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Manganese in PDB 3kv2: High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha)

Enzymatic activity of High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha)

All present enzymatic activity of High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha):
3.5.3.1;

Protein crystallography data

The structure of High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha), PDB code: 3kv2 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 / 1.55
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.497, 90.497, 69.604, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 17.8

Manganese Binding Sites:

The binding sites of Manganese atom in the High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha) (pdb code 3kv2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha), PDB code: 3kv2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3kv2

Go back to Manganese Binding Sites List in 3kv2
Manganese binding site 1 out of 4 in the High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn514

b:11.1
occ:1.00
 OD1 A:ASP124 2.1 10.7 1.0
OH1 A:NNH901 2.3 13.8 1.0
OD2 A:ASP234 2.3 12.0 1.0
ND1 A:HIS126 2.3 10.8 1.0
OD2 A:ASP232 2.3 10.5 1.0
OD1 A:ASP234 2.3 10.0 1.0
CG A:ASP234 2.6 11.3 1.0
NH1 A:NNH901 3.0 12.2 1.0
CG A:ASP124 3.1 9.8 1.0
CE1 A:HIS126 3.1 10.6 1.0
CG A:ASP232 3.2 11.6 1.0
MN A:MN515 3.3 11.4 1.0
OD2 A:ASP124 3.3 11.9 1.0
CG A:HIS126 3.4 10.5 1.0
NH2 A:NNH901 3.5 10.2 1.0
CE A:NNH901 3.6 11.8 1.0
OD1 A:ASP232 3.7 12.7 1.0
CB A:HIS126 3.9 9.4 1.0
N A:HIS126 4.0 9.0 1.0
N A:ALA125 4.1 7.7 1.0
CB A:ASP232 4.1 11.1 1.0
CB A:ASP234 4.2 12.0 1.0
NE2 A:HIS126 4.3 11.7 1.0
CB A:ASP124 4.4 10.3 1.0
CD2 A:HIS126 4.5 9.5 1.0
CA A:HIS126 4.5 9.1 1.0
OG1 A:THR246 4.6 14.3 1.0
CB A:ALA125 4.7 8.2 1.0
O A:HOH480 4.7 45.9 1.0
O A:HOH347 4.7 11.7 1.0
ND A:NNH901 4.8 11.6 1.0
C A:ALA125 4.8 6.3 1.0
CA A:ALA125 4.8 7.8 1.0
CA A:ASP124 4.8 9.7 1.0
OD2 A:ASP128 4.8 11.2 1.0
C A:ASP124 4.9 7.8 1.0
OD1 A:ASP128 4.9 9.4 1.0
C A:ASP234 5.0 8.6 1.0
CA A:ASP234 5.0 10.2 1.0

Manganese binding site 2 out of 4 in 3kv2

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Manganese binding site 2 out of 4 in the High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn515

b:11.4
occ:1.00
 OH1 A:NNH901 2.0 13.8 1.0
OD2 A:ASP124 2.1 11.9 1.0
OD2 A:ASP128 2.2 11.2 1.0
OD2 A:ASP232 2.3 10.5 1.0
ND1 A:HIS101 2.3 12.6 1.0
O A:HOH480 3.0 45.9 1.0
CG A:ASP124 3.1 9.8 1.0
NH1 A:NNH901 3.1 12.2 1.0
CG A:ASP128 3.2 8.9 1.0
MN A:MN514 3.3 11.1 1.0
CE1 A:HIS101 3.3 12.1 1.0
CG A:HIS101 3.3 13.0 1.0
CG A:ASP232 3.3 11.6 1.0
OD1 A:ASP124 3.5 10.7 1.0
CB A:HIS101 3.6 11.7 1.0
OD1 A:ASP128 3.6 9.4 1.0
CB A:ASP232 3.7 11.1 1.0
CE A:NNH901 4.3 11.8 1.0
NE1 A:TRP122 4.4 10.8 1.0
CB A:ASP124 4.4 10.3 1.0
OD1 A:ASP232 4.4 12.7 1.0
NE2 A:HIS101 4.4 11.9 1.0
O A:HIS141 4.4 11.3 1.0
CD2 A:HIS101 4.5 13.7 1.0
NH2 A:NNH901 4.5 10.2 1.0
CB A:ASP128 4.5 11.7 1.0
CZ2 A:TRP122 4.6 10.6 1.0
CG A:GLU277 4.8 12.6 1.0
OE2 A:GLU277 4.8 14.2 1.0
CE2 A:TRP122 4.8 11.0 1.0
CB A:HIS126 4.9 9.4 1.0
ND1 A:HIS126 4.9 10.8 1.0
O A:HIS126 5.0 9.5 1.0

Manganese binding site 3 out of 4 in 3kv2

Go back to Manganese Binding Sites List in 3kv2
Manganese binding site 3 out of 4 in the High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn514

b:13.8
occ:1.00
 OH1 B:NNH902 2.1 21.8 1.0
OD1 B:ASP234 2.2 13.7 1.0
OD1 B:ASP124 2.2 12.6 1.0
OD2 B:ASP232 2.3 15.4 1.0
OD2 B:ASP234 2.3 12.3 1.0
ND1 B:HIS126 2.4 17.1 1.0
CG B:ASP234 2.6 15.0 1.0
NH1 B:NNH902 2.9 21.9 1.0
CG B:ASP124 3.1 11.6 1.0
CG B:ASP232 3.1 13.5 1.0
CE1 B:HIS126 3.2 18.0 1.0
MN B:MN515 3.3 15.3 1.0
OD2 B:ASP124 3.4 12.7 1.0
CG B:HIS126 3.5 17.8 1.0
NH2 B:NNH902 3.6 21.3 1.0
CE B:NNH902 3.6 20.7 1.0
OD1 B:ASP232 3.7 12.4 1.0
CB B:HIS126 3.9 14.5 1.0
N B:HIS126 3.9 13.1 1.0
CB B:ASP234 4.1 14.4 1.0
CB B:ASP232 4.1 12.5 1.0
N B:ALA125 4.1 12.4 1.0
OG1 B:THR246 4.3 23.6 1.0
NE2 B:HIS126 4.3 16.9 1.0
CB B:ASP124 4.5 13.0 1.0
CD2 B:HIS126 4.5 17.7 1.0
CA B:HIS126 4.5 13.3 1.0
CB B:ALA125 4.5 10.3 1.0
O B:HOH475 4.6 40.3 1.0
O B:HOH340 4.7 12.8 1.0
CA B:ALA125 4.7 10.5 1.0
ND B:NNH902 4.8 18.1 1.0
C B:ALA125 4.8 10.6 1.0
OD2 B:ASP128 4.8 12.9 1.0
CA B:ASP124 4.9 12.0 1.0
OD1 B:ASP128 4.9 14.1 1.0
C B:ASP234 4.9 12.2 1.0
CA B:ASP234 4.9 11.9 1.0
C B:ASP124 5.0 12.3 1.0

Manganese binding site 4 out of 4 in 3kv2

Go back to Manganese Binding Sites List in 3kv2
Manganese binding site 4 out of 4 in the High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of High Resolution Structure of Human Arginase I in Complex with the Strong Inhibitor N(Omega)-Hydroxy-Nor-L-Arginine (Nor-Noha) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn515

b:15.3
occ:1.00
 OH1 B:NNH902 2.0 21.8 1.0
OD2 B:ASP128 2.1 12.9 1.0
OD2 B:ASP124 2.2 12.7 1.0
ND1 B:HIS101 2.4 15.1 1.0
OD2 B:ASP232 2.4 15.4 1.0
O B:HOH475 3.0 40.3 1.0
NH1 B:NNH902 3.1 21.9 1.0
CG B:ASP124 3.2 11.6 1.0
CG B:ASP128 3.2 13.8 1.0
MN B:MN514 3.3 13.8 1.0
CG B:HIS101 3.3 15.7 1.0
CE1 B:HIS101 3.4 12.6 1.0
CG B:ASP232 3.4 13.5 1.0
OD1 B:ASP124 3.5 12.6 1.0
CB B:HIS101 3.5 16.1 1.0
OD1 B:ASP128 3.6 14.1 1.0
CB B:ASP232 3.7 12.5 1.0
CE B:NNH902 4.2 20.7 1.0
NE1 B:TRP122 4.4 15.2 1.0
O B:HIS141 4.4 16.1 1.0
NE2 B:HIS101 4.5 13.4 1.0
CD2 B:HIS101 4.5 16.1 1.0
NH2 B:NNH902 4.5 21.3 1.0
CB B:ASP124 4.5 13.0 1.0
CB B:ASP128 4.5 13.2 1.0
OD1 B:ASP232 4.5 12.4 1.0
CZ2 B:TRP122 4.6 15.1 1.0
CG B:GLU277 4.7 17.5 1.0
O B:HIS126 4.8 14.2 1.0
CE2 B:TRP122 4.8 16.7 1.0
CB B:HIS126 4.9 14.5 1.0
ND1 B:HIS126 4.9 17.1 1.0
OD1 B:ASP234 5.0 13.7 1.0
OE2 B:GLU277 5.0 20.6 1.0

Reference:

L.Di Costanzo, M.Ilies, K.J.Thorn, D.W.Christianson. Inhibition of Human Arginase I By Substrate and Product Analogues. Arch.Biochem.Biophys. V. 496 101 2010.
ISSN: ISSN 0003-9861
PubMed: 20153713
DOI: 10.1016/J.ABB.2010.02.004
Page generated: Sat Oct 5 16:46:04 2024

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