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Manganese in PDB 4ixv: Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)

Enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)

All present enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-):
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-), PDB code: 4ixv was solved by A.Cousido-Siah, A.Mitschler, F.X.Ruiz, D.Whitehouse, P.Beckett, M.C.Vanzandt, M.K.Ji, T.Ryder, R.Jagdmann, M.Andreoli, J.Olczak, M.Mazur, W.Czestkowski, W.Piotrowska, 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) 33.83 / 2.30
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.123, 128.123, 159.362, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23.2

Other elements in 4ixv:

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) (pdb code 4ixv). 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 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-), PDB code: 4ixv:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4ixv

Go back to Manganese Binding Sites List in 4ixv
Manganese binding site 1 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)


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 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:8.5
occ:1.00
 OD2 A:ASP147 2.1 4.9 1.0
OD2 A:ASP143 2.1 5.0 1.0
O12 A:XA1405 2.2 7.9 1.0
ND1 A:HIS120 2.3 6.5 1.0
OD2 A:ASP251 2.4 7.7 1.0
O27 A:XA1405 2.4 6.5 1.0
B10 A:XA1405 2.9 10.6 1.0
CG A:ASP147 3.1 5.9 1.0
CG A:ASP143 3.2 7.1 1.0
CG A:HIS120 3.2 7.4 1.0
CE1 A:HIS120 3.2 8.5 1.0
CG A:ASP251 3.3 7.8 1.0
MN A:MN402 3.4 9.5 1.0
OD1 A:ASP147 3.4 9.1 1.0
CB A:HIS120 3.5 6.6 1.0
OD1 A:ASP143 3.5 5.9 1.0
CB A:ASP251 3.6 5.4 1.0
O11 A:XA1405 3.7 7.1 1.0
C9 A:XA1405 4.2 6.0 1.0
NE1 A:TRP141 4.2 9.9 1.0
NE2 A:HIS120 4.3 6.9 1.0
CD2 A:HIS120 4.3 4.6 1.0
O A:HIS160 4.4 11.3 1.0
OD1 A:ASP251 4.5 5.4 1.0
CB A:ASP147 4.5 10.7 1.0
CB A:ASP143 4.5 4.3 1.0
CZ2 A:TRP141 4.6 4.9 1.0
CE2 A:TRP141 4.8 6.2 1.0
CG A:GLU296 4.8 8.1 1.0
CA A:ASP251 5.0 8.6 1.0
CA A:HIS120 5.0 8.1 1.0

Manganese binding site 2 out of 6 in 4ixv

Go back to Manganese Binding Sites List in 4ixv
Manganese binding site 2 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)


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 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:9.5
occ:1.00
 O12 A:XA1405 2.2 7.9 1.0
ND1 A:HIS145 2.2 6.8 1.0
OD2 A:ASP253 2.2 7.4 1.0
OD1 A:ASP143 2.2 5.9 1.0
OD2 A:ASP251 2.4 7.7 1.0
OD1 A:ASP253 2.5 9.6 1.0
CG A:ASP253 2.7 8.0 1.0
O11 A:XA1405 2.9 7.1 1.0
CE1 A:HIS145 3.0 5.5 1.0
B10 A:XA1405 3.0 10.6 1.0
CG A:ASP143 3.2 7.1 1.0
CG A:ASP251 3.2 7.8 1.0
CG A:HIS145 3.3 12.7 1.0
MN A:MN401 3.4 8.5 1.0
OD2 A:ASP143 3.4 5.0 1.0
CB A:HIS145 3.7 8.8 1.0
OD1 A:ASP251 3.7 5.4 1.0
O27 A:XA1405 4.0 6.5 1.0
N A:HIS145 4.0 5.4 1.0
CB A:ASP251 4.1 5.4 1.0
OG1 A:THR265 4.1 9.1 0.2
NE2 A:HIS145 4.2 6.2 1.0
CB A:ASP253 4.2 4.2 1.0
N A:ALA144 4.3 6.4 1.0
C9 A:XA1405 4.3 6.0 1.0
CD2 A:HIS145 4.3 3.5 1.0
C8 A:XA1405 4.5 10.6 1.0
OD1 A:ASP147 4.5 9.1 1.0
CA A:HIS145 4.5 9.5 1.0
CB A:ASP143 4.6 4.3 1.0
CB A:ALA144 4.7 6.2 1.0
O A:HOH510 4.8 7.0 1.0
C A:ALA144 4.8 7.9 1.0
OD2 A:ASP147 4.8 4.9 1.0
CA A:ALA144 4.8 6.0 1.0
CA A:ASP143 5.0 7.2 1.0

Manganese binding site 3 out of 6 in 4ixv

Go back to Manganese Binding Sites List in 4ixv
Manganese binding site 3 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)


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 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:8.5
occ:1.00
 OD2 B:ASP147 2.1 7.9 1.0
OD2 B:ASP143 2.1 4.8 1.0
O27 B:XA1405 2.3 9.0 1.0
OD2 B:ASP251 2.3 6.4 1.0
ND1 B:HIS120 2.3 9.3 1.0
O12 B:XA1405 2.4 7.6 1.0
B10 B:XA1405 2.9 9.0 1.0
CG B:ASP147 3.1 10.1 1.0
CG B:ASP143 3.1 7.2 1.0
CG B:HIS120 3.2 8.6 1.0
CE1 B:HIS120 3.3 7.6 1.0
OD1 B:ASP147 3.3 7.6 1.0
CG B:ASP251 3.3 9.3 1.0
MN B:MN402 3.3 10.8 1.0
CB B:HIS120 3.5 5.8 1.0
OD1 B:ASP143 3.5 8.0 1.0
O11 B:XA1405 3.6 5.7 1.0
CB B:ASP251 3.6 7.5 1.0
C9 B:XA1405 4.2 8.1 1.0
NE1 B:TRP141 4.3 5.1 1.0
CD2 B:HIS120 4.4 11.2 1.0
NE2 B:HIS120 4.4 10.5 1.0
CB B:ASP147 4.4 8.7 1.0
O B:HIS160 4.5 6.0 1.0
CB B:ASP143 4.5 5.7 1.0
OD1 B:ASP251 4.5 5.5 1.0
CZ2 B:TRP141 4.7 9.4 1.0
CE2 B:TRP141 4.8 7.2 1.0
CG B:GLU296 4.9 8.2 1.0
CA B:ASP251 4.9 5.6 1.0
CA B:HIS120 5.0 3.2 1.0

Manganese binding site 4 out of 6 in 4ixv

Go back to Manganese Binding Sites List in 4ixv
Manganese binding site 4 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)


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 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:10.8
occ:1.00
 OD1 B:ASP143 2.2 8.0 1.0
O12 B:XA1405 2.3 7.6 1.0
ND1 B:HIS145 2.3 7.2 1.0
OD2 B:ASP253 2.3 8.1 1.0
OD1 B:ASP253 2.4 9.8 1.0
OD2 B:ASP251 2.5 6.4 1.0
CG B:ASP253 2.7 9.7 1.0
O11 B:XA1405 2.8 5.7 1.0
B10 B:XA1405 3.0 9.0 1.0
CE1 B:HIS145 3.1 6.8 1.0
CG B:ASP143 3.1 7.2 1.0
CG B:ASP251 3.2 9.3 1.0
CG B:HIS145 3.3 9.7 1.0
MN B:MN401 3.3 8.5 1.0
OD2 B:ASP143 3.4 4.8 1.0
CB B:HIS145 3.7 5.3 1.0
OD1 B:ASP251 3.7 5.5 1.0
O27 B:XA1405 3.9 9.0 1.0
N B:HIS145 4.1 7.1 1.0
CB B:ASP251 4.1 7.5 1.0
N B:ALA144 4.2 7.1 1.0
OG1 B:THR265 4.2 41.0 0.6
CB B:ASP253 4.2 5.0 1.0
NE2 B:HIS145 4.3 7.6 1.0
C9 B:XA1405 4.3 8.1 1.0
CD2 B:HIS145 4.4 10.7 1.0
OD1 B:ASP147 4.4 7.6 1.0
C8 B:XA1405 4.5 8.3 1.0
CA B:HIS145 4.5 10.0 1.0
CB B:ASP143 4.5 5.7 1.0
CB B:ALA144 4.6 8.0 1.0
O B:HOH566 4.8 13.0 1.0
CA B:ALA144 4.8 8.6 1.0
OD2 B:ASP147 4.8 7.9 1.0
C B:ALA144 4.8 11.0 1.0
CA B:ASP143 4.9 6.4 1.0
C B:ASP143 5.0 9.1 1.0

Manganese binding site 5 out of 6 in 4ixv

Go back to Manganese Binding Sites List in 4ixv
Manganese binding site 5 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)


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 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:10.5
occ:1.00
 O12 C:XA1405 2.1 9.3 1.0
OD1 C:ASP143 2.2 5.7 1.0
OD2 C:ASP253 2.2 12.2 1.0
ND1 C:HIS145 2.3 6.0 1.0
OD2 C:ASP251 2.3 11.4 1.0
OD1 C:ASP253 2.6 8.8 1.0
CG C:ASP253 2.7 11.7 1.0
O11 C:XA1405 3.0 13.7 1.0
B10 C:XA1405 3.0 12.1 1.0
CE1 C:HIS145 3.1 8.9 1.0
CG C:ASP251 3.2 11.8 1.0
CG C:ASP143 3.2 7.1 1.0
CG C:HIS145 3.3 14.1 1.0
MN C:MN402 3.4 10.3 1.0
OD2 C:ASP143 3.5 8.7 1.0
CB C:HIS145 3.7 9.8 1.0
OD1 C:ASP251 3.8 8.0 1.0
O27 C:XA1405 4.0 6.9 1.0
N C:HIS145 4.0 8.2 1.0
CB C:ASP251 4.1 6.2 1.0
OG1 C:THR265 4.2 9.5 0.1
N C:ALA144 4.2 6.3 1.0
CB C:ASP253 4.3 8.8 1.0
NE2 C:HIS145 4.3 7.6 1.0
C9 C:XA1405 4.3 11.6 1.0
CD2 C:HIS145 4.4 8.7 1.0
OD1 C:ASP147 4.4 7.3 1.0
CA C:HIS145 4.5 12.5 1.0
C8 C:XA1405 4.5 11.1 1.0
CB C:ASP143 4.6 5.7 1.0
CB C:ALA144 4.6 3.3 1.0
O C:HOH555 4.8 10.0 1.0
CA C:ALA144 4.8 6.5 1.0
C C:ALA144 4.8 8.4 1.0
OD2 C:ASP147 4.9 10.6 1.0
CA C:ASP143 4.9 8.4 1.0

Manganese binding site 6 out of 6 in 4ixv

Go back to Manganese Binding Sites List in 4ixv
Manganese binding site 6 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-)


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 2D: {(5R)-5-Amino-5-Carboxy-5-[1-(4-Chlorobenzyl)Piperidin-4- Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:10.3
occ:1.00
 OD2 C:ASP147 2.1 10.6 1.0
ND1 C:HIS120 2.2 7.2 1.0
OD2 C:ASP143 2.2 8.7 1.0
O12 C:XA1405 2.2 9.3 1.0
O27 C:XA1405 2.3 6.9 1.0
OD2 C:ASP251 2.4 11.4 1.0
B10 C:XA1405 2.9 12.1 1.0
CG C:ASP147 3.1 7.8 1.0
CG C:HIS120 3.1 8.8 1.0
CE1 C:HIS120 3.1 9.6 1.0
CG C:ASP143 3.2 7.1 1.0
OD1 C:ASP147 3.3 7.3 1.0
CG C:ASP251 3.3 11.8 1.0
MN C:MN401 3.4 10.5 1.0
CB C:HIS120 3.4 8.1 1.0
OD1 C:ASP143 3.5 5.7 1.0
CB C:ASP251 3.6 6.2 1.0
O11 C:XA1405 3.7 13.7 1.0
C9 C:XA1405 4.1 11.6 1.0
NE2 C:HIS120 4.2 11.9 1.0
CD2 C:HIS120 4.2 10.6 1.0
NE1 C:TRP141 4.3 8.2 1.0
OD1 C:ASP251 4.4 8.0 1.0
O C:HIS160 4.4 8.7 1.0
CB C:ASP147 4.5 8.1 1.0
CB C:ASP143 4.6 5.7 1.0
CZ2 C:TRP141 4.7 7.1 1.0
CG C:GLU296 4.8 7.8 1.0
CE2 C:TRP141 4.9 10.7 1.0
CA C:HIS120 4.9 10.9 1.0
CA C:ASP251 4.9 7.7 1.0

Reference:

A.Golebiowski, D.Whitehouse, R.P.Beckett, M.Van Zandt, M.K.Ji, T.R.Ryder, E.Jagdmann, M.Andreoli, Y.Lee, R.Sheeler, B.Conway, J.Olczak, M.Mazur, W.Czestkowski, W.Piotrowska, A.Cousido-Siah, F.X.Ruiz, A.Mitschler, A.Podjarny, H.Schroeter. Synthesis of Quaternary Alpha-Amino Acid-Based Arginase Inhibitors Via the Ugi Reaction. Bioorg.Med.Chem.Lett. V. 23 4837 2013.
ISSN: ISSN 0960-894X
PubMed: 23886684
DOI: 10.1016/J.BMCL.2013.06.092
Page generated: Sat Aug 16 14:21:21 2025

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