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Manganese in PDB 1zpg: Arginase I Covalently Modified with Propylamine at Q19C

Enzymatic activity of Arginase I Covalently Modified with Propylamine at Q19C

All present enzymatic activity of Arginase I Covalently Modified with Propylamine at Q19C:
3.5.3.1;

Protein crystallography data

The structure of Arginase I Covalently Modified with Propylamine at Q19C, PDB code: 1zpg was solved by D.M.Colleluori, R.S.Reczkowski, F.A.Emig, E.Cama, J.D.Cox, L.R.Scolnick, K.Compher, K.Jude, S.Han, R.E.Viola, D.W.Christianson, D.E.Ash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.87 / 1.90
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 88.184, 88.184, 106.652, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 22

Manganese Binding Sites:

The binding sites of Manganese atom in the Arginase I Covalently Modified with Propylamine at Q19C (pdb code 1zpg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Arginase I Covalently Modified with Propylamine at Q19C, PDB code: 1zpg:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1zpg

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Manganese binding site 1 out of 6 in the Arginase I Covalently Modified with Propylamine at Q19C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase I Covalently Modified with Propylamine at Q19C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:14.8
occ:1.00
 OD2 A:ASP234 2.1 13.2 1.0
OD1 A:ASP124 2.2 14.3 1.0
O A:HOH542 2.2 13.1 1.0
ND1 A:HIS126 2.3 14.0 1.0
OD2 A:ASP232 2.3 12.6 1.0
OD1 A:ASP234 2.4 13.2 1.0
CG A:ASP234 2.6 12.7 1.0
CE1 A:HIS126 3.1 14.9 1.0
CG A:ASP124 3.1 14.3 1.0
CG A:ASP232 3.1 14.8 1.0
MN A:MN502 3.2 14.9 1.0
OD2 A:ASP124 3.4 14.4 1.0
CG A:HIS126 3.4 14.2 1.0
OD1 A:ASP232 3.6 12.7 1.0
CB A:HIS126 3.9 13.6 1.0
N A:HIS126 4.0 14.5 1.0
O A:HOH575 4.1 26.6 1.0
CB A:ASP234 4.1 12.3 1.0
CB A:ASP232 4.1 14.9 1.0
N A:ALA125 4.2 13.2 1.0
NE2 A:HIS126 4.2 15.8 1.0
CD2 A:HIS126 4.4 14.7 1.0
CB A:ASP124 4.5 12.9 1.0
OD1 A:ASP128 4.5 17.7 1.0
CA A:HIS126 4.6 13.7 1.0
OD2 A:ASP128 4.6 17.9 1.0
O A:HOH515 4.6 15.9 1.0
CB A:ALA125 4.8 14.3 1.0
CA A:ASP124 4.8 12.1 1.0
C A:ALA125 4.9 13.2 1.0
CA A:ALA125 4.9 13.1 1.0
CG A:ASP128 5.0 18.6 1.0
C A:ASP124 5.0 11.8 1.0

Manganese binding site 2 out of 6 in 1zpg

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Manganese binding site 2 out of 6 in the Arginase I Covalently Modified with Propylamine at Q19C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase I Covalently Modified with Propylamine at Q19C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:14.9
occ:1.00
 OD2 A:ASP124 2.1 14.4 1.0
OD2 A:ASP128 2.1 17.9 1.0
O A:HOH542 2.1 13.1 1.0
OD2 A:ASP232 2.1 12.6 1.0
ND1 A:HIS101 2.2 13.7 1.0
CG A:ASP124 3.1 14.3 1.0
CG A:ASP128 3.1 18.6 1.0
CG A:HIS101 3.1 16.8 1.0
CE1 A:HIS101 3.2 15.2 1.0
CG A:ASP232 3.2 14.8 1.0
MN A:MN501 3.2 14.8 1.0
OD1 A:ASP124 3.4 14.3 1.0
CB A:HIS101 3.4 16.3 1.0
OD1 A:ASP128 3.5 17.7 1.0
O A:HOH575 3.6 26.6 1.0
CB A:ASP232 3.7 14.9 1.0
NE2 A:HIS101 4.3 15.5 1.0
OD1 A:ASP232 4.3 12.7 1.0
CD2 A:HIS101 4.3 14.5 1.0
NE1 A:TRP122 4.3 13.5 1.0
CB A:ASP124 4.4 12.9 1.0
CB A:ASP128 4.5 15.8 1.0
CZ2 A:TRP122 4.6 14.4 1.0
CG A:GLU277 4.7 16.9 1.0
OE2 A:GLU277 4.8 16.9 1.0
O A:ALA141 4.8 19.2 1.0
CE2 A:TRP122 4.8 13.7 1.0
OD2 A:ASP234 4.8 13.2 1.0
ND1 A:HIS126 4.9 14.0 1.0
CA A:HIS101 4.9 17.1 1.0
CA A:ASP232 5.0 13.8 1.0
OD1 A:ASP234 5.0 13.2 1.0

Manganese binding site 3 out of 6 in 1zpg

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Manganese binding site 3 out of 6 in the Arginase I Covalently Modified with Propylamine at Q19C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase I Covalently Modified with Propylamine at Q19C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:13.3
occ:1.00
 O B:HOH547 2.2 14.3 1.0
OD1 B:ASP124 2.2 11.0 1.0
ND1 B:HIS126 2.2 11.8 1.0
OD2 B:ASP234 2.3 11.2 1.0
OD2 B:ASP232 2.3 9.5 1.0
OD1 B:ASP234 2.4 11.7 1.0
CG B:ASP234 2.7 13.3 1.0
CE1 B:HIS126 3.0 12.9 1.0
CG B:ASP124 3.1 12.5 1.0
CG B:ASP232 3.1 11.3 1.0
MN B:MN504 3.2 12.3 1.0
OD2 B:ASP124 3.3 14.3 1.0
CG B:HIS126 3.4 12.3 1.0
OD1 B:ASP232 3.7 10.3 1.0
CB B:HIS126 3.8 11.1 1.0
N B:HIS126 4.0 11.8 1.0
CB B:ASP232 4.1 9.9 1.0
CB B:ASP234 4.2 12.0 1.0
O B:HOH581 4.2 23.5 1.0
N B:ALA125 4.2 11.1 1.0
NE2 B:HIS126 4.2 15.3 1.0
OD1 B:ASP128 4.4 13.1 1.0
CD2 B:HIS126 4.4 13.4 1.0
CB B:ASP124 4.5 12.0 1.0
CA B:HIS126 4.5 11.2 1.0
O B:HOH520 4.6 13.7 1.0
OD2 B:ASP128 4.6 12.9 1.0
CB B:ALA125 4.8 12.3 1.0
CA B:ASP124 4.8 11.5 1.0
C B:ALA125 4.9 11.3 1.0
CG B:ASP128 4.9 14.4 1.0
CA B:ALA125 5.0 11.0 1.0

Manganese binding site 4 out of 6 in 1zpg

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Manganese binding site 4 out of 6 in the Arginase I Covalently Modified with Propylamine at Q19C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase I Covalently Modified with Propylamine at Q19C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:12.3
occ:1.00
 ND1 B:HIS101 2.1 13.3 1.0
OD2 B:ASP128 2.1 12.9 1.0
OD2 B:ASP124 2.1 14.3 1.0
O B:HOH547 2.2 14.3 1.0
OD2 B:ASP232 2.2 9.5 1.0
CG B:HIS101 3.1 15.2 1.0
CE1 B:HIS101 3.1 15.1 1.0
CG B:ASP128 3.1 14.4 1.0
CG B:ASP124 3.1 12.5 1.0
MN B:MN503 3.2 13.3 1.0
CG B:ASP232 3.3 11.3 1.0
CB B:HIS101 3.4 15.6 1.0
OD1 B:ASP128 3.5 13.1 1.0
OD1 B:ASP124 3.5 11.0 1.0
CB B:ASP232 3.7 9.9 1.0
O B:HOH581 3.9 23.5 1.0
NE2 B:HIS101 4.2 15.6 1.0
CD2 B:HIS101 4.2 14.8 1.0
NE1 B:TRP122 4.3 11.0 1.0
OD1 B:ASP232 4.4 10.3 1.0
CB B:ASP128 4.5 12.9 1.0
CB B:ASP124 4.5 12.0 1.0
CZ2 B:TRP122 4.5 12.4 1.0
CG B:GLU277 4.7 15.6 1.0
CE2 B:TRP122 4.8 11.7 1.0
O B:ALA141 4.8 17.1 1.0
OE2 B:GLU277 4.8 18.0 1.0
CA B:HIS101 4.9 14.8 1.0
ND1 B:HIS126 4.9 11.8 1.0
OD2 B:ASP234 4.9 11.2 1.0
CA B:ASP232 5.0 10.4 1.0
OD1 B:ASP234 5.0 11.7 1.0

Manganese binding site 5 out of 6 in 1zpg

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Manganese binding site 5 out of 6 in the Arginase I Covalently Modified with Propylamine at Q19C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase I Covalently Modified with Propylamine at Q19C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:13.2
occ:1.00
 O C:HOH550 2.2 12.0 1.0
OD1 C:ASP124 2.2 9.7 1.0
OD2 C:ASP232 2.3 10.6 1.0
OD2 C:ASP234 2.3 11.7 1.0
ND1 C:HIS126 2.3 12.1 1.0
OD1 C:ASP234 2.4 13.1 1.0
CG C:ASP234 2.7 12.8 1.0
CG C:ASP124 3.1 13.0 1.0
CE1 C:HIS126 3.1 11.7 1.0
CG C:ASP232 3.1 12.4 1.0
MN C:MN506 3.2 13.6 1.0
CG C:HIS126 3.4 10.8 1.0
OD2 C:ASP124 3.4 12.7 1.0
OD1 C:ASP232 3.7 10.9 1.0
CB C:HIS126 3.8 10.7 1.0
N C:HIS126 4.0 12.3 1.0
CB C:ASP232 4.1 10.3 1.0
O C:HOH622 4.1 27.8 1.0
CB C:ASP234 4.2 12.6 1.0
N C:ALA125 4.2 11.6 1.0
NE2 C:HIS126 4.3 11.6 1.0
CD2 C:HIS126 4.5 12.9 1.0
CB C:ASP124 4.5 11.3 1.0
OD1 C:ASP128 4.5 13.1 1.0
CA C:HIS126 4.5 11.7 1.0
OD2 C:ASP128 4.6 12.8 1.0
O C:HOH523 4.7 14.5 1.0
CB C:ALA125 4.8 13.1 1.0
CA C:ASP124 4.8 12.4 1.0
C C:ALA125 4.9 11.2 1.0
CG C:ASP128 4.9 14.8 1.0
CA C:ALA125 4.9 11.5 1.0
C C:ASP124 5.0 11.6 1.0

Manganese binding site 6 out of 6 in 1zpg

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Manganese binding site 6 out of 6 in the Arginase I Covalently Modified with Propylamine at Q19C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase I Covalently Modified with Propylamine at Q19C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn506

b:13.6
occ:1.00
 OD2 C:ASP128 2.1 12.8 1.0
OD2 C:ASP124 2.1 12.7 1.0
ND1 C:HIS101 2.2 13.9 1.0
O C:HOH550 2.3 12.0 1.0
OD2 C:ASP232 2.3 10.6 1.0
CG C:ASP124 3.1 13.0 1.0
CG C:ASP128 3.1 14.8 1.0
CG C:HIS101 3.2 14.2 1.0
MN C:MN505 3.2 13.2 1.0
CE1 C:HIS101 3.2 13.6 1.0
CG C:ASP232 3.3 12.4 1.0
OD1 C:ASP124 3.4 9.7 1.0
CB C:HIS101 3.4 16.2 1.0
OD1 C:ASP128 3.5 13.1 1.0
CB C:ASP232 3.7 10.3 1.0
O C:HOH622 3.8 27.8 1.0
NE1 C:TRP122 4.3 13.6 1.0
NE2 C:HIS101 4.3 14.7 1.0
CD2 C:HIS101 4.3 13.8 1.0
OD1 C:ASP232 4.4 10.9 1.0
CB C:ASP128 4.4 13.8 1.0
CB C:ASP124 4.4 11.3 1.0
CZ2 C:TRP122 4.5 12.7 1.0
CG C:GLU277 4.7 14.6 1.0
CE2 C:TRP122 4.7 12.4 1.0
OE2 C:GLU277 4.7 16.4 1.0
O C:ALA141 4.8 16.7 1.0
OD2 C:ASP234 4.9 11.7 1.0
CA C:HIS101 4.9 15.3 1.0
ND1 C:HIS126 4.9 12.1 1.0
OD1 C:ASP234 5.0 13.1 1.0

Reference:

D.M.Colleluori, R.S.Reczkowski, F.A.Emig, E.Cama, J.D.Cox, L.R.Scolnick, K.Compher, K.Jude, S.Han, R.E.Viola, D.W.Christianson, D.E.Ash. Probing the Role of the Hyper-Reactive Histidine Residue of Arginase. Arch.Biochem.Biophys. V. 444 15 2005.
ISSN: ISSN 0003-9861
PubMed: 16266687
DOI: 10.1016/J.ABB.2005.09.009
Page generated: Sat Oct 5 13:18:11 2024

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