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Manganese in PDB 8e5n: Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10

Enzymatic activity of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10

All present enzymatic activity of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10:
3.5.3.1;

Protein crystallography data

The structure of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10, PDB code: 8e5n was solved by R.L.Palte, S.Gathiaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.88 / 2.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.423, 287.535, 67.351, 90, 90.2, 90
R / Rfree (%) 23.7 / 29.6

Other elements in 8e5n:

The structure of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 (pdb code 8e5n). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10, PDB code: 8e5n:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 8e5n

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Manganese binding site 1 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:15.4
occ:1.00
 OD2 A:ASP232 2.3 25.8 1.0
OD2 A:ASP124 2.3 25.7 1.0
OD2 A:ASP128 2.4 9.1 1.0
ND1 A:HIS101 2.5 18.9 1.0
CG A:ASP124 3.2 23.0 1.0
CG A:ASP128 3.2 9.4 1.0
CG A:HIS101 3.3 17.4 1.0
MN A:MN1002 3.3 19.2 1.0
OD1 A:ASP124 3.3 23.5 1.0
CB A:HIS101 3.4 17.6 1.0
CG A:ASP232 3.4 23.8 1.0
OD1 A:ASP128 3.5 8.8 1.0
CE1 A:HIS101 3.6 18.8 1.0
CB A:ASP232 3.9 18.7 1.0
O A:HIS141 4.5 19.5 1.0
OD1 A:ASP232 4.5 24.7 1.0
CB A:ASP128 4.5 10.7 1.0
CD2 A:HIS101 4.5 17.7 1.0
NE1 A:TRP122 4.5 18.7 1.0
CB A:ASP124 4.6 18.2 1.0
NE2 A:HIS101 4.7 18.3 1.0
CG A:GLU277 4.8 25.1 1.0
CZ2 A:TRP122 4.8 18.7 1.0
CA A:HIS101 4.9 17.7 1.0
OD2 A:ASP234 4.9 18.4 1.0
OD1 A:ASP234 5.0 17.9 1.0

Manganese binding site 2 out of 12 in 8e5n

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Manganese binding site 2 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1002

b:19.2
occ:1.00
 ND1 A:HIS126 2.2 20.8 1.0
OD1 A:ASP124 2.3 23.5 1.0
OD2 A:ASP234 2.4 18.4 1.0
OD1 A:ASP234 2.8 17.9 1.0
CG A:ASP234 3.0 17.5 1.0
CG A:HIS126 3.0 18.9 1.0
CE1 A:HIS126 3.2 21.6 1.0
CB A:HIS126 3.3 16.1 1.0
MN A:MN1001 3.3 15.4 1.0
CG A:ASP124 3.3 23.0 1.0
OD2 A:ASP232 3.5 25.8 1.0
N A:HIS126 3.5 14.8 1.0
OD2 A:ASP124 3.7 25.7 1.0
CA A:HIS126 4.0 14.9 1.0
OG1 A:THR246 4.0 23.0 1.0
CG A:ASP232 4.1 23.8 1.0
CD2 A:HIS126 4.2 20.2 1.0
OD1 A:ASP128 4.2 8.8 1.0
N A:ALA125 4.2 15.7 1.0
NE2 A:HIS126 4.2 21.6 1.0
C28 A:UL01003 4.3 15.6 1.0
OD2 A:ASP128 4.4 9.1 1.0
CB A:ASP234 4.5 16.2 1.0
C A:ALA125 4.5 15.1 1.0
OD1 A:ASP232 4.5 24.7 1.0
CB A:ALA125 4.5 15.2 1.0
CB A:ASP124 4.6 18.2 1.0
CA A:ALA125 4.7 15.3 1.0
CG A:ASP128 4.7 9.4 1.0
O A:HIS126 4.7 14.1 1.0
C A:HIS126 4.8 14.8 1.0
C29 A:UL01003 4.9 15.4 1.0
CB A:ASP232 4.9 18.7 1.0
O A:THR246 5.0 19.0 1.0
C A:ASP124 5.0 16.4 1.0

Manganese binding site 3 out of 12 in 8e5n

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Manganese binding site 3 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1001

b:21.2
occ:1.00
 OD2 B:ASP128 2.0 16.8 1.0
OD2 B:ASP124 2.2 19.1 1.0
ND1 B:HIS101 2.3 23.6 1.0
OD2 B:ASP232 2.3 23.3 1.0
CG B:ASP128 2.9 15.7 1.0
CG B:HIS101 3.2 22.1 1.0
MN B:MN1002 3.2 16.6 1.0
CB B:HIS101 3.2 19.7 1.0
CG B:ASP124 3.2 17.4 1.0
CG B:ASP232 3.3 19.8 1.0
OD1 B:ASP128 3.3 15.5 1.0
CE1 B:HIS101 3.4 24.3 1.0
CB B:ASP232 3.7 14.4 1.0
OD1 B:ASP124 3.7 18.0 1.0
O B:HIS141 4.1 22.4 1.0
CB B:ASP128 4.2 14.9 1.0
CD2 B:HIS101 4.4 23.4 1.0
OD1 B:ASP232 4.4 20.5 1.0
NE2 B:HIS101 4.5 24.4 1.0
CB B:ASP124 4.5 13.5 1.0
CZ2 B:TRP122 4.6 18.6 1.0
CG B:GLU277 4.6 24.1 1.0
ND1 B:HIS141 4.6 28.8 1.0
NE1 B:TRP122 4.7 18.5 1.0
CA B:HIS101 4.8 19.1 1.0
OD1 B:ASP234 4.8 18.6 1.0
OE2 B:GLU277 4.9 26.5 1.0
CE2 B:TRP122 4.9 18.3 1.0
O B:HIS126 4.9 10.3 1.0

Manganese binding site 4 out of 12 in 8e5n

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Manganese binding site 4 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1002

b:16.6
occ:1.00
 OD1 B:ASP124 2.0 18.0 1.0
OD1 B:ASP234 2.0 18.6 1.0
OD2 B:ASP232 2.1 23.3 1.0
OD2 B:ASP234 2.4 19.8 1.0
CG B:ASP234 2.5 17.7 1.0
ND1 B:HIS126 2.6 7.0 1.0
CG B:ASP124 2.8 17.4 1.0
CG B:ASP232 3.0 19.8 1.0
OD2 B:ASP124 3.0 19.1 1.0
MN B:MN1001 3.2 21.2 1.0
CE1 B:HIS126 3.3 6.8 1.0
OD1 B:ASP232 3.5 20.5 1.0
CG B:HIS126 3.9 6.5 1.0
CB B:ASP234 4.0 13.7 1.0
CB B:ASP232 4.0 14.4 1.0
CB B:ASP124 4.2 13.5 1.0
N B:HIS126 4.3 8.9 1.0
CB B:HIS126 4.4 7.8 1.0
N B:ALA125 4.4 10.2 1.0
OG1 B:THR246 4.4 21.2 1.0
OD1 B:ASP128 4.4 15.5 1.0
OD2 B:ASP128 4.5 16.8 1.0
NE2 B:HIS126 4.6 6.7 1.0
CA B:ASP124 4.7 11.9 1.0
O B:HIS126 4.8 10.3 1.0
CA B:ASP234 4.8 11.9 1.0
CG B:ASP128 4.8 15.7 1.0
CD2 B:HIS126 4.9 6.6 1.0
CA B:HIS126 4.9 8.8 1.0
C B:ASP234 4.9 12.8 1.0
C28 B:UL01003 5.0 23.9 1.0
CB B:ALA125 5.0 8.9 1.0
C B:ASP124 5.0 11.4 1.0

Manganese binding site 5 out of 12 in 8e5n

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Manganese binding site 5 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1001

b:26.8
occ:1.00
 OD2 C:ASP124 2.2 16.3 1.0
OD2 C:ASP232 2.4 25.1 1.0
OD2 C:ASP128 2.4 15.9 1.0
ND1 C:HIS101 2.8 12.4 1.0
CG C:ASP124 3.0 14.7 1.0
MN C:MN1002 3.1 26.5 1.0
OD1 C:ASP124 3.1 14.5 1.0
CG C:ASP128 3.2 15.2 1.0
OD1 C:ASP128 3.3 16.3 1.0
CB C:HIS101 3.4 14.1 1.0
CG C:ASP232 3.4 22.2 1.0
CG C:HIS101 3.5 11.8 1.0
CB C:ASP232 3.8 17.5 1.0
CE1 C:HIS101 3.9 12.4 1.0
O C:HIS141 4.2 18.8 1.0
OD2 C:ASP234 4.2 25.2 1.0
CB C:ASP124 4.4 13.2 1.0
OD1 C:ASP232 4.5 22.9 1.0
OD1 C:ASP234 4.5 22.9 1.0
CB C:ASP128 4.6 13.0 1.0
CD2 C:HIS101 4.8 11.5 1.0
CG C:ASP234 4.8 22.4 1.0
CD C:GLU277 4.8 28.0 1.0
CZ2 C:TRP122 4.9 10.5 1.0
NE1 C:TRP122 4.9 11.2 1.0
CA C:HIS101 4.9 15.4 1.0
CG C:GLU277 4.9 22.0 1.0
NE2 C:HIS101 4.9 12.1 1.0
OE1 C:GLU277 5.0 31.0 1.0

Manganese binding site 6 out of 12 in 8e5n

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Manganese binding site 6 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1002

b:26.5
occ:1.00
 OD2 C:ASP234 2.1 25.2 1.0
OD1 C:ASP124 2.1 14.5 1.0
OD1 C:ASP234 2.3 22.9 1.0
CG C:ASP234 2.5 22.4 1.0
ND1 C:HIS126 2.6 18.0 1.0
OD2 C:ASP232 2.9 25.1 1.0
MN C:MN1001 3.1 26.8 1.0
CG C:ASP124 3.2 14.7 1.0
CE1 C:HIS126 3.6 18.7 1.0
OD2 C:ASP124 3.6 16.3 1.0
CG C:HIS126 3.6 16.0 1.0
CB C:HIS126 3.8 14.8 1.0
CG C:ASP232 3.8 22.2 1.0
OG1 C:THR246 3.9 22.1 1.0
N C:HIS126 3.9 14.0 1.0
CB C:ASP234 4.0 17.2 1.0
N C:ALA125 4.1 13.9 1.0
OD1 C:ASP128 4.4 16.3 1.0
CB C:ASP124 4.5 13.2 1.0
CA C:HIS126 4.5 14.5 1.0
OD1 C:ASP232 4.5 22.9 1.0
CB C:ALA125 4.6 14.0 1.0
CB C:ASP232 4.6 17.5 1.0
NE2 C:HIS126 4.7 18.6 1.0
CD2 C:HIS126 4.7 17.0 1.0
CA C:ALA125 4.7 14.0 1.0
C C:ALA125 4.7 14.0 1.0
C28 C:UL01003 4.8 19.2 1.0
C29 C:UL01003 4.8 19.3 1.0
OE1 C:GLU277 4.8 31.0 1.0
CA C:ASP124 4.9 12.4 1.0
OD2 C:ASP128 4.9 15.9 1.0
O C:THR246 4.9 19.1 1.0
C C:ASP124 4.9 13.5 1.0
CA C:ASP234 5.0 15.2 1.0

Manganese binding site 7 out of 12 in 8e5n

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Manganese binding site 7 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1001

b:40.2
occ:1.00
 ND1 D:HIS101 2.1 13.4 1.0
OD2 D:ASP128 2.2 26.9 1.0
OD2 D:ASP232 2.5 15.9 1.0
CG D:HIS101 2.9 12.3 1.0
CG D:ASP128 3.0 24.2 1.0
CB D:HIS101 3.0 12.2 1.0
CE1 D:HIS101 3.2 13.4 1.0
OD2 D:ASP124 3.2 26.3 1.0
OD1 D:ASP128 3.2 24.1 1.0
MN D:MN1002 3.3 35.7 1.0
CG D:ASP124 3.5 22.6 1.0
CG D:ASP232 3.6 14.7 1.0
OD1 D:ASP124 3.7 24.0 1.0
O D:HIS141 3.8 13.7 1.0
CD2 D:HIS101 4.1 12.7 1.0
CB D:ASP232 4.2 15.0 1.0
NE2 D:HIS101 4.2 13.2 1.0
CB D:ASP128 4.3 19.6 1.0
NE1 D:TRP122 4.5 9.6 1.0
CB D:ASP124 4.5 15.2 1.0
CA D:HIS101 4.6 11.9 1.0
OD1 D:ASP232 4.6 13.0 1.0
OE2 D:GLU277 4.6 36.0 1.0
ND1 D:HIS126 4.8 15.8 1.0
CZ2 D:TRP122 4.8 9.7 1.0
CG D:GLU277 4.8 29.0 1.0
OD1 D:ASP234 4.8 24.0 1.0

Manganese binding site 8 out of 12 in 8e5n

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Manganese binding site 8 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1002

b:35.7
occ:1.00
 OD1 D:ASP234 2.0 24.0 1.0
ND1 D:HIS126 2.2 15.8 1.0
OD1 D:ASP124 2.3 24.0 1.0
OD2 D:ASP232 2.5 15.9 1.0
CE1 D:HIS126 2.6 16.1 1.0
CG D:ASP234 2.9 25.2 1.0
OD2 D:ASP234 3.1 27.8 1.0
CG D:ASP124 3.1 22.6 1.0
OD2 D:ASP124 3.3 26.3 1.0
MN D:MN1001 3.3 40.2 1.0
CG D:HIS126 3.4 14.3 1.0
CG D:ASP232 3.5 14.7 1.0
OG1 D:THR246 3.7 21.9 1.0
NE2 D:HIS126 3.8 16.4 1.0
OD1 D:ASP232 3.9 13.0 1.0
CB D:HIS126 4.2 13.1 1.0
CD2 D:HIS126 4.2 15.4 1.0
CB D:ASP234 4.3 21.4 1.0
N D:HIS126 4.4 12.9 1.0
OD1 D:ASP128 4.4 24.1 1.0
N D:ALA125 4.4 12.7 1.0
CB D:ASP124 4.6 15.2 1.0
CB D:ASP232 4.7 15.0 1.0
C29 D:UL01003 4.7 16.2 1.0
O D:THR246 4.7 20.8 1.0
C28 D:UL01003 4.8 16.2 1.0
CB D:ALA125 4.8 12.8 1.0
ND1 D:HIS101 4.9 13.4 1.0
CA D:HIS126 4.9 12.8 1.0
CB D:THR246 5.0 20.8 1.0

Manganese binding site 9 out of 12 in 8e5n

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Manganese binding site 9 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1001

b:25.0
occ:1.00
 OD2 E:ASP124 2.0 18.3 1.0
OD2 E:ASP128 2.0 24.0 1.0
ND1 E:HIS101 2.5 32.9 1.0
OD2 E:ASP232 2.8 32.5 1.0
CG E:ASP128 2.8 21.8 1.0
CG E:ASP124 2.9 17.2 1.0
OD1 E:ASP128 3.0 21.1 1.0
OD1 E:ASP124 3.2 18.3 1.0
CG E:HIS101 3.2 30.9 1.0
MN E:MN1002 3.3 22.0 1.0
CB E:HIS101 3.4 28.4 1.0
CE1 E:HIS101 3.4 33.4 1.0
CG E:ASP232 3.7 30.5 1.0
O E:HIS141 3.8 29.9 1.0
CB E:ASP232 4.0 25.7 1.0
CB E:ASP128 4.2 20.2 1.0
NE1 E:TRP122 4.2 18.6 1.0
CB E:ASP124 4.3 13.7 1.0
CD2 E:HIS101 4.4 32.0 1.0
NE2 E:HIS101 4.4 33.3 1.0
CZ2 E:TRP122 4.7 19.1 1.0
CE2 E:TRP122 4.8 18.5 1.0
OD1 E:ASP234 4.9 25.5 1.0
OD1 E:ASP232 4.9 31.5 1.0
CA E:HIS101 4.9 26.9 1.0
C28 E:UL01003 4.9 26.2 1.0
OE2 E:GLU277 5.0 40.3 1.0

Manganese binding site 10 out of 12 in 8e5n

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Manganese binding site 10 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1002

b:22.0
occ:1.00
 OD1 E:ASP124 2.0 18.3 1.0
OD2 E:ASP234 2.2 28.9 1.0
OD1 E:ASP234 2.3 25.5 1.0
ND1 E:HIS126 2.4 13.4 1.0
CG E:ASP234 2.6 25.9 1.0
OD2 E:ASP232 2.7 32.5 1.0
CG E:ASP124 3.1 17.2 1.0
CE1 E:HIS126 3.1 13.3 1.0
MN E:MN1001 3.3 25.0 1.0
OD2 E:ASP124 3.5 18.3 1.0
CG E:HIS126 3.6 12.5 1.0
CG E:ASP232 3.6 30.5 1.0
N E:ALA125 3.9 10.6 1.0
N E:HIS126 4.0 11.0 1.0
CB E:HIS126 4.1 12.3 1.0
CB E:ASP234 4.1 22.1 1.0
OG1 E:THR246 4.1 21.8 1.0
OD1 E:ASP232 4.3 31.5 1.0
NE2 E:HIS126 4.3 13.5 1.0
CB E:ALA125 4.4 10.1 1.0
CB E:ASP232 4.4 25.7 1.0
CB E:ASP124 4.4 13.7 1.0
OD1 E:ASP128 4.5 21.1 1.0
CD2 E:HIS126 4.6 13.1 1.0
CA E:ALA125 4.6 10.3 1.0
C28 E:UL01003 4.6 26.2 1.0
CA E:HIS126 4.7 12.3 1.0
C E:ALA125 4.7 10.3 1.0
CA E:ASP124 4.8 12.3 1.0
C E:ASP124 4.9 11.3 1.0
OD2 E:ASP128 5.0 24.0 1.0
O E:HIS126 5.0 15.1 1.0
O E:HOH1101 5.0 3.0 1.0

Reference:

S.Gathiaka, R.L.Palte, S.S.So, X.Chai, J.Richard Miller, R.Kuvelkar, J.Wen, S.Cifelli, A.Kreamer, A.Liaw, D.G.Mclaren, C.Fischer. Discovery of Non-Boronic Acid Arginase 1 Inhibitors Through Virtual Screening and Biophysical Methods. Bioorg.Med.Chem.Lett. 29193 2023.
ISSN: ESSN 1464-3405
PubMed: 36822300
DOI: 10.1016/J.BMCL.2023.129193
Page generated: Sun Oct 6 11:38:19 2024

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