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Manganese in PDB 3skk: Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure

Enzymatic activity of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure

All present enzymatic activity of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure, PDB code: 3skk was solved by K.J.Thorn, L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.78 / 1.70
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.094, 90.094, 69.362, 90.00, 90.00, 120.00
R / Rfree (%) 13.6 / 17.8

Other elements in 3skk:

The structure of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure (pdb code 3skk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure, PDB code: 3skk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3skk

Go back to Manganese Binding Sites List in 3skk
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:7.8
occ:1.00
 O2 A:4U7551 2.2 8.1 1.0
OD1 A:ASP124 2.2 6.5 1.0
OD1 A:ASP234 2.3 7.9 1.0
OD2 A:ASP232 2.3 7.4 1.0
ND1 A:HIS126 2.3 9.1 1.0
OD2 A:ASP234 2.4 7.3 1.0
CG A:ASP234 2.7 8.1 1.0
O4 A:4U7551 2.8 9.0 1.0
B1 A:4U7551 3.0 7.7 1.0
CE1 A:HIS126 3.1 9.2 1.0
CG A:ASP124 3.2 7.9 1.0
CG A:ASP232 3.2 8.3 1.0
MN A:MN502 3.4 8.1 1.0
CG A:HIS126 3.4 8.0 1.0
OD2 A:ASP124 3.5 8.1 1.0
OD1 A:ASP232 3.7 8.1 1.0
CB A:HIS126 3.9 9.1 1.0
O3 A:4U7551 3.9 8.3 1.0
N A:HIS126 4.1 7.4 1.0
C6 A:4U7551 4.1 9.2 1.0
CB A:ASP232 4.2 7.0 1.0
N A:ALA125 4.2 7.1 1.0
CB A:ASP234 4.2 8.0 1.0
C5 A:4U7551 4.2 9.7 1.0
NE2 A:HIS126 4.3 9.1 1.0
CD2 A:HIS126 4.5 8.6 1.0
CB A:ASP124 4.5 7.4 1.0
OD2 A:ASP128 4.6 8.3 1.0
CA A:HIS126 4.6 7.5 1.0
O A:HOH377 4.6 9.0 1.0
CB A:ALA125 4.7 7.2 1.0
OD1 A:ASP128 4.8 8.8 1.0
CA A:ALA125 4.8 7.2 1.0
C A:ALA125 4.8 6.6 1.0
O A:HOH564 4.8 11.7 1.0
CA A:ASP124 4.9 7.4 1.0
C A:ASP124 5.0 6.8 1.0

Manganese binding site 2 out of 4 in 3skk

Go back to Manganese Binding Sites List in 3skk
Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:8.1
occ:1.00
 OD1 A:ASP128 2.1 8.8 1.0
OD2 A:ASP124 2.1 8.1 1.0
OD2 A:ASP232 2.2 7.4 1.0
ND1 A:HIS101 2.2 8.7 1.0
O3 A:4U7551 2.3 8.3 1.0
O2 A:4U7551 2.3 8.1 1.0
B1 A:4U7551 2.8 7.7 1.0
CG A:ASP128 3.1 8.5 1.0
CG A:ASP124 3.1 7.9 1.0
CE1 A:HIS101 3.2 7.3 1.0
CG A:ASP232 3.2 8.3 1.0
CG A:HIS101 3.2 7.6 1.0
MN A:MN501 3.4 7.8 1.0
OD2 A:ASP128 3.4 8.3 1.0
O4 A:4U7551 3.4 9.0 1.0
OD1 A:ASP124 3.5 6.5 1.0
CB A:HIS101 3.5 9.0 1.0
CB A:ASP232 3.5 7.0 1.0
C6 A:4U7551 4.1 9.2 1.0
OD1 A:ASP232 4.3 8.1 1.0
NE2 A:HIS101 4.3 7.7 1.0
CD2 A:HIS101 4.3 8.1 1.0
NE1 A:TRP122 4.3 8.7 1.0
O A:HIS141 4.4 8.0 1.0
CB A:ASP128 4.4 8.4 1.0
CB A:ASP124 4.4 7.4 1.0
CZ2 A:TRP122 4.6 9.0 1.0
CE2 A:TRP122 4.8 8.4 1.0
CG A:GLU277 4.9 8.8 1.0
CA A:ASP232 4.9 7.1 1.0

Manganese binding site 3 out of 4 in 3skk

Go back to Manganese Binding Sites List in 3skk
Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:11.8
occ:1.00
 O2 B:4U7552 2.2 10.9 1.0
OD1 B:ASP234 2.2 11.8 1.0
OD1 B:ASP124 2.2 10.7 1.0
ND1 B:HIS126 2.3 12.2 1.0
OD2 B:ASP232 2.3 11.4 1.0
OD2 B:ASP234 2.4 12.0 1.0
CG B:ASP234 2.7 13.5 1.0
O4 B:4U7552 2.8 13.2 1.0
B1 B:4U7552 3.1 13.3 1.0
CG B:ASP232 3.1 11.0 1.0
CE1 B:HIS126 3.2 13.0 1.0
CG B:ASP124 3.2 10.9 1.0
MN B:MN504 3.3 11.8 1.0
CG B:HIS126 3.3 13.4 1.0
OD2 B:ASP124 3.6 10.9 1.0
OD1 B:ASP232 3.6 9.8 1.0
CB B:HIS126 3.6 11.9 1.0
O3 B:4U7552 4.0 13.3 1.0
CB B:ASP232 4.0 10.9 1.0
N B:HIS126 4.0 11.1 1.0
C6 B:4U7552 4.1 12.8 1.0
CB B:ASP234 4.2 11.4 1.0
C5 B:4U7552 4.2 12.6 1.0
N B:ALA125 4.3 9.4 1.0
NE2 B:HIS126 4.3 13.8 1.0
CD2 B:HIS126 4.4 12.5 1.0
CA B:HIS126 4.5 11.8 1.0
OD1 B:ASP128 4.5 12.0 1.0
CB B:ASP124 4.6 9.6 1.0
O B:HOH669 4.8 13.1 1.0
OD2 B:ASP128 4.8 12.0 1.0
O B:HOH445 4.8 12.6 1.0
CB B:ALA125 4.8 10.2 1.0
CA B:ASP124 4.9 9.9 1.0
C B:ALA125 4.9 9.4 1.0
CA B:ALA125 4.9 9.6 1.0

Manganese binding site 4 out of 4 in 3skk

Go back to Manganese Binding Sites List in 3skk
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:11.8
occ:1.00
 OD2 B:ASP128 2.2 12.0 1.0
ND1 B:HIS101 2.2 10.7 1.0
O2 B:4U7552 2.3 10.9 1.0
OD2 B:ASP124 2.3 10.9 1.0
OD2 B:ASP232 2.3 11.4 1.0
O3 B:4U7552 2.4 13.3 1.0
B1 B:4U7552 2.8 13.3 1.0
CG B:ASP128 3.1 12.0 1.0
CE1 B:HIS101 3.2 9.6 1.0
CG B:HIS101 3.2 10.7 1.0
CG B:ASP124 3.2 10.9 1.0
CG B:ASP232 3.3 11.0 1.0
MN B:MN503 3.3 11.8 1.0
OD1 B:ASP128 3.4 12.0 1.0
OD1 B:ASP124 3.4 10.7 1.0
CB B:HIS101 3.5 13.2 1.0
O4 B:4U7552 3.5 13.2 1.0
CB B:ASP232 3.6 10.9 1.0
C6 B:4U7552 4.0 12.8 1.0
NE2 B:HIS101 4.3 11.0 1.0
CD2 B:HIS101 4.3 12.7 1.0
O B:HIS141 4.4 15.1 1.0
NE1 B:TRP122 4.4 10.5 1.0
OD1 B:ASP232 4.4 9.8 1.0
CB B:ASP128 4.5 11.9 1.0
CZ2 B:TRP122 4.5 11.4 1.0
CB B:ASP124 4.6 9.6 1.0
CG B:GLU277 4.8 11.5 1.0
CE2 B:TRP122 4.8 12.0 1.0
CA B:ASP232 4.9 10.3 1.0
CA B:HIS101 5.0 13.1 1.0
CB B:HIS126 5.0 11.9 1.0

Reference:

M.Ilies, L.Di Costanzo, D.P.Dowling, K.J.Thorn, D.W.Christianson. Binding of Alpha,Alpha-Disubstituted Amino Acids to Arginase Suggests New Avenues For Inhibitor Design J.Med.Chem. 2011.
ISSN: ISSN 0022-2623
PubMed: 21728378
DOI: 10.1021/JM200443B
Page generated: Sat Oct 5 17:53:32 2024

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