Atomistry » Manganese » PDB 2pal-2qgi » 2pho
Atomistry »
  Manganese »
    PDB 2pal-2qgi »
      2pho »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy