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Manganese in PDB 6q9p: Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh

Enzymatic activity of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh

All present enzymatic activity of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh, PDB code: 6q9p was solved by Y.Grobben, J.C.M.Uitdehaag, G.J.R.Zaman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.99 / 1.66
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 89.980, 89.980, 69.131, 90.00, 90.00, 120.00
R / Rfree (%) 14.8 / 17.8

Other elements in 6q9p:

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh (pdb code 6q9p). 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-1 at pH 9.0 in Complex with Abh, PDB code: 6q9p:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6q9p

Go back to Manganese Binding Sites List in 6q9p
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh


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-1 at pH 9.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:17.2
occ:1.00
 OD2 A:ASP128 2.2 17.3 1.0
OD2 A:ASP124 2.2 15.0 1.0
O1 A:ABH403 2.3 21.2 1.0
OD2 A:ASP232 2.3 18.2 1.0
O2 A:ABH403 2.3 26.8 1.0
ND1 A:HIS101 2.3 14.8 1.0
B A:ABH403 2.9 23.1 1.0
CG A:ASP128 3.1 15.0 1.0
CG A:HIS101 3.2 14.3 1.0
CG A:ASP124 3.2 15.4 1.0
CG A:ASP232 3.3 16.4 1.0
CB A:HIS101 3.3 15.8 1.0
OD1 A:ASP128 3.3 15.5 1.0
CE1 A:HIS101 3.3 13.4 1.0
MN A:MN402 3.4 18.5 1.0
OD1 A:ASP124 3.5 17.2 1.0
CB A:ASP232 3.6 16.4 1.0
O3 A:ABH403 3.8 20.8 1.0
CE A:ABH403 4.1 21.4 1.0
NA A:NA404 4.2 29.2 1.0
CD2 A:HIS101 4.4 14.6 1.0
NE1 A:TRP122 4.4 16.8 1.0
OD1 A:ASP232 4.4 15.5 1.0
O A:HIS141 4.4 17.3 1.0
NE2 A:HIS101 4.4 15.0 1.0
CB A:ASP128 4.5 14.5 1.0
CB A:ASP124 4.5 15.4 1.0
CZ2 A:TRP122 4.6 18.2 1.0
OD2 A:ASP234 4.8 19.2 1.0
CE2 A:TRP122 4.8 16.3 1.0
CA A:HIS101 4.9 15.2 1.0
OE2 A:GLU277 4.9 18.4 1.0
CG A:GLU277 4.9 17.2 1.0
CA A:ASP232 5.0 15.9 1.0

Manganese binding site 2 out of 4 in 6q9p

Go back to Manganese Binding Sites List in 6q9p
Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh


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-1 at pH 9.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:18.5
occ:1.00
 ND1 A:HIS126 2.0 16.4 1.0
OD1 A:ASP124 2.1 17.2 1.0
O1 A:ABH403 2.1 21.2 1.0
OD2 A:ASP234 2.1 19.2 1.0
OD1 A:ASP234 2.6 13.7 1.0
CG A:ASP234 2.7 16.5 1.0
OD2 A:ASP232 2.7 18.2 1.0
O3 A:ABH403 2.9 20.8 1.0
CE1 A:HIS126 2.9 14.9 1.0
B A:ABH403 3.0 23.1 1.0
CG A:HIS126 3.0 15.1 1.0
CG A:ASP124 3.1 15.4 1.0
NA A:NA404 3.2 29.2 1.0
OD2 A:ASP124 3.4 15.0 1.0
CB A:HIS126 3.4 15.4 1.0
MN A:MN401 3.4 17.2 1.0
CG A:ASP232 3.5 16.4 1.0
N A:HIS126 3.8 13.8 1.0
O2 A:ABH403 3.9 26.8 1.0
OD1 A:ASP232 4.0 15.5 1.0
OG1 A:THR246 4.1 21.2 1.0
NE2 A:HIS126 4.1 16.9 1.0
CD2 A:HIS126 4.1 15.7 1.0
CE A:ABH403 4.1 21.4 1.0
CB A:ASP234 4.2 16.2 1.0
N A:ALA125 4.2 13.2 1.0
OD1 A:ASP128 4.3 15.5 1.0
CA A:HIS126 4.3 14.7 1.0
CB A:ASP232 4.4 16.4 1.0
CD A:ABH403 4.4 22.0 1.0
CB A:ASP124 4.4 15.4 1.0
CB A:ALA125 4.6 14.8 1.0
C A:ALA125 4.7 13.2 1.0
CA A:ALA125 4.7 14.1 1.0
CA A:ASP124 4.8 14.2 1.0
O A:HOH593 4.8 19.3 1.0
OD2 A:ASP128 4.8 17.3 1.0
C A:ASP124 4.9 14.2 1.0
O A:HIS126 4.9 15.8 1.0
CG A:ASP128 5.0 15.0 1.0

Manganese binding site 3 out of 4 in 6q9p

Go back to Manganese Binding Sites List in 6q9p
Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh


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-1 at pH 9.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:20.3
occ:1.00
 OD2 B:ASP128 2.1 20.4 1.0
OD2 B:ASP124 2.1 15.8 1.0
O1 B:ABH403 2.2 18.0 1.0
ND1 B:HIS101 2.2 17.9 1.0
OD2 B:ASP232 2.3 16.9 1.0
O2 B:ABH403 2.3 23.4 1.0
B B:ABH403 2.8 20.6 1.0
CG B:ASP128 3.0 18.4 1.0
CG B:ASP124 3.1 16.1 1.0
CG B:HIS101 3.2 18.8 1.0
CE1 B:HIS101 3.2 18.9 1.0
CG B:ASP232 3.3 18.1 1.0
OD1 B:ASP128 3.3 18.5 1.0
CB B:HIS101 3.4 18.7 1.0
MN B:MN402 3.4 21.7 1.0
OD1 B:ASP124 3.4 18.5 1.0
CB B:ASP232 3.6 17.0 1.0
O3 B:ABH403 3.7 23.0 1.0
CE B:ABH403 4.1 20.8 1.0
NA B:NA404 4.2 38.4 1.0
CD2 B:HIS101 4.3 19.0 1.0
NE1 B:TRP122 4.3 18.4 1.0
NE2 B:HIS101 4.3 19.2 1.0
O B:HIS141 4.4 22.6 1.0
CB B:ASP128 4.4 18.0 1.0
OD1 B:ASP232 4.4 16.9 1.0
CB B:ASP124 4.5 16.9 1.0
CZ2 B:TRP122 4.5 20.7 1.0
CE2 B:TRP122 4.8 19.7 1.0
CA B:HIS101 4.9 18.0 1.0
CG B:GLU277 4.9 21.9 1.0
OE2 B:GLU277 5.0 24.1 1.0
CA B:ASP232 5.0 17.2 1.0
OD2 B:ASP234 5.0 20.9 1.0

Manganese binding site 4 out of 4 in 6q9p

Go back to Manganese Binding Sites List in 6q9p
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh


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-1 at pH 9.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:21.7
occ:1.00
 OD1 B:ASP124 2.1 18.5 1.0
OD2 B:ASP234 2.1 20.9 1.0
ND1 B:HIS126 2.2 17.5 1.0
O1 B:ABH403 2.2 18.0 1.0
OD1 B:ASP234 2.6 16.4 1.0
OD2 B:ASP232 2.7 16.9 1.0
CG B:ASP234 2.7 17.7 1.0
O3 B:ABH403 2.8 23.0 1.0
B B:ABH403 3.0 20.6 1.0
CE1 B:HIS126 3.0 16.5 1.0
CG B:ASP124 3.1 16.1 1.0
NA B:NA404 3.1 38.4 1.0
CG B:HIS126 3.3 18.1 1.0
MN B:MN401 3.4 20.3 1.0
OD2 B:ASP124 3.4 15.8 1.0
CG B:ASP232 3.4 18.1 1.0
CB B:HIS126 3.7 17.3 1.0
O2 B:ABH403 3.9 23.4 1.0
OD1 B:ASP232 3.9 16.9 1.0
N B:HIS126 4.0 15.8 1.0
CE B:ABH403 4.1 20.8 1.0
OG1 B:THR246 4.1 21.8 1.0
N B:ALA125 4.2 15.8 1.0
NE2 B:HIS126 4.2 17.3 1.0
CB B:ASP234 4.2 16.0 1.0
CD B:ABH403 4.2 20.4 1.0
OD1 B:ASP128 4.3 18.5 1.0
CD2 B:HIS126 4.3 17.9 1.0
CB B:ASP232 4.3 17.0 1.0
CB B:ASP124 4.5 16.9 1.0
CA B:HIS126 4.5 16.5 1.0
CB B:ALA125 4.6 15.0 1.0
CA B:ALA125 4.7 14.8 1.0
C B:ALA125 4.7 15.2 1.0
OD2 B:ASP128 4.8 20.4 1.0
CA B:ASP124 4.9 16.2 1.0
O B:HOH536 4.9 22.5 1.0
C B:ASP124 4.9 15.8 1.0
CG B:ASP128 5.0 18.4 1.0

Reference:

Y.Grobben, J.C.M.Uitdehaag, G.J.R.Zaman. Structural Insights Into Human Arginase-1 pH Dependence and Its Inhibition By the Small Molecule Inhibitor Cb-1158 J.Struct.Biol. 2019.
ISSN: ESSN 1095-8657
DOI: 10.1016/J.YJSBX.2019.100014
Page generated: Sun Oct 6 05:56:22 2024

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