIR1000 3.8 53.9 1.0 N A:HIS126 4.0 22.7 1.0 CB A:ASP234 4.1 28.0 1.0 CB A:ASP232 4.1 26.5 1.0 O A:HOH820 4.1 22.1 1.0 NE2 A:HIS126 4.2 24.1 1.0 N A:ALA125 4.2 19.0 1.0 CD2 A:HIS126 4.3 25.9 1.0 OD1 A:ASP128 4.4 31.6 1.0 O A:HOH861 4.5 28.9 1.0 CA A:HIS126 4.5 25.7 1.0 CB A:ASP124 4.5 24.1 1.0 OG1 A:THR246 4.6 36.9 1.0 OD2 A:ASP128 4.7 34.5 1.0 CA A:ASP124 4.8 24.0 1.0 C A:ALA125 4.8 21.4 1.0 CB A:ALA125 4.9 21.1 1.0 CA A:ALA125 4.9 20.6 1.0 O A:THR246 4.9 33.2 1.0 C A:ASP124 5.0 23.8 1.0 CG A:ASP128 5.0 33.7 1.0

Manganese binding site 2 out of 6 in the Arginase-Dinor-Noha Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase-Dinor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:29.9 occ:1.00 OD2 A:ASP128 2.0 34.5 1.0 OD2 A:ASP124 2.0 26.3 1.0 O A:HOH820 2.3 22.1 1.0 ND1 A:HIS101 2.3 35.1 1.0 OD2 A:ASP232 2.4 29.9 1.0 OH1 A:DIR1000 2.9 52.5 1.0 CG A:ASP128 3.0 33.7 1.0 CG A:ASP124 3.1 22.0 1.0 CG A:ASP232 3.2 30.0 1.0 CG A:HIS101 3.2 34.3 1.0 CE1 A:HIS101 3.3 33.7 1.0 OD1 A:ASP128 3.3 31.6 1.0 MN A:MN500 3.4 27.4 1.0 CB A:HIS101 3.5 33.7 1.0 CB A:ASP232 3.5 26.5 1.0 OD1 A:ASP124 3.5 23.1 1.0 NH1 A:DIR1000 4.0 52.8 1.0 NE1 A:TRP122 4.2 28.8 1.0 OD1 A:ASP232 4.3 28.9 1.0 O A:HIS141 4.4 37.1 1.0 CB A:ASP124 4.4 24.1 1.0 CB A:ASP128 4.4 31.7 1.0 CD2 A:HIS101 4.4 35.2 1.0 NE2 A:HIS101 4.4 37.6 1.0 CZ2 A:TRP122 4.6 27.1 1.0 CE2 A:TRP122 4.8 27.3 1.0 CA A:ASP232 4.8 28.6 1.0 OD2 A:ASP234 4.8 34.7 1.0 CG A:GLU277 4.9 30.5 1.0 CA A:HIS101 5.0 33.7 1.0

Manganese binding site 3 out of 6 in the Arginase-Dinor-Noha Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase-Dinor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:31.6 occ:1.00 ND1 B:HIS126 2.1 27.6 1.0 OD2 B:ASP232 2.1 27.3 1.0 OD2 B:ASP234 2.2 32.4 1.0 OD1 B:ASP124 2.3 24.6 1.0 OH1 B:DIR1001 2.4 56.9 1.0 OD1 B:ASP234 2.5 32.1 1.0 CG B:ASP234 2.7 31.7 1.0 CE1 B:HIS126 3.0 29.1 1.0 CG B:ASP124 3.1 21.2 1.0 CG B:HIS126 3.1 26.2 1.0 CG B:ASP232 3.2 28.7 1.0 NH1 B:DIR1001 3.3 59.1 1.0 OD2 B:ASP124 3.3 18.3 1.0 MN B:MN503 3.4 32.0 1.0 CB B:HIS126 3.5 25.3 1.0 NH2 B:DIR1001 3.6 58.4 1.0 CD B:DIR1001 3.8 58.0 1.0 OD1 B:ASP232 3.9 28.8 1.0 N B:HIS126 3.9 24.5 1.0 CB B:ASP232 4.1 23.4 1.0 N B:ALA125 4.1 23.0 1.0 NE2 B:HIS126 4.1 28.4 1.0 CB B:ASP234 4.2 26.1 1.0 CD2 B:HIS126 4.2 28.1 1.0 CA B:HIS126 4.3 25.4 1.0 O B:HOH790 4.4 26.9 1.0 OD1 B:ASP128 4.4 31.9 1.0 CB B:ASP124 4.5 21.7 1.0 O B:HOH860 4.6 30.2 1.0 OD2 B:ASP128 4.6 29.7 1.0 C B:ALA125 4.7 23.1 1.0 CB B:ALA125 4.8 22.7 1.0 CA B:ASP124 4.8 25.1 1.0 CA B:ALA125 4.8 24.3 1.0 C B:ASP124 4.9 25.4 1.0 CG B:ASP128 5.0 31.6 1.0

Manganese binding site 4 out of 6 in the Arginase-Dinor-Noha Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase-Dinor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:32.0 occ:1.00 OD2 B:ASP124 2.0 18.3 1.0 OD2 B:ASP128 2.1 29.7 1.0 O B:HOH790 2.2 26.9 1.0 ND1 B:HIS101 2.3 31.0 1.0 OD2 B:ASP232 2.5 27.3 1.0 OH1 B:DIR1001 2.9 56.9 1.0 CG B:ASP128 3.1 31.6 1.0 CG B:ASP124 3.1 21.2 1.0 CG B:ASP232 3.2 28.7 1.0 CG B:HIS101 3.3 32.6 1.0 CE1 B:HIS101 3.3 32.2 1.0 MN B:MN502 3.4 31.6 1.0 OD1 B:ASP128 3.4 31.9 1.0 CB B:HIS101 3.4 34.1 1.0 CB B:ASP232 3.5 23.4 1.0 OD1 B:ASP124 3.6 24.6 1.0 NH1 B:DIR1001 4.0 59.1 1.0 NE1 B:TRP122 4.2 26.7 1.0 OD1 B:ASP232 4.3 28.8 1.0 O B:HIS141 4.4 34.7 1.0 CB B:ASP124 4.4 21.7 1.0 CB B:ASP128 4.4 31.1 1.0 CD2 B:HIS101 4.4 31.9 1.0 NE2 B:HIS101 4.4 33.6 1.0 CZ2 B:TRP122 4.6 25.5 1.0 CE2 B:TRP122 4.8 24.6 1.0 CA B:ASP232 4.8 24.6 1.0 CG B:GLU277 4.9 30.6 1.0 OD2 B:ASP234 4.9 32.4 1.0 CA B:HIS101 5.0 34.3 1.0

Manganese binding site 5 out of 6 in the Arginase-Dinor-Noha Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase-Dinor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn504 b:25.1 occ:1.00 OD2 C:ASP232 2.0 19.6 1.0 OD2 C:ASP234 2.2 29.5 1.0 ND1 C:HIS126 2.2 21.8 1.0 OD1 C:ASP124 2.4 27.1 1.0 OH1 C:DIR1002 2.4 48.2 1.0 OD1 C:ASP234 2.5 26.5 1.0 CG C:ASP234 2.7 30.2 1.0 CE1 C:HIS126 3.0 24.3 1.0 CG C:ASP232 3.1 26.3 1.0 CG C:ASP124 3.2 22.9 1.0 CG C:HIS126 3.3 22.7 1.0 NH1 C:DIR1002 3.3 48.8 1.0 MN C:MN505 3.4 28.9 1.0 OD2 C:ASP124 3.4 19.6 1.0 NH2 C:DIR1002 3.5 52.7 1.0 CB C:HIS126 3.7 22.6 1.0 CD C:DIR1002 3.8 52.2 1.0 OD1 C:ASP232 3.8 25.6 1.0 N C:HIS126 4.0 22.8 1.0 CB C:ASP232 4.1 24.4 1.0 CB C:ASP234 4.2 26.6 1.0 NE2 C:HIS126 4.2 23.6 1.0 N C:ALA125 4.2 21.3 1.0 CD2 C:HIS126 4.3 22.4 1.0 O C:HOH791 4.3 20.9 1.0 OD1 C:ASP128 4.4 27.3 1.0 CA C:HIS126 4.5 23.4 1.0 OG1 C:THR246 4.5 29.1 1.0 CB C:ASP124 4.6 24.9 1.0 OD2 C:ASP128 4.6 28.3 1.0 C C:ALA125 4.8 21.9 1.0 CA C:ASP124 4.9 23.4 1.0 CB C:ALA125 4.9 20.9 1.0 CA C:ALA125 4.9 22.3 1.0 CG C:ASP128 4.9 27.6 1.0 C C:ASP124 5.0 24.7 1.0 O C:HOH803 5.0 17.1 1.0

Manganese binding site 6 out of 6 in the Arginase-Dinor-Noha Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase-Dinor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn505 b:28.9 occ:1.00 OD2 C:ASP128 2.1 28.3 1.0 OD2 C:ASP124 2.1 19.6 1.0 O C:HOH791 2.2 20.9 1.0 ND1 C:HIS101 2.3 29.6 1.0 OD2 C:ASP232 2.5 19.6 1.0 OH1 C:DIR1002 3.0 48.2 1.0 CG C:ASP128 3.1 27.6 1.0 CG C:HIS101 3.2 30.7 1.0 CG C:ASP124 3.2 22.9 1.0 CG C:ASP232 3.3 26.3 1.0 CE1 C:HIS101 3.3 30.2 1.0 CB C:HIS101 3.4 30.9 1.0 MN C:MN504 3.4 25.1 1.0 OD1 C:ASP128 3.5 27.3 1.0 CB C:ASP232 3.5 24.4 1.0 OD1 C:ASP124 3.6 27.1 1.0 NH1 C:DIR1002 4.1 48.8 1.0 NE1 C:TRP122 4.2 27.3 1.0 OD1 C:ASP232 4.3 25.6 1.0 CD2 C:HIS101 4.3 29.5 1.0 O C:HIS141 4.4 33.2 1.0 NE2 C:HIS101 4.4 32.1 1.0 CB C:ASP128 4.4 29.4 1.0 CB C:ASP124 4.5 24.9 1.0 CZ2 C:TRP122 4.5 24.1 1.0 CE2 C:TRP122 4.7 26.3 1.0 CA C:ASP232 4.8 27.1 1.0 CG C:GLU277 4.8 28.5 1.0 CA C:HIS101 4.9 32.0 1.0 OD2 C:ASP234 5.0 29.5 1.0

E.Cama, S.Pethe, J.-L.Boucher, S.Han, F.A.Emig, D.E.Ash, R.E.Viola, D.Mansuy, D.W.Christianson. Inhibitor Coordination Interactions in the Binuclear Manganese Cluster of Arginase Biochemistry V. 43 8987 2004.
ISSN: ISSN 0006-2960
PubMed: 15248756
DOI: 10.1021/BI0491705