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Manganese in PDB 3sjt: Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure

Enzymatic activity of Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure

All present enzymatic activity of Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure, PDB code: 3sjt 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) 34.07 / 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 (%) 12.9 / 16.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure (pdb code 3sjt). 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 the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure, PDB code: 3sjt:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3sjt

Go back to Manganese Binding Sites List in 3sjt
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure


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 the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn514

b:13.5
occ:1.00
 OD1 A:ASP234 2.2 14.6 1.0
OD1 A:ASP124 2.2 13.5 1.0
O2 A:5AB551 2.3 15.9 1.0
ND1 A:HIS126 2.3 14.2 1.0
OD2 A:ASP232 2.4 13.5 1.0
OD2 A:ASP234 2.5 13.2 1.0
CG A:ASP234 2.7 14.1 1.0
O4 A:5AB551 2.7 13.7 1.0
B1 A:5AB551 3.0 15.3 1.0
CE1 A:HIS126 3.1 14.8 1.0
CG A:ASP124 3.2 13.7 1.0
CG A:ASP232 3.3 13.5 1.0
MN A:MN515 3.4 14.0 1.0
CG A:HIS126 3.4 13.0 1.0
OD2 A:ASP124 3.5 13.7 1.0
CB A:HIS126 3.8 14.1 1.0
OD1 A:ASP232 3.8 14.7 1.0
O3 A:5AB551 3.9 13.9 1.0
N A:HIS126 4.1 13.2 1.0
C6 A:5AB551 4.1 15.0 1.0
CB A:ASP234 4.2 13.9 1.0
CB A:ASP232 4.2 14.3 1.0
N A:ALA125 4.3 13.2 1.0
NE2 A:HIS126 4.3 15.3 1.0
C5 A:5AB551 4.3 15.0 1.0
CD2 A:HIS126 4.4 14.3 1.0
OD1 A:ASP128 4.5 13.0 1.0
CA A:HIS126 4.5 12.7 1.0
CB A:ASP124 4.6 13.3 1.0
O A:HOH473 4.7 15.9 1.0
CB A:ALA125 4.8 12.1 1.0
C A:ALA125 4.8 12.4 1.0
CA A:ALA125 4.9 12.7 1.0
OD2 A:ASP128 4.9 15.2 1.0
CA A:ASP124 4.9 13.2 1.0

Manganese binding site 2 out of 4 in 3sjt

Go back to Manganese Binding Sites List in 3sjt
Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure


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 the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn515

b:14.0
occ:1.00
 OD2 A:ASP124 2.2 13.7 1.0
OD2 A:ASP128 2.2 15.2 1.0
ND1 A:HIS101 2.2 14.9 1.0
OD2 A:ASP232 2.4 13.5 1.0
O2 A:5AB551 2.4 15.9 1.0
O3 A:5AB551 2.4 13.9 1.0
B1 A:5AB551 2.9 15.3 1.0
CG A:ASP128 3.1 13.4 1.0
CG A:ASP124 3.2 13.7 1.0
CE1 A:HIS101 3.2 14.3 1.0
CG A:HIS101 3.2 13.7 1.0
CG A:ASP232 3.3 13.5 1.0
MN A:MN514 3.4 13.5 1.0
OD1 A:ASP128 3.4 13.0 1.0
CB A:HIS101 3.5 13.9 1.0
OD1 A:ASP124 3.5 13.5 1.0
CB A:ASP232 3.5 14.3 1.0
O4 A:5AB551 3.6 13.7 1.0
C6 A:5AB551 4.0 15.0 1.0
NE1 A:TRP122 4.2 14.0 1.0
NE2 A:HIS101 4.3 14.6 1.0
CD2 A:HIS101 4.3 15.1 1.0
O A:HIS141 4.4 15.0 1.0
OD1 A:ASP232 4.4 14.7 1.0
CB A:ASP128 4.5 14.7 1.0
CB A:ASP124 4.5 13.3 1.0
CZ2 A:TRP122 4.6 13.3 1.0
CE2 A:TRP122 4.8 14.8 1.0
CG A:GLU277 4.9 15.2 1.0
CA A:ASP232 4.9 12.3 1.0
CA A:HIS101 5.0 14.7 1.0

Manganese binding site 3 out of 4 in 3sjt

Go back to Manganese Binding Sites List in 3sjt
Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure


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 the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn514

b:16.2
occ:1.00
 OD1 B:ASP234 2.2 17.1 1.0
O2 B:5AB552 2.2 17.6 1.0
OD1 B:ASP124 2.2 16.4 1.0
ND1 B:HIS126 2.3 16.0 1.0
OD2 B:ASP232 2.4 16.9 1.0
OD2 B:ASP234 2.5 15.6 1.0
CG B:ASP234 2.7 17.7 1.0
O4 B:5AB552 2.9 17.8 1.0
B1 B:5AB552 3.1 17.9 1.0
CG B:ASP232 3.2 16.4 1.0
CE1 B:HIS126 3.2 16.9 1.0
CG B:ASP124 3.2 14.9 1.0
CG B:HIS126 3.3 15.6 1.0
MN B:MN515 3.4 17.3 1.0
OD2 B:ASP124 3.5 16.8 1.0
CB B:HIS126 3.7 16.3 1.0
OD1 B:ASP232 3.7 15.8 1.0
O3 B:5AB552 3.9 20.2 1.0
N B:HIS126 4.1 15.8 1.0
C6 B:5AB552 4.1 18.2 1.0
CB B:ASP232 4.2 14.8 1.0
CB B:ASP234 4.2 17.1 1.0
N B:ALA125 4.3 14.7 1.0
C5 B:5AB552 4.3 17.7 1.0
NE2 B:HIS126 4.4 18.1 1.0
CD2 B:HIS126 4.5 18.4 1.0
CA B:HIS126 4.5 16.3 1.0
OD1 B:ASP128 4.5 17.0 1.0
O B:HOH361 4.5 19.2 1.0
CB B:ASP124 4.6 14.1 1.0
CB B:ALA125 4.8 14.3 1.0
OD2 B:ASP128 4.8 15.6 1.0
C B:ALA125 4.9 14.7 1.0
CA B:ASP124 4.9 14.2 1.0
O B:HOH429 4.9 21.4 1.0
CA B:ALA125 4.9 15.4 1.0

Manganese binding site 4 out of 4 in 3sjt

Go back to Manganese Binding Sites List in 3sjt
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure


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 the Inhibitor Me-Abh, Resolution 1.60 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn515

b:17.3
occ:1.00
 OD2 B:ASP128 2.1 15.6 1.0
OD2 B:ASP124 2.1 16.8 1.0
ND1 B:HIS101 2.3 16.5 1.0
OD2 B:ASP232 2.4 16.9 1.0
O2 B:5AB552 2.4 17.6 1.0
O3 B:5AB552 2.4 20.2 1.0
B1 B:5AB552 2.9 17.9 1.0
CG B:ASP128 3.1 15.7 1.0
CG B:ASP124 3.1 14.9 1.0
CG B:HIS101 3.2 17.5 1.0
CE1 B:HIS101 3.3 15.5 1.0
CG B:ASP232 3.3 16.4 1.0
MN B:MN514 3.4 16.2 1.0
OD1 B:ASP128 3.4 17.0 1.0
OD1 B:ASP124 3.4 16.4 1.0
CB B:HIS101 3.5 19.0 1.0
CB B:ASP232 3.5 14.8 1.0
O4 B:5AB552 3.6 17.8 1.0
C6 B:5AB552 4.0 18.2 1.0
NE1 B:TRP122 4.3 15.7 1.0
NE2 B:HIS101 4.3 15.9 1.0
CD2 B:HIS101 4.4 17.7 1.0
O B:HIS141 4.4 19.2 1.0
OD1 B:ASP232 4.4 15.8 1.0
CB B:ASP128 4.4 16.6 1.0
CB B:ASP124 4.5 14.1 1.0
CZ2 B:TRP122 4.6 15.2 1.0
CG B:GLU277 4.8 18.8 1.0
CE2 B:TRP122 4.8 15.8 1.0
CA B:ASP232 4.9 16.0 1.0
CB B:HIS126 5.0 16.3 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. 2011.
ISSN: ISSN 0022-2623
PubMed: 21728378
DOI: 10.1021/JM200443B
Page generated: Sat Oct 5 17:53:23 2024

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