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Manganese in PDB 4i06: Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14

Enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14

All present enzymatic activity of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14, PDB code: 4i06 was solved by A.Cousido-Siah, A.Mitschler, F.X.Ruiz, D.L.Whitehouse, A.Golebiowski, M.Ji, M.Zhang, P.Beckett, R.Sheeler, M.Andreoli, B.Conway, K.Mahboubi, H.Schroeter, M.C.Van Zandt, A.Podjarny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.81 / 1.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.805, 127.805, 159.094, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14 (pdb code 4i06). 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 14, PDB code: 4i06:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4i06

Go back to Manganese Binding Sites List in 4i06
Manganese binding site 1 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:11.5
occ:1.00
 OD2 A:ASP147 2.1 10.1 1.0
OD2 A:ASP143 2.1 11.3 1.0
ND1 A:HIS120 2.2 11.9 1.0
O21 A:X8A406 2.3 10.9 1.0
O22 A:X8A406 2.3 12.4 1.0
OD2 A:ASP251 2.3 12.2 1.0
B19 A:X8A406 2.8 11.7 1.0
CG A:ASP147 3.1 11.8 1.0
CE1 A:HIS120 3.1 12.5 1.0
CG A:ASP143 3.1 14.1 1.0
CG A:HIS120 3.2 11.8 1.0
CG A:ASP251 3.3 11.6 1.0
MN A:MN402 3.4 11.7 1.0
OD1 A:ASP147 3.4 10.0 1.0
OD1 A:ASP143 3.4 11.0 1.0
CB A:HIS120 3.5 9.8 1.0
O20 A:X8A406 3.6 12.1 1.0
CB A:ASP251 3.6 9.5 1.0
C5 A:X8A406 4.2 12.2 1.0
NE2 A:HIS120 4.2 10.9 1.0
NE1 A:TRP141 4.2 12.1 1.0
CD2 A:HIS120 4.3 9.6 1.0
OD1 A:ASP251 4.4 9.7 1.0
CB A:ASP147 4.4 11.6 1.0
O A:HIS160 4.5 10.8 1.0
CB A:ASP143 4.5 8.2 1.0
CZ2 A:TRP141 4.5 12.3 1.0
CE2 A:TRP141 4.7 13.0 1.0
CG A:GLU296 4.8 11.1 1.0
CA A:ASP251 4.9 10.6 1.0
CG2 A:VAL295 5.0 9.5 1.0
CA A:HIS120 5.0 9.2 1.0

Manganese binding site 2 out of 6 in 4i06

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Manganese binding site 2 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:11.7
occ:1.00
 O22 A:X8A406 2.1 12.4 1.0
OD1 A:ASP143 2.2 11.0 1.0
OD2 A:ASP253 2.2 11.9 1.0
ND1 A:HIS145 2.2 12.5 1.0
OD2 A:ASP251 2.3 12.2 1.0
OD1 A:ASP253 2.4 10.8 1.0
CG A:ASP253 2.7 14.3 1.0
O20 A:X8A406 2.8 12.1 1.0
CE1 A:HIS145 3.1 11.6 1.0
B19 A:X8A406 3.1 11.7 1.0
CG A:ASP251 3.1 11.6 1.0
CG A:ASP143 3.2 14.1 1.0
CG A:HIS145 3.3 10.2 1.0
MN A:MN401 3.4 11.5 1.0
OD2 A:ASP143 3.5 11.3 1.0
OD1 A:ASP251 3.7 9.7 1.0
CB A:HIS145 3.7 9.4 1.0
O21 A:X8A406 4.0 10.9 1.0
OG1 A:THR265 4.0 12.6 0.3
N A:HIS145 4.0 9.6 1.0
CB A:ASP251 4.1 9.5 1.0
CB A:ASP253 4.2 11.0 1.0
N A:ALA144 4.2 9.9 1.0
NE2 A:HIS145 4.2 11.0 1.0
C5 A:X8A406 4.3 12.2 1.0
CD2 A:HIS145 4.4 13.7 1.0
C4 A:X8A406 4.4 12.5 1.0
OD1 A:ASP147 4.5 10.0 1.0
CA A:HIS145 4.5 10.2 1.0
CB A:ASP143 4.6 8.2 1.0
CB A:ALA144 4.6 10.9 1.0
O A:HOH513 4.6 13.2 1.0
CA A:ALA144 4.8 11.0 1.0
OD2 A:ASP147 4.8 10.1 1.0
C A:ALA144 4.8 12.4 1.0
CA A:ASP143 4.9 9.7 1.0
C A:ASP143 5.0 10.6 1.0

Manganese binding site 3 out of 6 in 4i06

Go back to Manganese Binding Sites List in 4i06
Manganese binding site 3 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:11.7
occ:1.00
 OD2 B:ASP147 2.1 12.0 1.0
OD2 B:ASP143 2.1 11.1 1.0
OD2 B:ASP251 2.2 10.1 1.0
O21 B:X8A406 2.2 13.5 1.0
ND1 B:HIS120 2.2 9.2 1.0
O22 B:X8A406 2.4 14.7 1.0
B19 B:X8A406 2.7 13.5 1.0
CG B:ASP147 3.1 13.8 1.0
CG B:ASP143 3.1 14.7 1.0
CE1 B:HIS120 3.2 12.2 1.0
CG B:HIS120 3.2 12.0 1.0
CG B:ASP251 3.2 11.2 1.0
MN B:MN402 3.3 12.0 1.0
OD1 B:ASP143 3.4 11.9 1.0
OD1 B:ASP147 3.4 12.4 1.0
CB B:HIS120 3.5 12.4 1.0
O20 B:X8A406 3.6 13.4 1.0
CB B:ASP251 3.6 11.1 1.0
C5 B:X8A406 4.1 12.6 1.0
NE1 B:TRP141 4.3 9.8 1.0
NE2 B:HIS120 4.3 10.6 1.0
CD2 B:HIS120 4.3 9.1 1.0
OD1 B:ASP251 4.3 11.6 1.0
O B:HIS160 4.4 10.6 1.0
CB B:ASP147 4.5 10.4 1.0
CB B:ASP143 4.5 9.0 1.0
CZ2 B:TRP141 4.6 11.1 1.0
CG B:GLU296 4.8 10.0 1.0
CE2 B:TRP141 4.8 10.9 1.0
CA B:ASP251 4.9 9.5 1.0
CG2 B:VAL295 4.9 10.0 1.0
CA B:HIS120 5.0 9.0 1.0
OD2 B:ASP253 5.0 9.8 1.0

Manganese binding site 4 out of 6 in 4i06

Go back to Manganese Binding Sites List in 4i06
Manganese binding site 4 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:12.0
occ:1.00
 O22 B:X8A406 2.0 14.7 1.0
OD1 B:ASP143 2.1 11.9 1.0
OD2 B:ASP253 2.2 9.8 1.0
ND1 B:HIS145 2.3 10.3 1.0
OD2 B:ASP251 2.4 10.1 1.0
OD1 B:ASP253 2.4 11.6 1.0
CG B:ASP253 2.6 10.8 1.0
O20 B:X8A406 2.8 13.4 1.0
B19 B:X8A406 3.1 13.5 1.0
CE1 B:HIS145 3.1 12.4 1.0
CG B:ASP251 3.1 11.2 1.0
CG B:ASP143 3.2 14.7 1.0
MN B:MN401 3.3 11.7 1.0
CG B:HIS145 3.4 13.3 1.0
OD2 B:ASP143 3.5 11.1 1.0
OD1 B:ASP251 3.6 11.6 1.0
CB B:HIS145 3.8 12.5 1.0
O21 B:X8A406 3.9 13.5 1.0
N B:HIS145 4.0 11.6 1.0
CB B:ASP251 4.1 11.1 1.0
OG1 B:THR265 4.1 39.1 1.0
CB B:ASP253 4.1 8.3 1.0
N B:ALA144 4.2 11.8 1.0
C5 B:X8A406 4.3 12.6 1.0
NE2 B:HIS145 4.3 10.9 1.0
C4 B:X8A406 4.4 13.8 1.0
CD2 B:HIS145 4.4 13.8 1.0
CA B:HIS145 4.5 10.1 1.0
CB B:ASP143 4.5 9.0 1.0
OD1 B:ASP147 4.5 12.4 1.0
CB B:ALA144 4.6 12.0 1.0
O B:HOH526 4.6 14.0 1.0
CA B:ALA144 4.7 11.1 1.0
C B:ALA144 4.8 14.2 1.0
OD2 B:ASP147 4.8 12.0 1.0
CA B:ASP143 4.9 9.4 1.0
C B:ASP143 5.0 9.7 1.0

Manganese binding site 5 out of 6 in 4i06

Go back to Manganese Binding Sites List in 4i06
Manganese binding site 5 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:11.7
occ:1.00
 O22 C:X8A406 2.1 13.0 1.0
OD1 C:ASP143 2.2 10.2 1.0
ND1 C:HIS145 2.2 11.7 1.0
OD2 C:ASP253 2.2 10.5 1.0
OD2 C:ASP251 2.2 11.2 1.0
OD1 C:ASP253 2.4 11.8 1.0
CG C:ASP253 2.7 13.7 1.0
O20 C:X8A406 2.7 14.2 1.0
CE1 C:HIS145 3.1 13.6 1.0
B19 C:X8A406 3.1 16.1 1.0
CG C:ASP251 3.1 13.3 1.0
CG C:ASP143 3.2 9.8 1.0
CG C:HIS145 3.3 9.7 1.0
MN C:MN402 3.4 11.8 1.0
OD2 C:ASP143 3.5 12.1 1.0
CB C:HIS145 3.7 12.6 1.0
OD1 C:ASP251 3.7 11.0 1.0
O21 C:X8A406 4.0 12.7 1.0
OG1 C:THR265 4.0 13.5 0.2
N C:HIS145 4.1 11.7 1.0
CB C:ASP251 4.1 12.5 1.0
CB C:ASP253 4.2 9.8 1.0
NE2 C:HIS145 4.2 10.9 1.0
N C:ALA144 4.3 11.2 1.0
C5 C:X8A406 4.3 10.6 1.0
C4 C:X8A406 4.3 13.5 1.0
CD2 C:HIS145 4.4 11.0 1.0
OD1 C:ASP147 4.5 12.1 1.0
CA C:HIS145 4.5 10.2 1.0
CB C:ASP143 4.6 11.9 1.0
O C:HOH526 4.6 13.8 1.0
CB C:ALA144 4.7 12.9 1.0
C C:ALA144 4.8 9.8 1.0
CA C:ALA144 4.8 9.4 1.0
OD2 C:ASP147 4.8 12.9 1.0
CA C:ASP143 4.9 10.8 1.0
O C:HOH549 5.0 18.1 1.0

Manganese binding site 6 out of 6 in 4i06

Go back to Manganese Binding Sites List in 4i06
Manganese binding site 6 out of 6 in the Crystal Structure of Human Arginase-2 Complexed with Inhibitor 14


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 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:11.8
occ:1.00
 OD2 C:ASP147 2.1 12.9 1.0
ND1 C:HIS120 2.1 10.6 1.0
OD2 C:ASP143 2.1 12.1 1.0
O22 C:X8A406 2.2 13.0 1.0
O21 C:X8A406 2.3 12.7 1.0
OD2 C:ASP251 2.3 11.2 1.0
B19 C:X8A406 2.7 16.1 1.0
CG C:ASP147 3.1 13.8 1.0
CE1 C:HIS120 3.1 13.1 1.0
CG C:HIS120 3.1 12.2 1.0
CG C:ASP143 3.1 9.8 1.0
CG C:ASP251 3.3 13.3 1.0
OD1 C:ASP147 3.3 12.1 1.0
MN C:MN401 3.4 11.7 1.0
CB C:HIS120 3.5 10.5 1.0
OD1 C:ASP143 3.5 10.2 1.0
O20 C:X8A406 3.5 14.2 1.0
CB C:ASP251 3.6 12.5 1.0
C5 C:X8A406 4.1 10.6 1.0
NE2 C:HIS120 4.2 14.1 1.0
CD2 C:HIS120 4.2 12.7 1.0
NE1 C:TRP141 4.3 11.6 1.0
OD1 C:ASP251 4.4 11.0 1.0
CB C:ASP147 4.5 10.7 1.0
O C:HIS160 4.5 12.3 1.0
CB C:ASP143 4.5 11.9 1.0
CZ2 C:TRP141 4.6 11.7 1.0
CE2 C:TRP141 4.8 14.4 1.0
CG C:GLU296 4.8 10.4 1.0
CA C:ASP251 4.9 12.0 1.0
CG2 C:VAL295 4.9 12.3 1.0
CA C:HIS120 5.0 13.8 1.0
CB C:HIS145 5.0 12.6 1.0

Reference:

M.C.Van Zandt, D.L.Whitehouse, A.Golebiowski, M.K.Ji, M.Zhang, R.P.Beckett, G.E.Jagdmann, T.R.Ryder, R.Sheeler, M.Andreoli, B.Conway, K.Mahboubi, G.D'angelo, A.Mitschler, A.Cousido-Siah, F.X.Ruiz, E.I.Howard, A.D.Podjarny, H.Schroeter. Discovery of (R)-2-Amino-6-Borono-2-(2-(Piperidin-1-Yl)Ethyl)Hexanoic Acid and Congeners As Highly Potent Inhibitors of Human Arginases I and II For Treatment of Myocardial Reperfusion Injury. J.Med.Chem. V. 56 2568 2013.
ISSN: ISSN 0022-2623
PubMed: 23472952
DOI: 10.1021/JM400014C
Page generated: Sat Oct 5 19:45:24 2024

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