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Manganese in PDB 2pho: Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution

Enzymatic activity of Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution

All present enzymatic activity of Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution, PDB code: 2pho was solved by 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) 34.18 / 1.95
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.610, 90.610, 69.630, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 21.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution (pdb code 2pho). 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 Complexed with Thiosemicarbazide at 1.95 Resolution, PDB code: 2pho:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2pho

Go back to Manganese Binding Sites List in 2pho
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution


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 Complexed with Thiosemicarbazide at 1.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn614

b:23.2
occ:1.00
 OD1 A:ASP234 1.9 23.1 1.0
OD1 A:ASP124 2.0 22.3 1.0
OD2 A:ASP232 2.2 23.7 1.0
ND1 A:HIS126 2.2 23.1 1.0
OD2 A:ASP234 2.3 23.9 1.0
S A:TSZ501 2.3 34.3 1.0
CG A:ASP234 2.4 21.8 1.0
CE1 A:HIS126 3.0 23.3 1.0
CG A:ASP124 3.2 23.1 1.0
CG A:ASP232 3.3 27.9 1.0
CG A:HIS126 3.4 23.7 1.0
MN A:MN615 3.4 25.7 1.0
C A:TSZ501 3.5 35.1 1.0
OD2 A:ASP124 3.6 24.1 1.0
N2 A:TSZ501 3.8 34.2 1.0
CB A:HIS126 3.9 24.9 1.0
CB A:ASP234 3.9 20.1 1.0
N A:HIS126 3.9 23.9 1.0
N A:ALA125 3.9 20.2 1.0
N3 A:TSZ501 4.0 34.0 1.0
OG1 A:THR246 4.0 20.3 1.0
OD1 A:ASP232 4.1 29.7 1.0
NE2 A:HIS126 4.2 21.6 1.0
CB A:ASP232 4.3 26.6 1.0
CD2 A:HIS126 4.4 22.6 1.0
CB A:ALA125 4.4 24.1 1.0
CB A:ASP124 4.4 23.7 1.0
O A:HOH626 4.4 29.9 1.0
CA A:HIS126 4.5 25.5 1.0
CA A:ALA125 4.6 21.4 1.0
O A:HOH621 4.6 19.6 1.0
C A:ALA125 4.6 22.5 1.0
CA A:ASP124 4.7 23.3 1.0
OD1 A:ASP128 4.7 16.7 1.0
C A:ASP124 4.8 21.7 1.0
C A:ASP234 4.8 18.3 1.0
OD2 A:ASP128 4.8 18.2 1.0
N1 A:TSZ501 4.8 36.4 1.0
CA A:ASP234 4.8 18.2 1.0
O A:ASP234 4.8 20.6 1.0
O A:THR246 4.9 24.8 1.0

Manganese binding site 2 out of 4 in 2pho

Go back to Manganese Binding Sites List in 2pho
Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution


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 Complexed with Thiosemicarbazide at 1.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn615

b:25.7
occ:1.00
 OD2 A:ASP128 2.1 18.2 1.0
OD2 A:ASP124 2.1 24.1 1.0
ND1 A:HIS101 2.2 33.7 1.0
O A:HOH626 2.4 29.9 1.0
OD2 A:ASP232 2.5 23.7 1.0
S A:TSZ501 2.6 34.3 1.0
CG A:ASP124 3.0 23.1 1.0
CE1 A:HIS101 3.1 34.9 1.0
CG A:ASP128 3.1 19.5 1.0
CG A:HIS101 3.2 33.3 1.0
OD1 A:ASP124 3.2 22.3 1.0
CG A:ASP232 3.3 27.9 1.0
MN A:MN614 3.4 23.2 1.0
CB A:HIS101 3.5 32.2 1.0
OD1 A:ASP128 3.5 16.7 1.0
C A:TSZ501 3.6 35.1 1.0
CB A:ASP232 3.6 26.6 1.0
OD1 A:ASP232 4.2 29.7 1.0
NE2 A:HIS101 4.2 33.5 1.0
N1 A:TSZ501 4.2 36.4 1.0
O A:HIS141 4.3 22.1 1.0
CD2 A:HIS101 4.3 34.2 1.0
NE1 A:TRP122 4.4 21.4 1.0
CB A:ASP124 4.4 23.7 1.0
CB A:ASP128 4.4 20.9 1.0
N3 A:TSZ501 4.5 34.0 1.0
N2 A:TSZ501 4.6 34.2 1.0
CG A:GLU277 4.7 17.6 1.0
CZ2 A:TRP122 4.7 19.4 1.0
OD1 A:ASP234 4.8 23.1 1.0
OD2 A:ASP234 4.8 23.9 1.0
OE2 A:GLU277 4.9 20.3 1.0
CE2 A:TRP122 4.9 20.4 1.0

Manganese binding site 3 out of 4 in 2pho

Go back to Manganese Binding Sites List in 2pho
Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution


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 Complexed with Thiosemicarbazide at 1.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn714

b:26.6
occ:1.00
 OD1 B:ASP234 1.8 35.9 1.0
OD1 B:ASP124 2.2 31.2 1.0
OD2 B:ASP232 2.2 28.5 1.0
O B:HOH722 2.3 37.4 1.0
ND1 B:HIS126 2.4 21.4 1.0
CG B:ASP234 2.4 34.8 1.0
OD2 B:ASP234 2.5 30.8 1.0
CG B:ASP232 3.0 30.9 1.0
CE1 B:HIS126 3.1 23.2 1.0
CG B:ASP124 3.2 29.9 1.0
MN B:MN715 3.5 37.3 1.0
O B:HOH808 3.5 42.3 1.0
OD2 B:ASP124 3.5 30.8 1.0
OD1 B:ASP232 3.5 30.8 1.0
CG B:HIS126 3.6 25.7 1.0
CB B:ASP234 3.9 33.0 1.0
CB B:ASP232 3.9 31.4 1.0
N B:ALA125 4.0 26.5 1.0
CB B:HIS126 4.0 25.9 1.0
N B:HIS126 4.1 27.4 1.0
OG1 B:THR246 4.1 31.9 1.0
NE2 B:HIS126 4.3 24.6 1.0
CB B:ALA125 4.5 27.5 1.0
CB B:ASP124 4.5 29.5 1.0
OD1 B:ASP128 4.6 25.2 1.0
CD2 B:HIS126 4.6 24.0 1.0
CA B:HIS126 4.7 27.7 1.0
CA B:ALA125 4.7 26.4 1.0
C B:ALA125 4.7 27.5 1.0
O B:HOH759 4.8 20.5 1.0
OD2 B:ASP128 4.8 23.6 1.0
CA B:ASP124 4.8 27.2 1.0
O B:THR246 4.9 34.0 1.0
CA B:ASP234 4.9 31.4 1.0
C B:ASP124 4.9 27.3 1.0
C B:ASP234 5.0 30.5 1.0

Manganese binding site 4 out of 4 in 2pho

Go back to Manganese Binding Sites List in 2pho
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide at 1.95 Resolution


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 Complexed with Thiosemicarbazide at 1.95 Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn715

b:37.3
occ:1.00
 OD2 B:ASP128 2.0 23.6 1.0
ND1 B:HIS101 2.2 41.8 1.0
OD2 B:ASP232 2.3 28.5 1.0
O B:HOH722 2.3 37.4 1.0
OD2 B:ASP124 2.3 30.8 1.0
CG B:ASP128 3.0 26.5 1.0
CG B:HIS101 3.1 42.1 1.0
CG B:ASP232 3.2 30.9 1.0
CB B:HIS101 3.3 43.2 1.0
CE1 B:HIS101 3.3 41.2 1.0
CG B:ASP124 3.3 29.9 1.0
OD1 B:ASP128 3.4 25.2 1.0
MN B:MN714 3.5 26.6 1.0
CB B:ASP232 3.6 31.4 1.0
OD1 B:ASP124 3.6 31.2 1.0
O B:HIS141 4.0 31.9 1.0
CD2 B:HIS101 4.3 41.8 1.0
OD1 B:ASP232 4.3 30.8 1.0
CB B:ASP128 4.3 26.7 1.0
NE2 B:HIS101 4.4 39.9 1.0
NE1 B:TRP122 4.4 25.4 1.0
O B:HOH808 4.5 42.3 1.0
OE2 B:GLU277 4.5 33.4 1.0
CB B:ASP124 4.7 29.5 1.0
CZ2 B:TRP122 4.7 26.0 1.0
CG B:GLU277 4.7 34.7 1.0
CA B:HIS101 4.8 42.7 1.0
CE2 B:TRP122 4.9 26.3 1.0
CA B:ASP232 4.9 30.5 1.0
OD1 B:ASP234 5.0 35.9 1.0

Reference:

L.Di Costanzo, M.E.Pique, D.W.Christianson. Crystal Structure of Human Arginase I Complexed with Thiosemicarbazide Reveals An Unusual Thiocarbonyl Mu-Sulfide Ligand in the Binuclear Manganese Cluster. J.Am.Chem.Soc. V. 129 6388 2007.
ISSN: ISSN 0002-7863
PubMed: 17469833
DOI: 10.1021/JA071567J
Page generated: Sat Oct 5 14:54:42 2024

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