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Manganese in PDB 4ixu: Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)

Enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-)

All present enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-):
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-), PDB code: 4ixu 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) 46.34 / 1.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.400, 127.400, 159.249, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.3

Other elements in 4ixu:

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) (pdb code 4ixu). 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 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-), PDB code: 4ixu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4ixu

Go back to Manganese Binding Sites List in 4ixu
Manganese binding site 1 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-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 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:7.9
occ:1.00
 OD2 A:ASP147 2.1 8.3 1.0
OD2 A:ASP143 2.1 8.5 1.0
ND1 A:HIS120 2.2 9.7 1.0
O12 A:38I406 2.2 9.2 1.0
O30 A:38I406 2.3 10.6 1.0
OD2 A:ASP251 2.3 7.2 1.0
B11 A:38I406 2.9 10.6 1.0
CG A:ASP147 3.1 8.7 1.0
CG A:ASP143 3.1 10.9 1.0
CE1 A:HIS120 3.1 9.7 1.0
CG A:HIS120 3.1 8.8 1.0
CG A:ASP251 3.3 12.1 1.0
MN A:MN402 3.3 8.4 1.0
OD1 A:ASP143 3.4 6.3 1.0
OD1 A:ASP147 3.4 7.1 1.0
CB A:HIS120 3.5 7.0 1.0
CB A:ASP251 3.6 6.2 1.0
O13 A:38I406 3.7 12.1 1.0
C10 A:38I406 4.1 10.8 1.0
NE2 A:HIS120 4.2 8.3 1.0
NE1 A:TRP141 4.3 6.9 1.0
CD2 A:HIS120 4.3 7.5 1.0
OD1 A:ASP251 4.4 5.3 1.0
CB A:ASP147 4.4 8.2 1.0
CB A:ASP143 4.5 6.0 1.0
O A:HIS160 4.5 11.3 1.0
CZ2 A:TRP141 4.6 7.6 1.0
CE2 A:TRP141 4.8 8.6 1.0
CG A:GLU296 4.8 8.1 1.0
CG2 A:VAL295 4.9 6.5 1.0
CA A:ASP251 4.9 4.8 1.0
CA A:HIS120 5.0 7.7 1.0
OE2 A:GLU296 5.0 11.5 1.0

Manganese binding site 2 out of 6 in 4ixu

Go back to Manganese Binding Sites List in 4ixu
Manganese binding site 2 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-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 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:8.4
occ:1.00
 OD1 A:ASP143 2.2 6.3 1.0
O12 A:38I406 2.2 9.2 1.0
OD2 A:ASP253 2.2 10.1 1.0
OD2 A:ASP251 2.2 7.2 1.0
ND1 A:HIS145 2.3 8.4 1.0
OD1 A:ASP253 2.5 7.4 1.0
CG A:ASP253 2.7 11.9 1.0
O13 A:38I406 2.9 12.1 1.0
B11 A:38I406 3.0 10.6 1.0
CG A:ASP251 3.1 12.1 1.0
CE1 A:HIS145 3.1 8.9 1.0
CG A:ASP143 3.2 10.9 1.0
CG A:HIS145 3.3 8.0 1.0
MN A:MN401 3.3 7.9 1.0
OD2 A:ASP143 3.5 8.5 1.0
CB A:HIS145 3.7 7.7 1.0
OD1 A:ASP251 3.7 5.3 1.0
O30 A:38I406 3.9 10.6 1.0
N A:HIS145 4.0 7.8 1.0
OG1 A:THR265 4.1 12.6 0.2
CB A:ASP251 4.1 6.2 1.0
N A:ALA144 4.2 6.6 1.0
CB A:ASP253 4.2 8.9 1.0
C10 A:38I406 4.3 10.8 1.0
NE2 A:HIS145 4.3 7.2 1.0
CD2 A:HIS145 4.4 8.8 1.0
C9 A:38I406 4.4 10.8 1.0
CA A:HIS145 4.5 6.4 1.0
CB A:ASP143 4.5 6.0 1.0
OD1 A:ASP147 4.5 7.1 1.0
CB A:ALA144 4.6 7.9 1.0
O A:HOH519 4.7 11.1 1.0
OD2 A:ASP147 4.8 8.3 1.0
CA A:ALA144 4.8 8.5 1.0
C A:ALA144 4.8 10.3 1.0
CA A:ASP143 4.9 8.2 1.0
C A:ASP143 5.0 7.4 1.0

Manganese binding site 3 out of 6 in 4ixu

Go back to Manganese Binding Sites List in 4ixu
Manganese binding site 3 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-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 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:8.4
occ:1.00
 OD2 B:ASP143 2.1 7.8 1.0
OD2 B:ASP147 2.1 10.8 1.0
ND1 B:HIS120 2.2 5.5 1.0
O30 B:38I406 2.2 11.8 1.0
OD2 B:ASP251 2.2 8.0 1.0
O12 B:38I406 2.2 9.2 1.0
B11 B:38I406 2.8 14.7 1.0
CG B:ASP147 3.1 12.1 1.0
CG B:ASP143 3.1 11.1 1.0
CG B:HIS120 3.2 8.6 1.0
CE1 B:HIS120 3.2 9.6 1.0
CG B:ASP251 3.2 9.7 1.0
MN B:MN402 3.3 10.0 1.0
OD1 B:ASP147 3.4 9.3 1.0
OD1 B:ASP143 3.4 8.8 1.0
CB B:HIS120 3.4 8.8 1.0
CB B:ASP251 3.6 7.7 1.0
O13 B:38I406 3.6 11.8 1.0
C10 B:38I406 4.1 12.6 1.0
NE1 B:TRP141 4.3 6.9 1.0
NE2 B:HIS120 4.3 8.4 1.0
CD2 B:HIS120 4.3 6.3 1.0
OD1 B:ASP251 4.4 8.9 1.0
CB B:ASP143 4.4 9.2 1.0
CB B:ASP147 4.4 9.4 1.0
O B:HIS160 4.5 8.1 1.0
CZ2 B:TRP141 4.6 10.3 1.0
CE2 B:TRP141 4.8 8.1 1.0
CG B:GLU296 4.8 7.0 1.0
CG2 B:VAL295 4.9 10.6 1.0
CA B:ASP251 4.9 4.5 1.0
CA B:HIS120 4.9 6.3 1.0

Manganese binding site 4 out of 6 in 4ixu

Go back to Manganese Binding Sites List in 4ixu
Manganese binding site 4 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-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 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:10.0
occ:1.00
 OD1 B:ASP143 2.1 8.8 1.0
O12 B:38I406 2.1 9.2 1.0
ND1 B:HIS145 2.2 9.7 1.0
OD2 B:ASP253 2.2 8.3 1.0
OD2 B:ASP251 2.4 8.0 1.0
OD1 B:ASP253 2.4 9.6 1.0
CG B:ASP253 2.7 11.0 1.0
O13 B:38I406 2.9 11.8 1.0
B11 B:38I406 2.9 14.7 1.0
CE1 B:HIS145 3.1 10.6 1.0
CG B:ASP143 3.1 11.1 1.0
CG B:ASP251 3.2 9.7 1.0
CG B:HIS145 3.3 11.8 1.0
MN B:MN401 3.3 8.4 1.0
OD2 B:ASP143 3.5 7.8 1.0
OD1 B:ASP251 3.7 8.9 1.0
CB B:HIS145 3.7 7.8 1.0
O30 B:38I406 3.9 11.8 1.0
N B:HIS145 4.0 9.6 1.0
CB B:ASP251 4.1 7.7 1.0
OG1 B:THR265 4.1 13.6 0.3
N B:ALA144 4.2 8.1 1.0
CB B:ASP253 4.2 6.7 1.0
NE2 B:HIS145 4.2 8.3 1.0
C10 B:38I406 4.2 12.6 1.0
CD2 B:HIS145 4.4 10.5 1.0
C9 B:38I406 4.4 15.0 1.0
CA B:HIS145 4.5 8.8 1.0
OD1 B:ASP147 4.5 9.3 1.0
CB B:ASP143 4.5 9.2 1.0
CB B:ALA144 4.5 7.3 1.0
O B:HOH564 4.7 13.1 1.0
CA B:ALA144 4.7 11.2 1.0
C B:ALA144 4.8 13.2 1.0
OD2 B:ASP147 4.8 10.8 1.0
CA B:ASP143 4.8 6.5 1.0
C B:ASP143 4.9 6.6 1.0

Manganese binding site 5 out of 6 in 4ixu

Go back to Manganese Binding Sites List in 4ixu
Manganese binding site 5 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-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 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:9.7
occ:1.00
 OD1 C:ASP143 2.2 6.9 1.0
ND1 C:HIS145 2.2 7.7 1.0
OD2 C:ASP253 2.2 12.0 1.0
OD2 C:ASP251 2.3 9.3 1.0
O12 C:38I406 2.3 12.6 1.0
OD1 C:ASP253 2.4 9.8 1.0
CG C:ASP253 2.7 13.5 1.0
O13 C:38I406 2.8 12.4 1.0
B11 C:38I406 2.9 16.1 1.0
CE1 C:HIS145 3.1 12.8 1.0
CG C:ASP251 3.1 11.8 1.0
CG C:ASP143 3.2 9.3 1.0
CG C:HIS145 3.3 6.4 1.0
MN C:MN402 3.4 9.0 1.0
OD2 C:ASP143 3.5 11.0 1.0
CB C:HIS145 3.7 10.2 1.0
OD1 C:ASP251 3.7 8.6 1.0
O30 C:38I406 3.9 12.3 1.0
N C:HIS145 4.0 10.4 1.0
OG1 C:THR265 4.1 10.8 0.3
CB C:ASP251 4.1 9.8 1.0
CB C:ASP253 4.2 8.7 1.0
N C:ALA144 4.2 8.9 1.0
NE2 C:HIS145 4.2 10.2 1.0
C10 C:38I406 4.2 12.5 1.0
CD2 C:HIS145 4.4 10.8 1.0
C9 C:38I406 4.4 15.5 1.0
CA C:HIS145 4.5 9.9 1.0
OD1 C:ASP147 4.5 10.4 1.0
CB C:ASP143 4.5 8.8 1.0
CB C:ALA144 4.7 11.5 1.0
O C:HOH511 4.7 11.1 1.0
CA C:ALA144 4.8 8.8 1.0
C C:ALA144 4.8 9.6 1.0
OD2 C:ASP147 4.8 13.3 1.0
CA C:ASP143 4.9 8.4 1.0
C C:ASP143 5.0 12.1 1.0

Manganese binding site 6 out of 6 in 4ixu

Go back to Manganese Binding Sites List in 4ixu
Manganese binding site 6 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-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 11D: {(5R)-5-Amino-5-Carboxy-5-[(3-Endo)-8-(3,4-Dichlorobenzyl)-8- Azabicyclo[3.2.1]Oct-3-Yl]Pentyl}(Trihydroxy)Borate(1-) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:9.0
occ:1.00
 ND1 C:HIS120 2.1 7.8 1.0
OD2 C:ASP147 2.1 13.3 1.0
O12 C:38I406 2.1 12.6 1.0
OD2 C:ASP143 2.1 11.0 1.0
OD2 C:ASP251 2.3 9.3 1.0
O30 C:38I406 2.3 12.3 1.0
B11 C:38I406 2.9 16.1 1.0
CE1 C:HIS120 3.0 11.6 1.0
CG C:ASP147 3.0 8.9 1.0
CG C:HIS120 3.1 11.2 1.0
CG C:ASP143 3.1 9.3 1.0
CG C:ASP251 3.3 11.8 1.0
OD1 C:ASP147 3.3 10.4 1.0
MN C:MN401 3.4 9.7 1.0
OD1 C:ASP143 3.4 6.9 1.0
CB C:HIS120 3.5 9.7 1.0
CB C:ASP251 3.6 9.8 1.0
O13 C:38I406 3.6 12.4 1.0
NE2 C:HIS120 4.1 9.5 1.0
C10 C:38I406 4.1 12.5 1.0
CD2 C:HIS120 4.2 7.3 1.0
NE1 C:TRP141 4.2 9.7 1.0
OD1 C:ASP251 4.4 8.6 1.0
CB C:ASP147 4.4 12.1 1.0
CB C:ASP143 4.4 8.8 1.0
O C:HIS160 4.5 11.9 1.0
CZ2 C:TRP141 4.6 9.9 1.0
CE2 C:TRP141 4.8 13.2 1.0
CG C:GLU296 4.8 9.2 1.0
CA C:ASP251 4.9 11.8 1.0
CG2 C:VAL295 4.9 9.6 1.0
CA C:HIS120 5.0 10.8 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 Oct 5 19:55:43 2024

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