Manganese in PDB 4gwc: Crystal Structure of MN2+2,ZN2+-Human Arginase I

All present enzymatic activity of Crystal Structure of MN2+2,ZN2+-Human Arginase I:
3.5.3.1;

The structure of Crystal Structure of MN2+2,ZN2+-Human Arginase I, PDB code: 4gwc was solved by E.L.D'antonio, Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.829, 90.829, 70.068, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 22.1

The structure of Crystal Structure of MN2+2,ZN2+-Human Arginase I also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of MN2+2,ZN2+-Human Arginase I (pdb code 4gwc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of MN2+2,ZN2+-Human Arginase I, PDB code: 4gwc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of MN2+2,ZN2+-Human Arginase I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of MN2+2,ZN2+-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:25.3 occ:1.00 OD1 A:ASP124 2.1 27.1 1.0 OD2 A:ASP234 2.1 23.8 1.0 ND1 A:HIS126 2.3 27.2 1.0 O A:HOH513 2.3 54.2 1.0 OD2 A:ASP232 2.4 31.2 1.0 OD1 A:ASP234 2.5 18.9 1.0 CG A:ASP234 2.7 22.0 1.0 CG A:ASP124 3.0 29.4 1.0 CE1 A:HIS126 3.2 27.4 1.0 OD2 A:ASP124 3.2 28.4 1.0 CG A:HIS126 3.3 29.0 1.0 MN A:MN402 3.3 23.9 1.0 CG A:ASP232 3.5 29.3 1.0 CB A:HIS126 3.6 29.5 1.0 N A:HIS126 3.8 26.3 1.0 O A:HOH505 4.0 41.4 1.0 N A:ALA125 4.1 22.9 1.0 OD1 A:ASP232 4.1 26.7 1.0 CB A:ASP234 4.1 22.6 1.0 O A:HOH511 4.2 31.8 1.0 CA A:HIS126 4.3 29.1 1.0 NE2 A:HIS126 4.3 26.7 1.0 OD2 A:ASP128 4.3 25.0 1.0 CD2 A:HIS126 4.4 26.6 1.0 CB A:ASP124 4.4 25.1 1.0 OG1 A:THR246 4.4 35.6 1.0 CB A:ASP232 4.5 29.0 1.0 CB A:ALA125 4.6 23.2 1.0 C A:ALA125 4.6 24.1 1.0 OD1 A:ASP128 4.7 27.3 1.0 CA A:ALA125 4.7 23.6 1.0 CA A:ASP124 4.8 23.4 1.0 C A:ASP124 4.9 22.6 1.0 CG A:ASP128 4.9 26.5 1.0 O A:HIS126 5.0 31.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of MN2+2,ZN2+-Human Arginase I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of MN2+2,ZN2+-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:23.9 occ:1.00 OD2 A:ASP124 2.0 28.4 1.0 ND1 A:HIS101 2.2 25.6 1.0 OD1 A:ASP128 2.2 27.3 1.0 OD2 A:ASP232 2.3 31.2 1.0 O A:HOH511 2.4 31.8 1.0 O A:HOH513 2.5 54.2 1.0 CE1 A:HIS101 3.1 26.9 1.0 CG A:ASP124 3.1 29.4 1.0 CG A:HIS101 3.2 25.7 1.0 CG A:ASP232 3.2 29.3 1.0 CG A:ASP128 3.2 26.5 1.0 MN A:MN401 3.3 25.3 1.0 CB A:HIS101 3.5 28.3 1.0 OD2 A:ASP128 3.5 25.0 1.0 CB A:ASP232 3.5 29.0 1.0 OD1 A:ASP124 3.6 27.1 1.0 OD1 A:ASP232 4.2 26.7 1.0 NE2 A:HIS101 4.2 26.5 1.0 CD2 A:HIS101 4.3 28.8 1.0 O A:HIS141 4.3 24.5 1.0 CB A:ASP124 4.4 25.1 1.0 NE1 A:TRP122 4.5 27.1 1.0 CB A:ASP128 4.6 26.1 1.0 OD2 A:ASP234 4.6 23.8 1.0 CZ2 A:TRP122 4.6 27.8 1.0 CG A:GLU277 4.6 29.6 1.0 O A:HOH505 4.8 41.4 1.0 OD1 A:ASP234 4.9 18.9 1.0 CA A:ASP232 4.9 26.9 1.0 CE2 A:TRP122 4.9 26.9 1.0 CA A:HIS101 5.0 28.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of MN2+2,ZN2+-Human Arginase I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of MN2+2,ZN2+-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:23.8 occ:1.00 ND1 B:HIS126 2.1 24.0 1.0 OD2 B:ASP234 2.1 30.5 1.0 OD1 B:ASP124 2.2 20.4 1.0 OD2 B:ASP232 2.5 26.6 1.0 OD1 B:ASP234 2.5 26.5 1.0 CG B:ASP234 2.6 29.4 1.0 CE1 B:HIS126 2.8 26.9 1.0 CG B:ASP124 3.0 22.0 1.0 OD2 B:ASP124 3.2 23.6 1.0 CG B:HIS126 3.2 28.4 1.0 MN B:MN402 3.2 29.0 1.0 CG B:ASP232 3.3 28.9 1.0 O B:HOH501 3.4 37.9 1.0 CB B:HIS126 3.7 27.7 1.0 OD1 B:ASP232 3.9 26.6 1.0 N B:HIS126 3.9 24.0 1.0 NE2 B:HIS126 4.0 28.2 1.0 CB B:ASP234 4.1 27.8 1.0 N B:ALA125 4.1 21.2 1.0 CD2 B:HIS126 4.2 27.9 1.0 CB B:ASP232 4.3 28.9 1.0 OD2 B:ASP128 4.3 19.5 1.0 CB B:ASP124 4.4 21.8 1.0 CA B:HIS126 4.4 24.6 1.0 OD1 B:ASP128 4.5 23.4 1.0 CB B:ALA125 4.7 20.6 1.0 C B:ALA125 4.7 23.3 1.0 CA B:ALA125 4.8 22.1 1.0 CG B:ASP128 4.8 24.1 1.0 CA B:ASP124 4.8 21.8 1.0 C B:ASP124 4.9 21.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of MN2+2,ZN2+-Human Arginase I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of MN2+2,ZN2+-Human Arginase I within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:29.0 occ:1.00 OD1 B:ASP128 2.1 23.4 1.0 OD2 B:ASP124 2.1 23.6 1.0 OD2 B:ASP232 2.2 26.6 1.0 ND1 B:HIS101 2.3 26.2 1.0 O B:HOH501 2.9 37.9 1.0 CG B:ASP128 3.1 24.1 1.0 CG B:ASP124 3.2 22.0 1.0 CG B:HIS101 3.2 27.2 1.0 CG B:ASP232 3.2 28.9 1.0 MN B:MN401 3.2 23.8 1.0 CE1 B:HIS101 3.3 23.6 1.0 CB B:HIS101 3.4 28.8 1.0 OD2 B:ASP128 3.5 19.5 1.0 OD1 B:ASP124 3.6 20.4 1.0 CB B:ASP232 3.6 28.9 1.0 OD1 B:ASP232 4.3 26.6 1.0 CD2 B:HIS101 4.3 27.3 1.0 O B:HIS141 4.4 33.5 1.0 OD2 B:ASP234 4.4 30.5 1.0 NE2 B:HIS101 4.4 23.9 1.0 CB B:ASP128 4.4 23.3 1.0 CB B:ASP124 4.4 21.8 1.0 NE1 B:TRP122 4.4 26.1 1.0 CZ2 B:TRP122 4.6 26.8 1.0 CG B:GLU277 4.7 31.3 1.0 ND1 B:HIS126 4.8 24.0 1.0 OE2 B:GLU277 4.8 35.7 1.0 CE2 B:TRP122 4.8 26.0 1.0 CA B:HIS101 4.9 30.8 1.0 OD1 B:ASP234 4.9 26.5 1.0 CA B:ASP232 4.9 29.4 1.0

E.L.D'antonio, Y.Hai, D.W.Christianson. Structure and Function of Non-Native Metal Clusters in Human Arginase I. Biochemistry V. 51 8399 2012.
ISSN: ISSN 0006-2960
PubMed: 23061982
DOI: 10.1021/BI301145N