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Manganese in PDB 4ie2: Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H

Enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H

All present enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H, PDB code: 4ie2 was solved by A.Cousido-Siah, A.Mitschler, F.X.Ruiz, P.Beckett, M.C.Van Zandt, M.K.Ji, D.Whitehouse, T.Ryder, E.Jagdmann, M.Andreoli, A.Mazur, M.Padmanilayam, H.Schroeter, A.Golebiowski, A.Podjarny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.51 / 2.21
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.094, 128.094, 159.085, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H (pdb code 4ie2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H, PDB code: 4ie2:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4ie2

Go back to Manganese Binding Sites List in 4ie2
Manganese binding site 1 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H


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-2 Complexed with Inhibitor 1H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.8
occ:1.00
 OD2 A:ASP143 2.1 14.4 1.0
OD2 A:ASP147 2.1 14.9 1.0
ND1 A:HIS120 2.2 15.0 1.0
O13 A:1EC405 2.2 13.7 1.0
O11 A:1EC405 2.3 12.6 1.0
OD2 A:ASP251 2.3 15.5 1.0
B10 A:1EC405 2.7 14.8 1.0
CG A:ASP147 3.1 17.7 1.0
CG A:ASP143 3.1 14.6 1.0
CG A:HIS120 3.2 14.3 1.0
CE1 A:HIS120 3.2 14.8 1.0
CG A:ASP251 3.3 14.9 1.0
MN A:MN402 3.3 17.6 1.0
O23 A:1EC405 3.4 12.7 1.0
OD1 A:ASP147 3.4 15.2 1.0
CB A:HIS120 3.4 16.8 1.0
OD1 A:ASP143 3.5 13.8 1.0
CB A:ASP251 3.6 13.2 1.0
C9 A:1EC405 4.1 13.5 1.0
NE1 A:TRP141 4.3 18.1 1.0
NE2 A:HIS120 4.3 15.3 1.0
CD2 A:HIS120 4.3 12.1 1.0
OD1 A:ASP251 4.4 12.2 1.0
CB A:ASP143 4.4 12.5 1.0
CB A:ASP147 4.5 15.8 1.0
O A:HIS160 4.5 13.6 1.0
CZ2 A:TRP141 4.6 14.5 1.0
CG A:GLU296 4.8 14.4 1.0
CE2 A:TRP141 4.8 14.0 1.0
CG2 A:VAL295 4.9 11.8 1.0
CA A:ASP251 4.9 13.6 1.0
CA A:HIS120 4.9 14.1 1.0
OD2 A:ASP253 5.0 15.5 1.0
ND1 A:HIS145 5.0 17.9 1.0

Manganese binding site 2 out of 6 in 4ie2

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Manganese binding site 2 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H


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-2 Complexed with Inhibitor 1H within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:17.6
occ:1.00
 ND1 A:HIS145 2.1 17.9 1.0
OD1 A:ASP143 2.2 13.8 1.0
O13 A:1EC405 2.2 13.7 1.0
OD2 A:ASP253 2.2 15.5 1.0
OD2 A:ASP251 2.2 15.5 1.0
OD1 A:ASP253 2.5 16.8 1.0
CG A:ASP253 2.7 21.5 1.0
O23 A:1EC405 2.9 12.7 1.0
CE1 A:HIS145 3.0 13.9 1.0
CG A:ASP143 3.1 14.6 1.0
CG A:ASP251 3.1 14.9 1.0
CG A:HIS145 3.2 17.3 1.0
B10 A:1EC405 3.2 14.8 1.0
MN A:MN401 3.3 16.8 1.0
OD2 A:ASP143 3.4 14.4 1.0
CB A:HIS145 3.6 16.0 1.0
OD1 A:ASP251 3.7 12.2 1.0
N A:HIS145 4.0 13.8 1.0
CB A:ASP251 4.1 13.2 1.0
O11 A:1EC405 4.2 12.6 1.0
N A:ALA144 4.2 13.2 1.0
NE2 A:HIS145 4.2 14.3 1.0
CB A:ASP253 4.2 14.9 1.0
OG1 A:THR265 4.2 17.3 0.2
CD2 A:HIS145 4.3 11.4 1.0
C8 A:1EC405 4.4 18.4 1.0
C9 A:1EC405 4.4 13.5 1.0
OD1 A:ASP147 4.5 15.2 1.0
CA A:HIS145 4.5 14.9 1.0
CB A:ASP143 4.5 12.5 1.0
CB A:ALA144 4.7 16.1 1.0
OD2 A:ASP147 4.7 14.9 1.0
O A:HOH513 4.7 13.4 1.0
CA A:ALA144 4.8 16.2 1.0
C A:ALA144 4.8 16.6 1.0
CA A:ASP143 4.8 14.4 1.0
C A:ASP143 4.9 19.5 1.0

Manganese binding site 3 out of 6 in 4ie2

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Manganese binding site 3 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H


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-2 Complexed with Inhibitor 1H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:17.6
occ:1.00
 OD2 B:ASP143 2.0 10.7 1.0
OD2 B:ASP147 2.1 17.2 1.0
O11 B:1EC406 2.2 15.2 1.0
OD2 B:ASP251 2.2 14.8 1.0
O13 B:1EC406 2.3 17.0 1.0
ND1 B:HIS120 2.3 13.8 1.0
B10 B:1EC406 2.6 15.4 1.0
CG B:ASP147 3.1 18.7 1.0
CG B:ASP143 3.1 14.4 1.0
CG B:HIS120 3.2 17.9 1.0
CE1 B:HIS120 3.2 15.9 1.0
CG B:ASP251 3.2 16.6 1.0
MN B:MN402 3.3 18.9 1.0
O23 B:1EC406 3.3 17.1 1.0
OD1 B:ASP147 3.3 14.3 1.0
OD1 B:ASP143 3.4 13.4 1.0
CB B:HIS120 3.5 14.6 1.0
CB B:ASP251 3.6 13.7 1.0
C9 B:1EC406 4.1 17.6 1.0
NE1 B:TRP141 4.3 12.9 1.0
CD2 B:HIS120 4.3 13.7 1.0
NE2 B:HIS120 4.3 13.7 1.0
OD1 B:ASP251 4.4 14.3 1.0
CB B:ASP143 4.4 13.1 1.0
CB B:ASP147 4.5 17.4 1.0
O B:HIS160 4.5 14.1 1.0
CZ2 B:TRP141 4.7 16.7 1.0
CG B:GLU296 4.8 14.3 1.0
CE2 B:TRP141 4.8 13.8 1.0
CA B:ASP251 4.9 13.5 1.0
OD2 B:ASP253 5.0 16.2 1.0
CA B:HIS120 5.0 17.2 1.0
CG2 B:VAL295 5.0 14.4 1.0

Manganese binding site 4 out of 6 in 4ie2

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Manganese binding site 4 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H


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-2 Complexed with Inhibitor 1H within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:18.9
occ:1.00
 OD1 B:ASP143 2.1 13.4 1.0
OD2 B:ASP253 2.2 16.2 1.0
O13 B:1EC406 2.3 17.0 1.0
ND1 B:HIS145 2.3 16.4 1.0
OD1 B:ASP253 2.4 17.0 1.0
OD2 B:ASP251 2.4 14.8 1.0
CG B:ASP253 2.6 15.0 1.0
O23 B:1EC406 2.7 17.1 1.0
CG B:ASP143 3.1 14.4 1.0
CE1 B:HIS145 3.1 15.5 1.0
CG B:ASP251 3.2 16.6 1.0
B10 B:1EC406 3.2 15.4 1.0
MN B:MN401 3.3 17.6 1.0
CG B:HIS145 3.3 18.9 1.0
OD2 B:ASP143 3.4 10.7 1.0
CB B:HIS145 3.7 14.7 1.0
OD1 B:ASP251 3.7 14.3 1.0
N B:HIS145 4.0 15.7 1.0
O11 B:1EC406 4.1 15.2 1.0
CB B:ASP251 4.1 13.7 1.0
N B:ALA144 4.1 16.7 1.0
CB B:ASP253 4.2 13.1 1.0
OG1 B:THR265 4.2 36.9 1.0
NE2 B:HIS145 4.3 16.1 1.0
C9 B:1EC406 4.4 17.6 1.0
OD1 B:ASP147 4.4 14.3 1.0
CD2 B:HIS145 4.4 15.7 1.0
C8 B:1EC406 4.4 14.5 1.0
CA B:HIS145 4.5 15.5 1.0
CB B:ASP143 4.5 13.1 1.0
CB B:ALA144 4.6 14.0 1.0
OD2 B:ASP147 4.7 17.2 1.0
CA B:ALA144 4.7 18.3 1.0
C B:ALA144 4.8 20.3 1.0
O B:HOH544 4.8 17.8 1.0
CA B:ASP143 4.9 15.5 1.0
C B:ASP143 4.9 16.9 1.0

Manganese binding site 5 out of 6 in 4ie2

Go back to Manganese Binding Sites List in 4ie2
Manganese binding site 5 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:19.6
occ:1.00
 O13 C:1EC404 2.2 20.2 1.0
OD1 C:ASP143 2.2 13.9 1.0
OD2 C:ASP253 2.2 16.4 1.0
OD2 C:ASP251 2.3 17.3 1.0
ND1 C:HIS145 2.3 17.5 1.0
OD1 C:ASP253 2.5 18.1 1.0
O23 C:1EC404 2.6 21.3 1.0
CG C:ASP253 2.7 20.8 1.0
B10 C:1EC404 3.1 17.6 1.0
CG C:ASP251 3.1 18.7 1.0
CE1 C:HIS145 3.2 19.2 1.0
CG C:ASP143 3.2 14.1 1.0
CG C:HIS145 3.3 20.3 1.0
MN C:MN402 3.3 18.5 1.0
OD2 C:ASP143 3.5 14.8 1.0
CB C:HIS145 3.7 19.4 1.0
OD1 C:ASP251 3.8 16.5 1.0
O11 C:1EC404 4.0 17.5 1.0
N C:HIS145 4.0 14.8 1.0
CB C:ASP251 4.0 13.6 1.0
OG1 C:THR265 4.1 17.5 0.4
N C:ALA144 4.2 17.6 1.0
CB C:ASP253 4.2 16.9 1.0
C9 C:1EC404 4.3 19.7 1.0
C8 C:1EC404 4.3 16.9 1.0
NE2 C:HIS145 4.3 16.1 1.0
CD2 C:HIS145 4.4 16.1 1.0
OD1 C:ASP147 4.4 17.1 1.0
CA C:HIS145 4.5 17.1 1.0
CB C:ASP143 4.6 14.2 1.0
CB C:ALA144 4.7 15.1 1.0
O C:HOH536 4.7 16.8 1.0
CA C:ALA144 4.8 16.2 1.0
C C:ALA144 4.8 17.1 1.0
OD2 C:ASP147 4.8 20.4 1.0
CA C:ASP143 4.9 15.6 1.0
C C:ASP143 5.0 15.3 1.0

Manganese binding site 6 out of 6 in 4ie2

Go back to Manganese Binding Sites List in 4ie2
Manganese binding site 6 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 1H within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:18.5
occ:1.00
 O11 C:1EC404 2.1 17.5 1.0
OD2 C:ASP147 2.1 20.4 1.0
ND1 C:HIS120 2.2 14.7 1.0
OD2 C:ASP143 2.2 14.8 1.0
O13 C:1EC404 2.2 20.2 1.0
OD2 C:ASP251 2.4 17.3 1.0
B10 C:1EC404 2.6 17.6 1.0
CG C:ASP147 3.0 15.6 1.0
CG C:HIS120 3.1 18.0 1.0
CE1 C:HIS120 3.1 17.3 1.0
CG C:ASP143 3.2 14.1 1.0
OD1 C:ASP147 3.2 17.1 1.0
CG C:ASP251 3.3 18.7 1.0
O23 C:1EC404 3.3 21.3 1.0
MN C:MN401 3.3 19.6 1.0
CB C:HIS120 3.4 18.4 1.0
OD1 C:ASP143 3.5 13.9 1.0
CB C:ASP251 3.6 13.6 1.0
C9 C:1EC404 4.0 19.7 1.0
NE2 C:HIS120 4.2 17.3 1.0
CD2 C:HIS120 4.3 18.7 1.0
NE1 C:TRP141 4.3 16.6 1.0
CB C:ASP147 4.4 16.4 1.0
O C:HIS160 4.4 17.1 1.0
OD1 C:ASP251 4.4 16.5 1.0
CB C:ASP143 4.5 14.2 1.0
CZ2 C:TRP141 4.6 16.7 1.0
CE2 C:TRP141 4.8 21.3 1.0
CG C:GLU296 4.8 17.6 1.0
CA C:HIS120 4.9 18.4 1.0
CA C:ASP251 4.9 15.0 1.0

Reference:

A.Golebiowski, R.Paul Beckett, M.Van Zandt, M.K.Ji, D.Whitehouse, T.R.Ryder, E.Jagdmann, M.Andreoli, A.Mazur, M.Padmanilayam, A.Cousido-Siah, A.Mitschler, F.X.Ruiz, A.Podjarny, H.Schroeter. 2-Substituted-2-Amino-6-Boronohexanoic Acids As Arginase Inhibitors. Bioorg.Med.Chem.Lett. V. 23 2027 2013.
ISSN: ISSN 0960-894X
PubMed: 23453840
DOI: 10.1016/J.BMCL.2013.02.024
Page generated: Sat Oct 5 19:47:32 2024

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