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Manganese in PDB 3dj8: Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I

Enzymatic activity of Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I

All present enzymatic activity of Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I:
3.5.3.1;

Protein crystallography data

The structure of Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I, PDB code: 3dj8 was solved by L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.51
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.623, 90.623, 69.560, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 19.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I (pdb code 3dj8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I, PDB code: 3dj8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3dj8

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Manganese binding site 1 out of 4 in the Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with 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 Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn514

b:16.9
occ:1.00
 OD1 A:ASP124 2.1 15.3 1.0
OD1 A:ASP234 2.3 16.6 1.0
ND1 A:HIS126 2.3 15.6 1.0
OD2 A:ASP232 2.3 16.0 1.0
OD2 A:ASP234 2.4 14.1 1.0
OF A:EXY650 2.5 24.5 1.0
CG A:ASP234 2.7 15.8 1.0
CE1 A:HIS126 3.0 14.0 1.0
CG A:ASP124 3.1 14.1 1.0
CG A:ASP232 3.2 17.1 1.0
CF A:EXY650 3.3 24.4 1.0
MN A:MN515 3.4 15.6 1.0
CG A:HIS126 3.4 15.1 1.0
OD2 A:ASP124 3.4 15.9 1.0
OD1 A:ASP232 3.8 17.2 1.0
CB A:HIS126 3.9 16.5 1.0
CH A:EXY650 3.9 24.4 1.0
N A:HIS126 3.9 13.1 1.0
N A:ALA125 4.0 12.6 1.0
CB A:ASP234 4.2 16.1 1.0
OG1 A:THR246 4.2 19.2 1.0
CB A:ASP232 4.2 17.7 1.0
NE2 A:HIS126 4.2 16.8 1.0
CE A:EXY650 4.4 18.8 1.0
CD2 A:HIS126 4.4 15.1 1.0
CB A:ASP124 4.4 14.3 1.0
CA A:HIS126 4.5 14.9 1.0
OD1 A:ASP128 4.5 12.8 1.0
CD A:EXY650 4.6 19.3 1.0
CB A:ALA125 4.6 14.0 1.0
O A:HOH689 4.6 17.4 1.0
C A:ALA125 4.7 11.8 1.0
CA A:ALA125 4.7 12.9 1.0
CA A:ASP124 4.8 13.9 1.0
OD2 A:ASP128 4.8 18.1 1.0
C A:ASP124 4.9 12.8 1.0

Manganese binding site 2 out of 4 in 3dj8

Go back to Manganese Binding Sites List in 3dj8
Manganese binding site 2 out of 4 in the Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with 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 Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn515

b:15.6
occ:1.00
 OD2 A:ASP124 2.0 15.9 1.0
OD2 A:ASP128 2.1 18.1 1.0
OF A:EXY650 2.2 24.5 1.0
OD2 A:ASP232 2.2 16.0 1.0
ND1 A:HIS101 2.2 17.3 1.0
CH A:EXY650 2.8 24.4 1.0
CG A:ASP124 3.0 14.1 1.0
CG A:ASP128 3.1 14.7 1.0
CG A:ASP232 3.1 17.1 1.0
CG A:HIS101 3.2 16.4 1.0
CE1 A:HIS101 3.2 17.3 1.0
MN A:MN514 3.4 16.9 1.0
OD1 A:ASP124 3.4 15.3 1.0
CB A:HIS101 3.4 16.9 1.0
OD1 A:ASP128 3.4 12.8 1.0
CB A:ASP232 3.5 17.7 1.0
CF A:EXY650 3.6 24.4 1.0
OD1 A:ASP232 4.2 17.2 1.0
NE1 A:TRP122 4.3 17.1 1.0
NE2 A:HIS101 4.3 17.4 1.0
CD2 A:HIS101 4.3 16.6 1.0
CB A:ASP124 4.4 14.3 1.0
CB A:ASP128 4.5 16.4 1.0
O A:HIS141 4.5 14.8 1.0
CZ2 A:TRP122 4.5 16.9 1.0
CE A:EXY650 4.5 18.8 1.0
CG A:GLU277 4.7 16.7 1.0
CE2 A:TRP122 4.7 15.9 1.0
OE2 A:GLU277 4.8 17.4 1.0
CA A:ASP232 4.8 17.3 1.0
CA A:HIS101 4.9 14.8 1.0

Manganese binding site 3 out of 4 in 3dj8

Go back to Manganese Binding Sites List in 3dj8
Manganese binding site 3 out of 4 in the Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with 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 Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn514

b:19.8
occ:1.00
 OD1 B:ASP234 2.1 21.8 1.0
OF B:EXY751 2.2 24.5 1.0
ND1 B:HIS126 2.3 17.3 1.0
OD1 B:ASP124 2.3 15.4 1.0
OD2 B:ASP232 2.4 19.9 1.0
OD2 B:ASP234 2.5 20.1 1.0
CG B:ASP234 2.6 21.7 1.0
CF B:EXY751 2.9 24.4 1.0
CE1 B:HIS126 3.1 16.0 1.0
CG B:ASP124 3.2 15.8 1.0
CG B:ASP232 3.2 18.3 1.0
MN B:MN515 3.3 21.3 1.0
OD2 B:ASP124 3.4 17.2 1.0
CG B:HIS126 3.4 19.5 1.0
CH B:EXY751 3.4 24.4 1.0
OD1 B:ASP232 3.7 15.9 1.0
CB B:HIS126 3.8 17.9 1.0
N B:HIS126 4.0 15.8 1.0
CB B:ASP234 4.1 19.6 1.0
CE B:EXY751 4.2 18.8 1.0
CB B:ASP232 4.2 17.4 1.0
N B:ALA125 4.2 15.5 1.0
NE2 B:HIS126 4.3 17.8 1.0
CD2 B:HIS126 4.4 18.3 1.0
OD1 B:ASP128 4.5 15.8 1.0
CA B:HIS126 4.5 18.0 1.0
CD B:EXY751 4.5 19.3 1.0
CB B:ASP124 4.5 15.8 1.0
O B:HOH784 4.6 21.2 1.0
OD2 B:ASP128 4.7 18.2 1.0
CB B:ALA125 4.7 13.7 1.0
C B:ALA125 4.8 14.6 1.0
CA B:ALA125 4.9 14.8 1.0
CA B:ASP124 5.0 16.1 1.0

Manganese binding site 4 out of 4 in 3dj8

Go back to Manganese Binding Sites List in 3dj8
Manganese binding site 4 out of 4 in the Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with 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 Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn515

b:21.3
occ:1.00
 OD2 B:ASP124 2.1 17.2 1.0
OF B:EXY751 2.1 24.5 1.0
OD2 B:ASP128 2.1 18.2 1.0
OD2 B:ASP232 2.2 19.9 1.0
ND1 B:HIS101 2.3 22.3 1.0
CH B:EXY751 2.5 24.4 1.0
CG B:ASP124 3.1 15.8 1.0
CG B:ASP128 3.1 17.9 1.0
CG B:HIS101 3.2 21.5 1.0
CG B:ASP232 3.2 18.3 1.0
MN B:MN514 3.3 19.8 1.0
CE1 B:HIS101 3.3 20.1 1.0
CB B:HIS101 3.4 22.4 1.0
CF B:EXY751 3.4 24.4 1.0
OD1 B:ASP128 3.5 15.8 1.0
OD1 B:ASP124 3.6 15.4 1.0
CB B:ASP232 3.6 17.4 1.0
NE1 B:TRP122 4.3 17.8 1.0
OD1 B:ASP232 4.3 15.9 1.0
CD2 B:HIS101 4.4 23.1 1.0
CB B:ASP124 4.4 15.8 1.0
NE2 B:HIS101 4.4 21.4 1.0
CE B:EXY751 4.4 18.8 1.0
CB B:ASP128 4.5 19.3 1.0
O B:HIS141 4.6 21.1 1.0
CZ2 B:TRP122 4.6 18.2 1.0
CG B:GLU277 4.7 25.4 1.0
CE2 B:TRP122 4.8 18.8 1.0
CA B:ASP232 4.9 18.6 1.0
OD1 B:ASP234 4.9 21.8 1.0
CA B:HIS101 4.9 21.9 1.0
OE2 B:GLU277 5.0 28.3 1.0
O B:HIS126 5.0 18.1 1.0

Reference:

T.Y.Zakharian, L.Di Costanzo, D.W.Christianson. Synthesis of (2S)-2-Amino-7,8-Epoxyoctanoic Acid and Structure of Its Metal-Bridging Complex with Human Arginase I Org.Biomol.Chem. V. 6 3240 2008.
ISSN: ISSN 1477-0520
PubMed: 18802628
DOI: 10.1039/B811797G
Page generated: Sat Oct 5 16:04:29 2024

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