Manganese in PDB 1t4p: Arginase-Dehydro-Abh Complex

All present enzymatic activity of Arginase-Dehydro-Abh Complex:
3.5.3.1;

The structure of Arginase-Dehydro-Abh Complex, PDB code: 1t4p was solved by E.Cama, S.Pethe, J.-L.Boucher, S.Han, 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)	30.00 / 2.60
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	88.400, 88.400, 110.520, 90.00, 90.00, 120.00
R / Rfree (%)	26.4 / 29.2

The binding sites of Manganese atom in the Arginase-Dehydro-Abh Complex (pdb code 1t4p). 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-Dehydro-Abh Complex, PDB code: 1t4p:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Arginase-Dehydro-Abh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase-Dehydro-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:37.0 occ:1.00 OD2 A:ASP232 2.1 40.5 1.0 O12 A:2BH1000 2.2 27.5 1.0 OD2 A:ASP128 2.3 34.8 1.0 ND1 A:HIS101 2.3 42.0 1.0 OD2 A:ASP124 2.4 28.5 1.0 O11 A:2BH1000 2.5 28.1 1.0 B A:2BH1000 2.9 29.6 1.0 CG A:HIS101 3.2 42.7 1.0 CG A:ASP232 3.2 40.9 1.0 CG A:ASP128 3.3 35.5 1.0 MN A:MN504 3.3 35.2 1.0 CE1 A:HIS101 3.3 39.4 1.0 CB A:HIS101 3.4 44.5 1.0 CG A:ASP124 3.5 32.6 1.0 OD1 A:ASP128 3.6 34.7 1.0 CB A:ASP232 3.6 40.1 1.0 O13 A:2BH1000 3.7 32.8 1.0 OD1 A:ASP124 3.8 36.1 1.0 C09 A:2BH1000 3.9 28.4 1.0 OD1 A:ASP232 4.3 44.9 1.0 O A:HIS141 4.4 40.9 1.0 CD2 A:HIS101 4.4 41.8 1.0 NE2 A:HIS101 4.4 40.4 1.0 OE2 A:GLU277 4.4 50.2 1.0 NE1 A:TRP122 4.5 37.8 1.0 CG A:GLU277 4.5 44.8 1.0 OD2 A:ASP234 4.6 39.6 1.0 CB A:ASP128 4.6 36.9 1.0 CZ2 A:TRP122 4.6 34.3 1.0 CB A:ASP124 4.8 33.5 1.0 CA A:HIS101 4.9 47.7 1.0 CE2 A:TRP122 4.9 35.4 1.0 C08 A:2BH1000 4.9 28.8 1.0 CA A:ASP232 4.9 31.2 1.0 CD A:GLU277 5.0 47.8 1.0 ND1 A:HIS126 5.0 38.1 1.0

Manganese binding site 2 out of 6 in the Arginase-Dehydro-Abh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase-Dehydro-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn504 b:35.2 occ:1.00 O12 A:2BH1000 2.0 27.5 1.0 OD2 A:ASP234 2.1 39.6 1.0 ND1 A:HIS126 2.2 38.1 1.0 OD2 A:ASP232 2.4 40.5 1.0 OD1 A:ASP234 2.4 40.5 1.0 OD1 A:ASP124 2.4 36.1 1.0 CG A:ASP234 2.5 38.8 1.0 CE1 A:HIS126 3.0 38.3 1.0 CG A:ASP232 3.1 40.9 1.0 B A:2BH1000 3.3 29.6 1.0 O13 A:2BH1000 3.3 32.8 1.0 CG A:ASP124 3.3 32.6 1.0 MN A:MN502 3.3 37.0 1.0 CG A:HIS126 3.3 38.9 1.0 OD2 A:ASP124 3.4 28.5 1.0 OD1 A:ASP232 3.5 44.9 1.0 CB A:HIS126 3.8 37.7 1.0 CB A:ASP234 4.0 36.5 1.0 N A:HIS126 4.1 36.2 1.0 CB A:ASP232 4.1 40.1 1.0 O11 A:2BH1000 4.1 28.1 1.0 N A:ALA125 4.2 36.4 1.0 C09 A:2BH1000 4.2 28.4 1.0 NE2 A:HIS126 4.2 40.0 1.0 C08 A:2BH1000 4.3 28.8 1.0 CD2 A:HIS126 4.4 38.5 1.0 O A:HOH708 4.4 31.7 1.0 OD1 A:ASP128 4.5 34.7 1.0 CA A:HIS126 4.5 37.3 1.0 CB A:ASP124 4.6 33.5 1.0 CB A:ALA125 4.6 34.9 1.0 OD2 A:ASP128 4.7 34.8 1.0 C A:ALA125 4.9 35.1 1.0 CA A:ALA125 4.9 35.8 1.0

Manganese binding site 3 out of 6 in the Arginase-Dehydro-Abh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase-Dehydro-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn500 b:27.8 occ:1.00 O12 B:2BH1001 2.0 27.5 1.0 ND1 B:HIS126 2.1 31.1 1.0 OD2 B:ASP234 2.2 37.5 1.0 OD2 B:ASP232 2.3 40.9 1.0 OD1 B:ASP124 2.4 38.6 1.0 OD1 B:ASP234 2.5 36.6 1.0 CG B:ASP234 2.7 34.2 1.0 CE1 B:HIS126 3.0 32.6 1.0 CG B:ASP232 3.2 40.3 1.0 CG B:HIS126 3.2 30.5 1.0 B B:2BH1001 3.2 29.6 1.0 CG B:ASP124 3.2 35.6 1.0 MN B:MN501 3.3 30.5 1.0 O13 B:2BH1001 3.3 32.8 1.0 OD2 B:ASP124 3.4 32.0 1.0 CB B:HIS126 3.6 29.2 1.0 OD1 B:ASP232 3.7 40.3 1.0 N B:HIS126 4.0 36.7 1.0 O11 B:2BH1001 4.1 28.1 1.0 C09 B:2BH1001 4.1 28.4 1.0 NE2 B:HIS126 4.2 32.4 1.0 CB B:ASP234 4.2 33.4 1.0 CB B:ASP232 4.2 38.0 1.0 N B:ALA125 4.2 34.7 1.0 C08 B:2BH1001 4.2 28.8 1.0 CD2 B:HIS126 4.3 29.9 1.0 O B:HOH739 4.3 20.9 1.0 OD1 B:ASP128 4.4 28.4 1.0 CA B:HIS126 4.4 35.2 1.0 CB B:ALA125 4.6 35.9 1.0 CB B:ASP124 4.6 36.5 1.0 OD2 B:ASP128 4.6 22.6 1.0 C B:ALA125 4.8 34.3 1.0 CA B:ALA125 4.9 34.0 1.0 O B:HIS126 4.9 35.2 1.0 CG B:ASP128 5.0 26.7 1.0

Manganese binding site 4 out of 6 in the Arginase-Dehydro-Abh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase-Dehydro-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:30.5 occ:1.00 OD2 B:ASP232 2.1 40.9 1.0 O12 B:2BH1001 2.2 27.5 1.0 ND1 B:HIS101 2.3 25.5 1.0 OD2 B:ASP128 2.3 22.6 1.0 OD2 B:ASP124 2.4 32.0 1.0 O11 B:2BH1001 2.5 28.1 1.0 B B:2BH1001 2.9 29.6 1.0 CG B:ASP232 3.1 40.3 1.0 CG B:HIS101 3.2 27.3 1.0 MN B:MN500 3.3 27.8 1.0 CE1 B:HIS101 3.3 25.2 1.0 CG B:ASP128 3.3 26.7 1.0 CB B:HIS101 3.3 32.5 1.0 CG B:ASP124 3.4 35.6 1.0 CB B:ASP232 3.6 38.0 1.0 OD1 B:ASP128 3.6 28.4 1.0 OD1 B:ASP124 3.7 38.6 1.0 O13 B:2BH1001 3.7 32.8 1.0 C09 B:2BH1001 4.0 28.4 1.0 OD1 B:ASP232 4.3 40.3 1.0 CD2 B:HIS101 4.3 25.5 1.0 NE2 B:HIS101 4.4 25.5 1.0 OE2 B:GLU277 4.4 44.5 1.0 O B:HIS141 4.5 34.6 1.0 CG B:GLU277 4.5 42.6 1.0 NE1 B:TRP122 4.5 22.5 1.0 CB B:ASP128 4.6 31.2 1.0 CZ2 B:TRP122 4.7 21.2 1.0 OD2 B:ASP234 4.7 37.5 1.0 CB B:ASP124 4.7 36.5 1.0 CA B:HIS101 4.9 42.2 1.0 CA B:ASP232 4.9 34.7 1.0 C08 B:2BH1001 4.9 28.8 1.0 CE2 B:TRP122 5.0 22.4 1.0 CD B:GLU277 5.0 45.1 1.0 ND1 B:HIS126 5.0 31.1 1.0

Manganese binding site 5 out of 6 in the Arginase-Dehydro-Abh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase-Dehydro-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn503 b:42.3 occ:1.00 OD2 C:ASP232 2.1 40.9 1.0 O12 C:2BH1002 2.2 27.5 1.0 OD2 C:ASP124 2.2 38.5 1.0 ND1 C:HIS101 2.3 42.0 1.0 OD2 C:ASP128 2.3 37.7 1.0 O11 C:2BH1002 2.5 28.1 1.0 B C:2BH1002 2.9 29.6 1.0 CG C:ASP232 3.2 40.9 1.0 CG C:HIS101 3.2 41.8 1.0 CG C:ASP128 3.2 38.8 1.0 MN C:MN505 3.3 44.6 1.0 CG C:ASP124 3.3 40.5 1.0 CE1 C:HIS101 3.3 40.9 1.0 CB C:HIS101 3.4 44.4 1.0 OD1 C:ASP128 3.5 41.8 1.0 CB C:ASP232 3.6 40.5 1.0 OD1 C:ASP124 3.6 40.4 1.0 O13 C:2BH1002 3.7 32.8 1.0 C09 C:2BH1002 4.0 28.4 1.0 OD1 C:ASP232 4.3 41.3 1.0 CD2 C:HIS101 4.4 41.0 1.0 NE2 C:HIS101 4.4 41.7 1.0 NE1 C:TRP122 4.4 34.2 1.0 O C:HIS141 4.4 46.8 1.0 OE2 C:GLU277 4.5 53.3 1.0 OD2 C:ASP234 4.6 37.9 1.0 CB C:ASP128 4.6 39.4 1.0 CG C:GLU277 4.6 50.8 1.0 CB C:ASP124 4.6 40.6 1.0 CZ2 C:TRP122 4.7 32.6 1.0 CA C:ASP232 4.9 41.6 1.0 CE2 C:TRP122 4.9 33.6 1.0 C08 C:2BH1002 4.9 28.8 1.0 CA C:HIS101 4.9 48.2 1.0

Manganese binding site 6 out of 6 in the Arginase-Dehydro-Abh Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase-Dehydro-Abh Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn505 b:44.6 occ:1.00 O12 C:2BH1002 2.0 27.5 1.0 OD2 C:ASP234 2.1 37.9 1.0 ND1 C:HIS126 2.2 45.1 1.0 OD1 C:ASP124 2.3 40.4 1.0 OD2 C:ASP232 2.5 40.9 1.0 OD1 C:ASP234 2.5 38.6 1.0 CG C:ASP234 2.6 38.5 1.0 CE1 C:HIS126 3.1 43.9 1.0 CG C:ASP124 3.2 40.5 1.0 O13 C:2BH1002 3.2 32.8 1.0 B C:2BH1002 3.2 29.6 1.0 CG C:ASP232 3.2 40.9 1.0 MN C:MN503 3.3 42.3 1.0 CG C:HIS126 3.3 44.0 1.0 OD2 C:ASP124 3.4 38.5 1.0 OD1 C:ASP232 3.7 41.3 1.0 CB C:HIS126 3.7 41.9 1.0 N C:HIS126 4.0 40.5 1.0 O11 C:2BH1002 4.1 28.1 1.0 CB C:ASP234 4.1 37.2 1.0 C09 C:2BH1002 4.1 28.4 1.0 CB C:ASP232 4.2 40.5 1.0 N C:ALA125 4.2 38.1 1.0 C08 C:2BH1002 4.2 28.8 1.0 NE2 C:HIS126 4.3 43.2 1.0 OD1 C:ASP128 4.3 41.8 1.0 CD2 C:HIS126 4.4 41.8 1.0 CA C:HIS126 4.5 40.3 1.0 CB C:ASP124 4.6 40.6 1.0 O C:HOH774 4.6 29.0 1.0 CB C:ALA125 4.7 40.4 1.0 OD2 C:ASP128 4.8 37.7 1.0 C C:ALA125 4.8 39.6 1.0 CA C:ALA125 4.9 38.5 1.0 O C:HIS126 5.0 41.0 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