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Manganese in PDB 3gn0: Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)

Enzymatic activity of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)

All present enzymatic activity of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo):
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo), PDB code: 3gn0 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) 33.82 / 1.70
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 89.587, 89.587, 69.020, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 20.2

Other elements in 3gn0:

The structure of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo) also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo) (pdb code 3gn0). 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 Human Arginase I in Complex with Difluoromethylornithine (Dfmo), PDB code: 3gn0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3gn0

Go back to Manganese Binding Sites List in 3gn0
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Human Arginase I in Complex with Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn536

b:17.7
occ:1.00
 OD1 A:ASP124 2.0 17.2 1.0
O A:HOH437 2.2 16.7 1.0
OD2 A:ASP232 2.2 16.2 1.0
OD1 A:ASP234 2.2 18.8 1.0
ND1 A:HIS126 2.3 12.7 1.0
OD2 A:ASP234 2.4 18.2 1.0
CG A:ASP234 2.6 18.6 1.0
O A:HOH438 2.9 20.0 1.0
CG A:ASP124 3.0 18.2 1.0
CE1 A:HIS126 3.0 12.6 1.0
CG A:ASP232 3.1 18.7 1.0
OD2 A:ASP124 3.3 17.7 1.0
MN A:MN537 3.3 15.7 1.0
CG A:HIS126 3.4 13.0 1.0
OD1 A:ASP232 3.7 18.8 1.0
CB A:HIS126 3.9 15.1 1.0
OG1 A:THR246 3.9 16.8 1.0
N A:HIS126 3.9 14.4 1.0
N A:ALA125 4.0 14.8 1.0
CB A:ASP234 4.1 16.4 1.0
CB A:ASP232 4.1 18.1 1.0
O A:HOH435 4.2 30.2 1.0
NEO A:DMO551 4.2 22.5 1.0
NE2 A:HIS126 4.2 14.6 1.0
CB A:ASP124 4.4 17.0 1.0
CD2 A:HIS126 4.4 10.6 1.0
CA A:HIS126 4.5 14.3 1.0
CB A:ALA125 4.6 11.7 1.0
OD1 A:ASP128 4.6 16.3 1.0
OD2 A:ASP128 4.6 17.1 1.0
O A:HOH426 4.7 12.8 1.0
CDO A:DMO551 4.7 25.3 1.0
O A:HOH433 4.7 72.8 1.0
CA A:ALA125 4.7 14.6 1.0
C A:ALA125 4.7 13.4 1.0
CA A:ASP124 4.8 15.2 1.0
O A:THR246 4.8 17.1 1.0
C A:ASP124 4.9 15.7 1.0

Manganese binding site 2 out of 4 in 3gn0

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Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Human Arginase I in Complex with Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn537

b:15.7
occ:1.00
 OD2 A:ASP124 2.0 17.7 1.0
ND1 A:HIS101 2.1 15.0 1.0
OD2 A:ASP128 2.1 17.1 1.0
O A:HOH437 2.1 16.7 1.0
OD2 A:ASP232 2.3 16.2 1.0
O A:HOH435 2.6 30.2 1.0
CG A:ASP124 3.0 18.2 1.0
CG A:HIS101 3.1 15.6 1.0
CE1 A:HIS101 3.1 15.2 1.0
CG A:ASP128 3.2 13.7 1.0
CG A:ASP232 3.2 18.7 1.0
MN A:MN536 3.3 17.7 1.0
CB A:HIS101 3.4 17.0 1.0
CB A:ASP232 3.5 18.1 1.0
OD1 A:ASP124 3.5 17.2 1.0
OD1 A:ASP128 3.6 16.3 1.0
O A:HOH438 3.8 20.0 1.0
NEO A:DMO551 4.0 22.5 1.0
NE2 A:HIS101 4.2 14.0 1.0
CD2 A:HIS101 4.2 15.1 1.0
CB A:ASP124 4.3 17.0 1.0
OD1 A:ASP232 4.3 18.8 1.0
O A:HIS141 4.3 18.0 1.0
NE1 A:TRP122 4.4 16.6 1.0
CB A:ASP128 4.4 16.6 1.0
CG A:GLU277 4.6 15.8 1.0
OE2 A:GLU277 4.6 14.5 1.0
CZ2 A:TRP122 4.6 19.1 1.0
CA A:ASP232 4.8 16.4 1.0
CE2 A:TRP122 4.8 17.0 1.0
CA A:HIS101 4.9 17.4 1.0
OD2 A:ASP234 4.9 18.2 1.0
OD1 A:ASP234 5.0 18.8 1.0

Manganese binding site 3 out of 4 in 3gn0

Go back to Manganese Binding Sites List in 3gn0
Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Human Arginase I in Complex with Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn536

b:19.2
occ:1.00
 O B:HOH429 1.9 21.6 1.0
OD1 B:ASP234 2.0 19.0 1.0
OD1 B:ASP124 2.3 15.4 1.0
ND1 B:HIS126 2.3 19.2 1.0
OD2 B:ASP232 2.5 21.1 1.0
OD2 B:ASP234 2.5 18.4 1.0
CG B:ASP234 2.6 20.6 1.0
CE1 B:HIS126 3.0 21.1 1.0
CG B:ASP124 3.1 14.3 1.0
CG B:ASP232 3.1 20.2 1.0
OD2 B:ASP124 3.3 16.4 1.0
O B:HOH430 3.3 25.2 1.0
MN B:MN537 3.3 20.4 1.0
CG B:HIS126 3.4 20.7 1.0
OD1 B:ASP232 3.5 18.2 1.0
OG1 B:THR246 3.9 20.0 1.0
CB B:HIS126 3.9 18.2 1.0
O B:HOH432 4.0 26.3 1.0
N B:HIS126 4.0 17.6 1.0
CB B:ASP234 4.1 19.6 1.0
NEO B:DMO552 4.1 32.2 1.0
CB B:ASP232 4.1 17.1 1.0
N B:ALA125 4.2 17.5 1.0
NE2 B:HIS126 4.2 21.1 1.0
CD2 B:HIS126 4.4 21.0 1.0
CB B:ASP124 4.5 15.9 1.0
CA B:HIS126 4.6 18.5 1.0
OD1 B:ASP128 4.6 17.0 1.0
O B:HOH339 4.6 14.9 1.0
CB B:ALA125 4.7 15.0 1.0
CDO B:DMO552 4.7 32.5 1.0
OD2 B:ASP128 4.7 15.6 1.0
O B:THR246 4.7 22.5 1.0
C B:ALA125 4.8 16.2 1.0
CA B:ALA125 4.8 15.4 1.0
CA B:ASP124 4.9 16.7 1.0
C B:ASP124 5.0 17.1 1.0

Manganese binding site 4 out of 4 in 3gn0

Go back to Manganese Binding Sites List in 3gn0
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Human Arginase I in Complex with Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn537

b:20.4
occ:1.00
 ND1 B:HIS101 2.1 18.2 1.0
O B:HOH429 2.1 21.6 1.0
OD2 B:ASP128 2.1 15.6 1.0
OD2 B:ASP124 2.2 16.4 1.0
OD2 B:ASP232 2.2 21.1 1.0
O B:HOH432 2.3 26.3 1.0
CG B:HIS101 3.0 19.6 1.0
CE1 B:HIS101 3.1 19.1 1.0
CG B:ASP128 3.2 16.0 1.0
CG B:ASP232 3.2 20.2 1.0
CG B:ASP124 3.3 14.3 1.0
CB B:HIS101 3.3 20.1 1.0
MN B:MN536 3.3 19.2 1.0
CB B:ASP232 3.5 17.1 1.0
OD1 B:ASP128 3.6 17.0 1.0
OD1 B:ASP124 3.7 15.4 1.0
O B:HOH430 4.0 25.2 1.0
NEO B:DMO552 4.0 32.2 1.0
CD2 B:HIS101 4.2 21.2 1.0
NE2 B:HIS101 4.2 19.5 1.0
O B:HIS141 4.3 22.3 1.0
OD1 B:ASP232 4.4 18.2 1.0
CG B:GLU277 4.4 23.9 1.0
NE1 B:TRP122 4.4 20.0 1.0
OE2 B:GLU277 4.5 23.7 1.0
CB B:ASP128 4.5 16.1 1.0
CB B:ASP124 4.5 15.9 1.0
CZ2 B:TRP122 4.6 19.4 1.0
CA B:HIS101 4.8 20.2 1.0
OD1 B:ASP234 4.8 19.0 1.0
CE2 B:TRP122 4.8 20.7 1.0
CA B:ASP232 4.9 17.7 1.0
CD B:GLU277 4.9 24.6 1.0

Reference:

M.Ilies, L.Di Costanzo, D.P.Dowling, K.J.Thorn, D.W.Christianson. Binding of Alpha,Alpha-Disubstituted Amino Acids to Arginase Suggests New Avenues For Inhibitor Design J.Med.Chem. V. 54 5432 2011.
ISSN: ISSN 0022-2623
PubMed: 21728378
DOI: 10.1021/JM200443B
Page generated: Sat Oct 5 16:23:52 2024

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