Manganese in PDB 1t4r: Arginase-Descarboxy-Nor-Noha Complex

All present enzymatic activity of Arginase-Descarboxy-Nor-Noha Complex:
3.5.3.1;

The structure of Arginase-Descarboxy-Nor-Noha Complex, PDB code: 1t4r 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 / 2.60
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	88.300, 88.300, 113.200, 90.00, 90.00, 120.00
R / Rfree (%)	25.5 / 29.1

The binding sites of Manganese atom in the Arginase-Descarboxy-Nor-Noha Complex (pdb code 1t4r). 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-Descarboxy-Nor-Noha Complex, PDB code: 1t4r:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Arginase-Descarboxy-Nor-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-Descarboxy-Nor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:30.4 occ:1.00 ND1 A:HIS126 2.0 45.8 1.0 OD2 A:ASP234 2.2 42.1 1.0 OD1 A:ASP124 2.3 40.2 1.0 OD2 A:ASP232 2.3 39.3 1.0 OD1 A:ASP234 2.4 40.2 1.0 O16 A:AHI1000 2.5 62.4 1.0 CG A:ASP234 2.7 41.8 1.0 CE1 A:HIS126 2.8 44.2 1.0 MN A:MN501 3.0 44.6 1.0 CG A:HIS126 3.1 44.8 1.0 CG A:ASP124 3.1 38.7 1.0 CG A:ASP232 3.1 37.5 1.0 OD2 A:ASP124 3.3 38.5 1.0 NP1 A:AHI1000 3.4 64.6 1.0 N10 A:AHI1000 3.4 65.3 1.0 CB A:HIS126 3.7 43.9 1.0 C09 A:AHI1000 3.7 65.8 1.0 OD1 A:ASP232 3.7 36.6 1.0 N A:HIS126 3.8 42.5 1.0 NE2 A:HIS126 4.0 44.0 1.0 OG1 A:THR246 4.0 45.0 1.0 CB A:ASP232 4.1 37.4 1.0 CD2 A:HIS126 4.1 43.5 1.0 CB A:ASP234 4.2 39.0 1.0 N A:ALA125 4.2 40.8 1.0 CA A:HIS126 4.4 44.2 1.0 OD1 A:ASP128 4.5 48.5 1.0 CB A:ASP124 4.5 40.8 1.0 O A:HOH766 4.6 88.8 1.0 O A:HOH691 4.7 29.9 1.0 C A:ALA125 4.7 42.6 1.0 OD2 A:ASP128 4.8 50.2 1.0 CB A:ALA125 4.8 40.0 1.0 CA A:ALA125 4.9 40.9 1.0 CA A:ASP124 4.9 41.1 1.0 N08 A:AHI1000 4.9 65.6 1.0 O A:HIS126 4.9 46.2 1.0

Manganese binding site 2 out of 6 in the Arginase-Descarboxy-Nor-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-Descarboxy-Nor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:44.6 occ:1.00 OD2 A:ASP124 2.1 38.5 1.0 OD2 A:ASP232 2.2 39.3 1.0 OD2 A:ASP128 2.3 50.2 1.0 O16 A:AHI1000 2.3 62.4 1.0 ND1 A:HIS101 2.4 49.8 1.0 O A:HOH766 2.8 88.8 1.0 MN A:MN500 3.0 30.4 1.0 CG A:ASP124 3.1 38.7 1.0 CG A:ASP128 3.1 49.6 1.0 CG A:ASP232 3.2 37.5 1.0 OD1 A:ASP128 3.3 48.5 1.0 CE1 A:HIS101 3.3 48.7 1.0 CG A:HIS101 3.4 50.9 1.0 NP1 A:AHI1000 3.5 64.6 1.0 OD1 A:ASP124 3.5 40.2 1.0 CB A:ASP232 3.6 37.4 1.0 CB A:HIS101 3.6 50.9 1.0 OD1 A:ASP232 4.3 36.6 1.0 NE1 A:TRP122 4.4 40.8 1.0 CB A:ASP124 4.4 40.8 1.0 NE2 A:HIS101 4.5 50.9 1.0 CD2 A:HIS101 4.5 50.6 1.0 C09 A:AHI1000 4.5 65.8 1.0 OD2 A:ASP234 4.6 42.1 1.0 CB A:ASP128 4.6 49.5 1.0 ND1 A:HIS126 4.6 45.8 1.0 O A:HIS141 4.7 51.4 1.0 CZ2 A:TRP122 4.7 41.2 1.0 N10 A:AHI1000 4.7 65.3 1.0 CB A:HIS126 4.8 43.9 1.0 CG A:GLU277 4.8 47.5 1.0 OD1 A:ASP234 4.8 40.2 1.0 O A:HIS126 4.8 46.2 1.0 OE2 A:GLU277 4.9 45.3 1.0 CE2 A:TRP122 4.9 41.4 1.0 CA A:ASP232 4.9 39.9 1.0

Manganese binding site 3 out of 6 in the Arginase-Descarboxy-Nor-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-Descarboxy-Nor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:33.1 occ:1.00 ND1 B:HIS126 2.0 37.9 1.0 OD1 B:ASP124 2.1 30.7 1.0 OD2 B:ASP232 2.2 38.2 1.0 OD2 B:ASP234 2.2 36.5 1.0 OD1 B:ASP234 2.4 38.2 1.0 O16 B:AHI1001 2.5 62.6 1.0 CG B:ASP234 2.6 37.6 1.0 CE1 B:HIS126 2.9 39.2 1.0 MN B:MN503 3.0 35.3 1.0 CG B:ASP124 3.0 29.3 1.0 CG B:ASP232 3.0 35.3 1.0 CG B:HIS126 3.1 36.8 1.0 OD2 B:ASP124 3.2 27.1 1.0 NP1 B:AHI1001 3.4 64.6 1.0 N10 B:AHI1001 3.6 65.1 1.0 CB B:HIS126 3.6 35.4 1.0 OD1 B:ASP232 3.7 36.4 1.0 C09 B:AHI1001 3.8 65.5 1.0 N B:HIS126 3.9 35.5 1.0 CB B:ASP232 3.9 34.4 1.0 NE2 B:HIS126 4.0 38.6 1.0 N B:ALA125 4.1 30.7 1.0 CB B:ASP234 4.1 35.3 1.0 CD2 B:HIS126 4.2 36.6 1.0 OG1 B:THR246 4.2 44.9 1.0 CA B:HIS126 4.4 36.0 1.0 CB B:ASP124 4.4 29.3 1.0 OD1 B:ASP128 4.5 41.4 1.0 O B:HOH716 4.6 87.4 1.0 O B:HOH698 4.7 17.4 1.0 OD2 B:ASP128 4.7 45.7 1.0 CB B:ALA125 4.8 32.2 1.0 C B:ALA125 4.8 33.6 1.0 CA B:ASP124 4.8 29.8 1.0 CA B:ALA125 4.9 33.2 1.0 O B:HIS126 4.9 35.3 1.0 C B:ASP124 5.0 30.6 1.0 O B:ASP234 5.0 34.5 1.0

Manganese binding site 4 out of 6 in the Arginase-Descarboxy-Nor-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-Descarboxy-Nor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:35.3 occ:1.00 OD2 B:ASP124 2.1 27.1 1.0 O16 B:AHI1001 2.2 62.6 1.0 OD2 B:ASP128 2.2 45.7 1.0 OD2 B:ASP232 2.3 38.2 1.0 ND1 B:HIS101 2.5 42.5 1.0 O B:HOH716 2.8 87.4 1.0 MN B:MN502 3.0 33.1 1.0 CG B:ASP128 3.1 42.7 1.0 CG B:ASP124 3.1 29.3 1.0 OD1 B:ASP128 3.3 41.4 1.0 CG B:ASP232 3.3 35.3 1.0 NP1 B:AHI1001 3.4 64.6 1.0 OD1 B:ASP124 3.4 30.7 1.0 CG B:HIS101 3.4 43.4 1.0 CE1 B:HIS101 3.4 42.0 1.0 CB B:HIS101 3.6 44.7 1.0 CB B:ASP232 3.7 34.4 1.0 OD1 B:ASP232 4.4 36.4 1.0 C09 B:AHI1001 4.5 65.5 1.0 CB B:ASP124 4.5 29.3 1.0 O B:HIS141 4.5 45.6 1.0 NE1 B:TRP122 4.5 32.4 1.0 ND1 B:HIS126 4.5 37.9 1.0 CB B:ASP128 4.5 42.9 1.0 NE2 B:HIS101 4.5 42.8 1.0 OD2 B:ASP234 4.6 36.5 1.0 CD2 B:HIS101 4.6 42.0 1.0 CB B:HIS126 4.6 35.4 1.0 N10 B:AHI1001 4.7 65.1 1.0 CG B:GLU277 4.7 37.0 1.0 CZ2 B:TRP122 4.7 31.0 1.0 OE2 B:GLU277 4.8 37.3 1.0 OD1 B:ASP234 4.8 38.2 1.0 O B:HIS126 4.8 35.3 1.0 CE2 B:TRP122 5.0 30.6 1.0 CG B:HIS126 5.0 36.8 1.0

Manganese binding site 5 out of 6 in the Arginase-Descarboxy-Nor-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-Descarboxy-Nor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn504 b:26.6 occ:1.00 ND1 C:HIS126 2.1 30.9 1.0 OD1 C:ASP124 2.1 35.0 1.0 OD2 C:ASP232 2.1 32.0 1.0 OD2 C:ASP234 2.3 35.0 1.0 OD1 C:ASP234 2.4 34.0 1.0 O16 C:AHI1002 2.5 62.8 1.0 CG C:ASP234 2.6 35.2 1.0 CE1 C:HIS126 2.9 30.4 1.0 CG C:ASP124 3.0 34.1 1.0 MN C:MN505 3.0 38.8 1.0 CG C:ASP232 3.0 30.2 1.0 CG C:HIS126 3.2 29.4 1.0 OD2 C:ASP124 3.2 33.7 1.0 NP1 C:AHI1002 3.4 64.7 1.0 N10 C:AHI1002 3.6 65.5 1.0 CB C:HIS126 3.6 28.5 1.0 OD1 C:ASP232 3.7 27.5 1.0 C09 C:AHI1002 3.8 65.4 1.0 N C:HIS126 3.9 32.4 1.0 CB C:ASP232 4.0 29.3 1.0 NE2 C:HIS126 4.1 31.4 1.0 OG1 C:THR246 4.1 37.8 1.0 N C:ALA125 4.1 32.2 1.0 CB C:ASP234 4.2 33.3 1.0 CD2 C:HIS126 4.2 29.4 1.0 CA C:HIS126 4.4 32.0 1.0 CB C:ASP124 4.4 32.1 1.0 OD1 C:ASP128 4.5 38.0 1.0 O C:HOH768 4.6 87.6 1.0 OD2 C:ASP128 4.7 38.8 1.0 C C:ALA125 4.8 32.9 1.0 CA C:ASP124 4.8 31.7 1.0 CB C:ALA125 4.8 33.5 1.0 CA C:ALA125 4.8 33.4 1.0 O C:HIS126 4.9 33.6 1.0 C C:ASP124 4.9 32.8 1.0

Manganese binding site 6 out of 6 in the Arginase-Descarboxy-Nor-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-Descarboxy-Nor-Noha Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn505 b:38.8 occ:1.00 OD2 C:ASP124 2.2 33.7 1.0 OD2 C:ASP128 2.2 38.8 1.0 O16 C:AHI1002 2.3 62.8 1.0 OD2 C:ASP232 2.3 32.0 1.0 ND1 C:HIS101 2.4 31.5 1.0 O C:HOH768 2.7 87.6 1.0 MN C:MN504 3.0 26.6 1.0 CG C:ASP128 3.1 36.7 1.0 CG C:ASP124 3.1 34.1 1.0 CG C:ASP232 3.3 30.2 1.0 CG C:HIS101 3.3 33.1 1.0 CE1 C:HIS101 3.4 32.8 1.0 OD1 C:ASP128 3.4 38.0 1.0 NP1 C:AHI1002 3.4 64.7 1.0 OD1 C:ASP124 3.5 35.0 1.0 CB C:HIS101 3.5 35.4 1.0 CB C:ASP232 3.7 29.3 1.0 OD1 C:ASP232 4.4 27.5 1.0 NE2 C:HIS101 4.5 33.4 1.0 NE1 C:TRP122 4.5 34.1 1.0 CD2 C:HIS101 4.5 32.5 1.0 CB C:ASP124 4.5 32.1 1.0 O C:HIS141 4.5 39.7 1.0 C09 C:AHI1002 4.5 65.4 1.0 CB C:ASP128 4.5 40.0 1.0 ND1 C:HIS126 4.6 30.9 1.0 CG C:GLU277 4.7 37.4 1.0 OD2 C:ASP234 4.7 35.0 1.0 CB C:HIS126 4.7 28.5 1.0 N10 C:AHI1002 4.8 65.5 1.0 CZ2 C:TRP122 4.8 34.8 1.0 OE2 C:GLU277 4.8 35.4 1.0 O C:HIS126 4.8 33.6 1.0 OD1 C:ASP234 4.9 34.0 1.0 CE2 C:TRP122 5.0 33.6 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