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Manganese in PDB 6q92: Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh

Enzymatic activity of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh

All present enzymatic activity of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh, PDB code: 6q92 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) 39.14 / 1.50
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.380, 90.380, 69.254, 90.00, 90.00, 120.00
R / Rfree (%) 13.5 / 14.7

Other elements in 6q92:

The structure of Crystal Structure of Human Arginase-1 at pH 7.0 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 7.0 in Complex with Abh (pdb code 6q92). 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 7.0 in Complex with Abh, PDB code: 6q92:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6q92

Go back to Manganese Binding Sites List in 6q92
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 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 7.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:7.8
occ:1.00
OD2 A:ASP128 2.1 8.7 1.0
OD2 A:ASP232 2.2 7.2 1.0
O2 A:ABH403 2.2 11.0 1.0
OD2 A:ASP124 2.2 7.3 1.0
ND1 A:HIS101 2.2 7.6 1.0
O1 A:ABH403 2.3 9.7 1.0
B A:ABH403 2.8 9.9 1.0
CG A:ASP128 3.1 8.1 1.0
CG A:ASP124 3.2 6.5 1.0
CG A:HIS101 3.2 8.0 1.0
CG A:ASP232 3.2 7.3 1.0
CE1 A:HIS101 3.3 8.1 1.0
OD1 A:ASP128 3.3 8.6 1.0
CB A:HIS101 3.4 8.1 1.0
MN A:MN402 3.4 6.2 1.0
OD1 A:ASP124 3.5 6.7 1.0
CB A:ASP232 3.6 7.3 1.0
O3 A:ABH403 3.7 9.4 1.0
CE A:ABH403 4.1 10.2 1.0
NA A:NA404 4.2 12.2 1.0
CD2 A:HIS101 4.3 8.0 1.0
NE2 A:HIS101 4.3 8.0 1.0
OD1 A:ASP232 4.4 7.4 1.0
NE1 A:TRP122 4.4 6.8 1.0
O A:HIS141 4.4 8.3 1.0
CB A:ASP128 4.5 7.8 1.0
CB A:ASP124 4.5 6.3 1.0
OD2 A:ASP234 4.6 8.7 1.0
CZ2 A:TRP122 4.6 6.8 1.0
CE2 A:TRP122 4.9 6.9 1.0
CG A:GLU277 4.9 9.9 1.0
CA A:HIS101 4.9 7.9 1.0
CA A:ASP232 5.0 7.4 1.0
OE2 A:GLU277 5.0 11.0 1.0

Manganese binding site 2 out of 4 in 6q92

Go back to Manganese Binding Sites List in 6q92
Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 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 7.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:6.2
occ:1.00
O1 A:ABH403 1.9 9.7 1.0
OD1 A:ASP124 2.0 6.7 1.0
ND1 A:HIS126 2.0 8.2 1.0
OD2 A:ASP234 2.0 8.7 1.0
CG A:ASP234 2.8 7.7 1.0
OD1 A:ASP234 2.8 7.4 1.0
CE1 A:HIS126 2.9 7.6 1.0
OD2 A:ASP232 3.0 7.2 1.0
CG A:ASP124 3.0 6.5 1.0
CG A:HIS126 3.0 7.6 1.0
B A:ABH403 3.1 9.9 1.0
O3 A:ABH403 3.1 9.4 1.0
NA A:NA404 3.4 12.2 1.0
CB A:HIS126 3.4 7.4 1.0
MN A:MN401 3.4 7.8 1.0
OD2 A:ASP124 3.4 7.3 1.0
CG A:ASP232 3.7 7.3 1.0
N A:HIS126 3.8 6.8 1.0
O2 A:ABH403 4.0 11.0 1.0
OG1 A:THR246 4.0 11.5 1.0
NE2 A:HIS126 4.1 8.0 1.0
CE A:ABH403 4.1 10.2 1.0
OD1 A:ASP128 4.1 8.6 1.0
N A:ALA125 4.1 6.3 1.0
CD2 A:HIS126 4.1 7.8 1.0
OD1 A:ASP232 4.2 7.4 1.0
CD A:ABH403 4.2 10.3 1.0
CA A:HIS126 4.2 7.1 1.0
CB A:ASP234 4.2 7.6 1.0
CB A:ASP124 4.4 6.3 1.0
CB A:ASP232 4.5 7.3 1.0
CB A:ALA125 4.5 6.6 1.0
C A:ALA125 4.6 6.5 1.0
CA A:ALA125 4.6 6.5 1.0
OD2 A:ASP128 4.7 8.7 1.0
CA A:ASP124 4.8 6.4 1.0
CG A:ASP128 4.8 8.1 1.0
O A:HIS126 4.8 7.5 1.0
C A:ASP124 4.9 6.3 1.0
C A:HIS126 5.0 7.0 1.0
O A:THR246 5.0 10.2 1.0

Manganese binding site 3 out of 4 in 6q92

Go back to Manganese Binding Sites List in 6q92
Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 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 7.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:9.6
occ:1.00
OD2 B:ASP124 2.1 7.4 1.0
OD2 B:ASP128 2.1 9.2 1.0
OD2 B:ASP232 2.2 8.7 1.0
ND1 B:HIS101 2.2 10.3 1.0
O1 B:ABH403 2.3 13.3 1.0
O2 B:ABH403 2.3 13.4 1.0
B B:ABH403 2.8 12.3 1.0
CG B:ASP124 3.1 7.3 1.0
CG B:ASP128 3.1 8.9 1.0
CE1 B:HIS101 3.2 10.3 1.0
CG B:HIS101 3.2 10.6 1.0
CG B:ASP232 3.3 9.0 1.0
MN B:MN402 3.4 7.8 1.0
OD1 B:ASP128 3.4 9.7 1.0
OD1 B:ASP124 3.5 7.7 1.0
CB B:HIS101 3.5 11.0 1.0
CB B:ASP232 3.6 9.2 1.0
O3 B:ABH403 3.7 11.8 1.0
CE B:ABH403 4.0 12.9 1.0
NA B:NA404 4.1 14.1 1.0
NE2 B:HIS101 4.3 10.1 1.0
CD2 B:HIS101 4.3 10.6 1.0
NE1 B:TRP122 4.3 9.3 1.0
OD1 B:ASP232 4.4 8.8 1.0
O B:HIS141 4.4 11.6 1.0
CB B:ASP124 4.5 7.7 1.0
CB B:ASP128 4.5 8.9 1.0
CZ2 B:TRP122 4.6 9.5 1.0
OD2 B:ASP234 4.6 10.4 1.0
CE2 B:TRP122 4.8 9.2 1.0
CG B:GLU277 4.9 13.0 1.0
CA B:ASP232 5.0 9.4 1.0
OE2 B:GLU277 5.0 14.1 1.0

Manganese binding site 4 out of 4 in 6q92

Go back to Manganese Binding Sites List in 6q92
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 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 7.0 in Complex with Abh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:7.8
occ:1.00
O1 B:ABH403 1.9 13.3 1.0
OD2 B:ASP234 2.0 10.4 1.0
OD1 B:ASP124 2.0 7.7 1.0
ND1 B:HIS126 2.0 9.2 1.0
CG B:ASP234 2.7 9.2 1.0
OD1 B:ASP234 2.8 10.1 1.0
CE1 B:HIS126 2.9 9.0 1.0
CG B:ASP124 3.0 7.3 1.0
OD2 B:ASP232 3.0 8.7 1.0
B B:ABH403 3.0 12.3 1.0
CG B:HIS126 3.1 9.1 1.0
O3 B:ABH403 3.1 11.8 1.0
NA B:NA404 3.3 14.1 1.0
OD2 B:ASP124 3.4 7.4 1.0
CB B:HIS126 3.4 8.8 1.0
MN B:MN401 3.4 9.6 1.0
CG B:ASP232 3.7 9.0 1.0
N B:HIS126 3.9 8.1 1.0
O2 B:ABH403 4.0 13.4 1.0
CE B:ABH403 4.0 12.9 1.0
OG1 B:THR246 4.1 13.3 1.0
NE2 B:HIS126 4.1 9.5 1.0
CD B:ABH403 4.1 13.2 1.0
N B:ALA125 4.1 7.6 1.0
CD2 B:HIS126 4.2 9.8 1.0
OD1 B:ASP232 4.2 8.8 1.0
OD1 B:ASP128 4.2 9.7 1.0
CB B:ASP234 4.2 9.2 1.0
CA B:HIS126 4.3 8.6 1.0
CB B:ASP124 4.4 7.7 1.0
CB B:ASP232 4.5 9.2 1.0
CB B:ALA125 4.6 7.5 1.0
OD2 B:ASP128 4.6 9.2 1.0
C B:ALA125 4.7 7.6 1.0
CA B:ALA125 4.7 7.6 1.0
CA B:ASP124 4.8 7.7 1.0
CG B:ASP128 4.8 8.9 1.0
C B:ASP124 4.9 7.6 1.0
O B:THR246 4.9 12.8 1.0
O B:HIS126 4.9 9.0 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 05:54:44 2024

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