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Manganese in PDB 3f80: (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A.

Enzymatic activity of (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A.

All present enzymatic activity of (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A.:
3.5.3.1;

Protein crystallography data

The structure of (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A., PDB code: 3f80 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 / 1.60
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.337, 90.337, 69.329, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 18.4

Manganese Binding Sites:

The binding sites of Manganese atom in the (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A. (pdb code 3f80). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A., PDB code: 3f80:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3f80

Go back to Manganese Binding Sites List in 3f80
Manganese binding site 1 out of 4 in the (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn514

b:10.8
occ:1.00
 O1 A:6HN551 2.2 14.2 1.0
OD1 A:ASP124 2.2 8.0 1.0
OD1 A:ASP234 2.2 9.1 1.0
ND1 A:HIS126 2.2 9.5 1.0
OD2 A:ASP232 2.3 9.9 1.0
OD2 A:ASP234 2.4 9.8 1.0
CG A:ASP234 2.7 10.8 1.0
CE1 A:HIS126 3.0 10.1 1.0
N1 A:6HN551 3.2 11.6 1.0
CG A:ASP124 3.2 8.7 1.0
CG A:ASP232 3.2 9.9 1.0
MN A:MN515 3.3 10.2 1.0
CG A:HIS126 3.4 10.0 1.0
OD2 A:ASP124 3.4 12.4 1.0
O2 A:6HN551 3.6 14.2 1.0
OD1 A:ASP232 3.8 11.3 1.0
CB A:HIS126 3.8 9.8 1.0
N A:HIS126 4.0 8.5 1.0
OG1 A:THR246 4.1 13.1 1.0
N A:ALA125 4.1 8.2 1.0
CB A:ASP232 4.2 9.2 1.0
CB A:ASP234 4.2 10.0 1.0
NE2 A:HIS126 4.2 12.0 1.0
CE A:6HN551 4.3 11.8 1.0
CD A:6HN551 4.3 10.8 1.0
CD2 A:HIS126 4.4 8.4 1.0
CB A:ASP124 4.5 9.0 1.0
CA A:HIS126 4.5 8.5 1.0
CB A:ALA125 4.6 9.4 1.0
O A:HOH409 4.7 9.1 1.0
OD1 A:ASP128 4.7 8.2 1.0
C A:ALA125 4.8 7.8 1.0
CA A:ALA125 4.8 9.2 1.0
CA A:ASP124 4.9 9.2 1.0
OD2 A:ASP128 4.9 10.7 1.0
O A:THR246 4.9 10.4 1.0
C A:ASP124 5.0 8.3 1.0

Manganese binding site 2 out of 4 in 3f80

Go back to Manganese Binding Sites List in 3f80
Manganese binding site 2 out of 4 in the (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn515

b:10.2
occ:1.00
 OD2 A:ASP124 2.1 12.4 1.0
O2 A:6HN551 2.2 14.2 1.0
ND1 A:HIS101 2.2 12.1 1.0
OD2 A:ASP128 2.3 10.7 1.0
OD2 A:ASP232 2.3 9.9 1.0
O1 A:6HN551 2.5 14.2 1.0
N1 A:6HN551 2.6 11.6 1.0
CG A:ASP124 3.1 8.7 1.0
CG A:HIS101 3.2 10.3 1.0
CE1 A:HIS101 3.2 10.9 1.0
CG A:ASP232 3.2 9.9 1.0
CG A:ASP128 3.2 9.6 1.0
MN A:MN514 3.3 10.8 1.0
OD1 A:ASP124 3.4 8.0 1.0
CB A:HIS101 3.5 10.8 1.0
OD1 A:ASP128 3.5 8.2 1.0
CB A:ASP232 3.5 9.2 1.0
CE A:6HN551 4.0 11.8 1.0
NE1 A:TRP122 4.3 9.7 1.0
NE2 A:HIS101 4.3 11.0 1.0
OD1 A:ASP232 4.3 11.3 1.0
CD2 A:HIS101 4.3 11.2 1.0
CB A:ASP124 4.4 9.0 1.0
O A:HIS141 4.5 9.8 1.0
CB A:ASP128 4.6 9.0 1.0
CZ2 A:TRP122 4.7 8.9 1.0
CG A:GLU277 4.7 9.7 1.0
CE2 A:TRP122 4.8 10.2 1.0
CA A:ASP232 4.9 9.8 1.0
OE2 A:GLU277 5.0 11.3 1.0
CA A:HIS101 5.0 9.7 1.0
ND1 A:HIS126 5.0 9.5 1.0
OD1 A:ASP234 5.0 9.1 1.0

Manganese binding site 3 out of 4 in 3f80

Go back to Manganese Binding Sites List in 3f80
Manganese binding site 3 out of 4 in the (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn514

b:12.7
occ:1.00
 OD1 B:ASP234 2.1 13.3 1.0
O1 A:6HN552 2.1 17.9 1.0
OD1 B:ASP124 2.2 12.7 1.0
OD2 B:ASP232 2.4 15.5 1.0
ND1 B:HIS126 2.4 14.3 1.0
OD2 B:ASP234 2.4 10.5 1.0
CG B:ASP234 2.6 14.2 1.0
CG B:ASP232 3.1 12.4 1.0
CE1 B:HIS126 3.2 14.9 1.0
N1 A:6HN552 3.2 16.6 1.0
CG B:ASP124 3.2 12.2 1.0
MN B:MN515 3.3 14.1 1.0
CG B:HIS126 3.5 14.7 1.0
OD2 B:ASP124 3.5 13.4 1.0
OD1 B:ASP232 3.6 11.1 1.0
O2 A:6HN552 3.7 16.3 1.0
CB B:HIS126 3.9 14.0 1.0
N B:HIS126 4.0 11.8 1.0
OG1 B:THR246 4.0 15.4 1.0
CB B:ASP234 4.1 13.8 1.0
CB B:ASP232 4.1 11.8 1.0
N B:ALA125 4.2 10.5 1.0
CD A:6HN552 4.3 16.2 1.0
CE A:6HN552 4.3 17.2 1.0
NE2 B:HIS126 4.3 14.4 1.0
CD2 B:HIS126 4.5 15.2 1.0
CB B:ASP124 4.5 12.1 1.0
CA B:HIS126 4.6 12.8 1.0
OD1 B:ASP128 4.6 12.4 1.0
O B:HOH333 4.7 13.0 1.0
CB B:ALA125 4.7 9.1 1.0
OD2 B:ASP128 4.8 10.1 1.0
C B:ALA125 4.8 9.4 1.0
CA B:ALA125 4.8 9.8 1.0
CA B:ASP124 4.9 11.6 1.0
O B:THR246 4.9 13.6 1.0
C B:ASP124 5.0 11.1 1.0

Manganese binding site 4 out of 4 in 3f80

Go back to Manganese Binding Sites List in 3f80
Manganese binding site 4 out of 4 in the (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Resolution 1.60 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn515

b:14.1
occ:1.00
 OD2 B:ASP124 2.1 13.4 1.0
OD2 B:ASP128 2.2 10.1 1.0
ND1 B:HIS101 2.2 15.2 1.0
OD2 B:ASP232 2.3 15.5 1.0
O2 A:6HN552 2.3 16.3 1.0
O1 A:6HN552 2.4 17.9 1.0
N1 A:6HN552 2.6 16.6 1.0
CG B:ASP124 3.1 12.2 1.0
CE1 B:HIS101 3.2 14.0 1.0
CG B:HIS101 3.2 15.0 1.0
CG B:ASP128 3.2 11.3 1.0
CG B:ASP232 3.2 12.4 1.0
MN B:MN514 3.3 12.7 1.0
OD1 B:ASP124 3.4 12.7 1.0
CB B:HIS101 3.5 15.2 1.0
CB B:ASP232 3.5 11.8 1.0
OD1 B:ASP128 3.5 12.4 1.0
CE A:6HN552 4.0 17.2 1.0
NE2 B:HIS101 4.3 14.4 1.0
CD2 B:HIS101 4.3 16.2 1.0
NE1 B:TRP122 4.3 11.9 1.0
OD1 B:ASP232 4.4 11.1 1.0
CB B:ASP124 4.5 12.1 1.0
O B:HIS141 4.5 14.5 1.0
CB B:ASP128 4.5 11.3 1.0
CZ2 B:TRP122 4.6 11.5 1.0
CG B:GLU277 4.6 18.1 1.0
CE2 B:TRP122 4.8 13.2 1.0
CA B:ASP232 4.9 11.5 1.0
OD1 B:ASP234 4.9 13.3 1.0
CD A:6HN552 5.0 16.2 1.0
CA B:HIS101 5.0 14.0 1.0

Reference:

T.Y.Zakharian, L.Di Costanzo, D.W.Christianson. (S)-2-Amino-6-Nitrohexanoic Acid Binds to Human Arginase I Through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. J.Am.Chem.Soc. V. 130 17254 2008.
ISSN: ISSN 0002-7863
PubMed: 19032027
DOI: 10.1021/JA807702Q
Page generated: Sat Oct 5 16:15:54 2024

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