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Manganese in PDB 4ie3: Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O

Enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O

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

Protein crystallography data

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O, PDB code: 4ie3 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) 25.96 / 2.35
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.086, 128.086, 159.079, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 19.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O (pdb code 4ie3). 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 Inhbitor 1O, PDB code: 4ie3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4ie3

Go back to Manganese Binding Sites List in 4ie3
Manganese binding site 1 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O


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 Inhbitor 1O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:13.3
occ:1.00
 OD2 A:ASP143 2.1 10.0 1.0
OD2 A:ASP147 2.1 13.6 1.0
ND1 A:HIS120 2.3 13.6 1.0
O22 A:1EE405 2.3 10.3 1.0
OD2 A:ASP251 2.3 12.4 1.0
O12 A:1EE405 2.4 10.8 1.0
B10 A:1EE405 2.8 14.5 1.0
CG A:ASP147 3.1 14.0 1.0
CG A:ASP143 3.1 13.7 1.0
CG A:HIS120 3.2 15.6 1.0
CE1 A:HIS120 3.2 16.2 1.0
CG A:ASP251 3.3 13.7 1.0
MN A:MN402 3.4 14.4 1.0
OD1 A:ASP147 3.4 14.2 1.0
CB A:HIS120 3.5 13.8 1.0
OD1 A:ASP143 3.5 12.4 1.0
O11 A:1EE405 3.5 11.9 1.0
CB A:ASP251 3.6 10.7 1.0
NE1 A:TRP141 4.3 12.1 1.0
C9 A:1EE405 4.3 12.5 1.0
NE2 A:HIS120 4.3 13.1 1.0
CD2 A:HIS120 4.3 9.1 1.0
OD1 A:ASP251 4.4 11.6 1.0
CB A:ASP147 4.5 12.6 1.0
CB A:ASP143 4.5 10.4 1.0
O A:HIS160 4.5 11.1 1.0
CZ2 A:TRP141 4.6 12.3 1.0
CE2 A:TRP141 4.8 11.0 1.0
CG A:GLU296 4.8 14.7 1.0
CA A:ASP251 4.9 11.8 1.0
CG2 A:VAL295 5.0 9.4 1.0
CA A:HIS120 5.0 10.6 1.0

Manganese binding site 2 out of 6 in 4ie3

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


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 Inhbitor 1O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:14.4
occ:1.00
 O12 A:1EE405 2.1 10.8 1.0
OD1 A:ASP143 2.2 12.4 1.0
OD2 A:ASP253 2.2 14.7 1.0
ND1 A:HIS145 2.2 12.3 1.0
OD2 A:ASP251 2.3 12.4 1.0
OD1 A:ASP253 2.5 12.1 1.0
CG A:ASP253 2.7 16.7 1.0
O11 A:1EE405 2.9 11.9 1.0
CE1 A:HIS145 3.1 12.3 1.0
CG A:ASP143 3.1 13.7 1.0
B10 A:1EE405 3.2 14.5 1.0
CG A:ASP251 3.2 13.7 1.0
CG A:HIS145 3.3 16.6 1.0
MN A:MN401 3.4 13.3 1.0
OD2 A:ASP143 3.4 10.0 1.0
CB A:HIS145 3.7 12.9 1.0
OD1 A:ASP251 3.7 11.6 1.0
N A:HIS145 3.9 12.6 1.0
O22 A:1EE405 4.1 10.3 1.0
CB A:ASP251 4.1 10.7 1.0
C8 A:1EE405 4.1 13.3 1.0
OG1 A:THR265 4.2 15.0 0.3
NE2 A:HIS145 4.2 11.6 1.0
N A:ALA144 4.2 10.3 1.0
CB A:ASP253 4.2 8.5 1.0
C9 A:1EE405 4.3 12.5 1.0
CD2 A:HIS145 4.4 9.2 1.0
CA A:HIS145 4.4 13.7 1.0
OD1 A:ASP147 4.5 14.2 1.0
CB A:ASP143 4.5 10.4 1.0
CB A:ALA144 4.6 9.1 1.0
C A:ALA144 4.8 13.7 1.0
CA A:ALA144 4.8 11.0 1.0
O A:HOH517 4.8 14.7 1.0
OD2 A:ASP147 4.8 13.6 1.0
CA A:ASP143 4.9 10.4 1.0
C A:ASP143 5.0 14.5 1.0

Manganese binding site 3 out of 6 in 4ie3

Go back to Manganese Binding Sites List in 4ie3
Manganese binding site 3 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O


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 Inhbitor 1O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:15.5
occ:1.00
 OD2 B:ASP143 2.1 9.5 1.0
OD2 B:ASP147 2.2 17.0 1.0
O22 B:1EE406 2.3 13.6 1.0
OD2 B:ASP251 2.3 13.3 1.0
ND1 B:HIS120 2.3 12.9 1.0
O12 B:1EE406 2.4 14.6 1.0
B10 B:1EE406 2.7 16.5 1.0
CG B:ASP147 3.1 17.4 1.0
CG B:ASP143 3.2 10.9 1.0
CG B:HIS120 3.2 16.3 1.0
OD1 B:ASP147 3.3 13.3 1.0
CE1 B:HIS120 3.3 11.5 1.0
MN B:MN402 3.3 15.2 1.0
CG B:ASP251 3.3 15.0 1.0
O11 B:1EE406 3.5 13.5 1.0
CB B:HIS120 3.5 12.9 1.0
OD1 B:ASP143 3.5 10.5 1.0
CB B:ASP251 3.7 10.2 1.0
C9 B:1EE406 4.2 13.4 1.0
NE1 B:TRP141 4.3 12.3 1.0
CD2 B:HIS120 4.4 12.9 1.0
NE2 B:HIS120 4.4 13.2 1.0
O B:HIS160 4.4 13.2 1.0
OD1 B:ASP251 4.4 12.1 1.0
CB B:ASP147 4.5 15.0 1.0
CB B:ASP143 4.5 8.3 1.0
CZ2 B:TRP141 4.7 11.7 1.0
CE2 B:TRP141 4.8 15.1 1.0
CG B:GLU296 4.9 13.2 1.0
CA B:HIS120 5.0 11.0 1.0
OD2 B:ASP253 5.0 13.2 1.0

Manganese binding site 4 out of 6 in 4ie3

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


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 Inhbitor 1O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:15.2
occ:1.00
 O12 B:1EE406 2.1 14.6 1.0
OD1 B:ASP143 2.1 10.5 1.0
OD2 B:ASP253 2.2 13.2 1.0
ND1 B:HIS145 2.3 14.7 1.0
OD1 B:ASP253 2.4 13.9 1.0
OD2 B:ASP251 2.4 13.3 1.0
CG B:ASP253 2.7 12.9 1.0
O11 B:1EE406 2.8 13.5 1.0
CG B:ASP143 3.1 10.9 1.0
CE1 B:HIS145 3.1 15.7 1.0
B10 B:1EE406 3.1 16.5 1.0
CG B:ASP251 3.2 15.0 1.0
MN B:MN401 3.3 15.5 1.0
CG B:HIS145 3.4 19.2 1.0
OD2 B:ASP143 3.4 9.5 1.0
OD1 B:ASP251 3.7 12.1 1.0
CB B:HIS145 3.8 12.0 1.0
N B:HIS145 4.0 14.1 1.0
O22 B:1EE406 4.1 13.6 1.0
CB B:ASP251 4.1 10.2 1.0
CB B:ASP253 4.2 11.6 1.0
N B:ALA144 4.2 11.2 1.0
OG1 B:THR265 4.2 36.4 1.0
NE2 B:HIS145 4.3 15.1 1.0
C8 B:1EE406 4.3 17.0 1.0
C9 B:1EE406 4.3 13.4 1.0
CD2 B:HIS145 4.4 15.8 1.0
OD1 B:ASP147 4.5 13.3 1.0
CB B:ASP143 4.5 8.3 1.0
CA B:HIS145 4.5 16.1 1.0
CB B:ALA144 4.6 10.7 1.0
CA B:ALA144 4.8 13.7 1.0
C B:ALA144 4.8 16.2 1.0
CA B:ASP143 4.8 12.9 1.0
O B:HOH557 4.9 17.9 1.0
OD2 B:ASP147 4.9 17.0 1.0
C B:ASP143 5.0 13.5 1.0

Manganese binding site 5 out of 6 in 4ie3

Go back to Manganese Binding Sites List in 4ie3
Manganese binding site 5 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O


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 Inhbitor 1O within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:15.8
occ:1.00
 O12 C:1EE405 2.1 16.7 1.0
OD2 C:ASP253 2.2 19.9 1.0
ND1 C:HIS145 2.2 11.0 1.0
OD1 C:ASP143 2.2 13.9 1.0
OD2 C:ASP251 2.3 14.5 1.0
OD1 C:ASP253 2.5 14.4 1.0
CG C:ASP253 2.7 16.9 1.0
O11 C:1EE405 3.0 19.1 1.0
CG C:ASP251 3.1 14.4 1.0
CE1 C:HIS145 3.2 16.3 1.0
B10 C:1EE405 3.2 18.6 1.0
CG C:ASP143 3.2 13.0 1.0
CG C:HIS145 3.3 20.1 1.0
MN C:MN402 3.4 14.8 1.0
OD2 C:ASP143 3.5 12.8 1.0
CB C:HIS145 3.6 13.7 1.0
OD1 C:ASP251 3.7 15.2 1.0
N C:HIS145 4.0 14.7 1.0
O22 C:1EE405 4.1 13.9 1.0
CB C:ASP251 4.1 9.3 1.0
CB C:ASP253 4.2 13.0 1.0
N C:ALA144 4.2 12.3 1.0
OG1 C:THR265 4.3 17.4 0.3
C8 C:1EE405 4.3 16.1 1.0
NE2 C:HIS145 4.3 15.8 1.0
C9 C:1EE405 4.3 15.4 1.0
CD2 C:HIS145 4.4 15.0 1.0
CA C:HIS145 4.4 17.4 1.0
OD1 C:ASP147 4.5 10.7 1.0
CB C:ASP143 4.6 11.6 1.0
CB C:ALA144 4.6 9.9 1.0
C C:ALA144 4.8 14.6 1.0
CA C:ALA144 4.8 15.3 1.0
O C:HOH590 4.8 12.6 1.0
OD2 C:ASP147 4.9 16.6 1.0
CA C:ASP143 4.9 13.9 1.0

Manganese binding site 6 out of 6 in 4ie3

Go back to Manganese Binding Sites List in 4ie3
Manganese binding site 6 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhbitor 1O


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 Inhbitor 1O within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:14.8
occ:1.00
 OD2 C:ASP147 2.1 16.6 1.0
ND1 C:HIS120 2.2 10.2 1.0
OD2 C:ASP143 2.2 12.8 1.0
O22 C:1EE405 2.3 13.9 1.0
O12 C:1EE405 2.3 16.7 1.0
OD2 C:ASP251 2.4 14.5 1.0
B10 C:1EE405 2.8 18.6 1.0
CG C:ASP147 3.0 13.8 1.0
CG C:HIS120 3.1 14.8 1.0
CE1 C:HIS120 3.2 15.3 1.0
OD1 C:ASP147 3.2 10.7 1.0
CG C:ASP143 3.2 13.0 1.0
CG C:ASP251 3.3 14.4 1.0
MN C:MN401 3.4 15.8 1.0
CB C:HIS120 3.4 13.7 1.0
OD1 C:ASP143 3.5 13.9 1.0
O11 C:1EE405 3.5 19.1 1.0
CB C:ASP251 3.6 9.3 1.0
C9 C:1EE405 4.2 15.4 1.0
NE2 C:HIS120 4.3 12.9 1.0
CD2 C:HIS120 4.3 14.5 1.0
NE1 C:TRP141 4.3 13.6 1.0
O C:HIS160 4.4 12.6 1.0
OD1 C:ASP251 4.4 15.2 1.0
CB C:ASP147 4.4 11.9 1.0
CB C:ASP143 4.6 11.6 1.0
CZ2 C:TRP141 4.7 13.1 1.0
CE2 C:TRP141 4.9 16.2 1.0
CA C:HIS120 4.9 14.0 1.0
CG C:GLU296 4.9 12.5 1.0
CB C:HIS145 5.0 13.7 1.0
CA C:ASP251 5.0 11.4 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 19:48:58 2024

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