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Manganese in PDB 1p8r: Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.

Enzymatic activity of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.

All present enzymatic activity of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.:
3.5.3.1;

Protein crystallography data

The structure of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I., PDB code: 1p8r was solved by E.Cama, F.A.Emig, D.E.Ash, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 500.00 / 2.50
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 91.000, 91.000, 69.300, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 20.1

Other elements in 1p8r:

The structure of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. (pdb code 1p8r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I., PDB code: 1p8r:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1p8r

Go back to Manganese Binding Sites List in 1p8r
Manganese binding site 1 out of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:18.2
occ:1.00
 ND1 A:HIS126 2.1 6.7 1.0
O1 A:S2C551 2.2 40.5 1.0
OD2 A:ASP234 2.3 22.4 1.0
OD2 A:ASP124 2.4 11.9 1.0
OD1 A:ASP234 2.4 21.6 1.0
OD2 A:ASP232 2.6 17.6 1.0
CG A:ASP234 2.7 19.6 1.0
CE1 A:HIS126 2.9 9.2 1.0
O3 A:S2C551 3.0 43.0 1.0
B A:S2C551 3.1 42.3 1.0
CG A:ASP124 3.2 10.3 1.0
OD1 A:ASP124 3.3 10.5 1.0
CG A:HIS126 3.3 7.9 1.0
CG A:ASP232 3.4 15.7 1.0
MN A:MN501 3.6 23.2 1.0
CE A:S2C551 3.7 43.6 1.0
CB A:HIS126 3.9 7.8 1.0
OD1 A:ASP232 3.9 14.5 1.0
N A:HIS126 4.0 9.1 1.0
NE2 A:HIS126 4.1 9.1 1.0
N A:ALA125 4.1 8.9 1.0
CB A:ASP234 4.2 16.8 1.0
O2 A:S2C551 4.3 40.8 1.0
CD2 A:HIS126 4.3 7.4 1.0
CB A:ASP232 4.4 14.6 1.0
CD A:S2C551 4.5 46.7 1.0
CA A:HIS126 4.5 8.3 1.0
CB A:ASP124 4.6 8.5 1.0
CB A:ALA125 4.7 8.1 1.0
OD2 A:ASP128 4.7 10.8 1.0
O A:THR246 4.8 16.9 1.0
C A:ALA125 4.8 7.9 1.0
CA A:ALA125 4.8 7.5 1.0
OD1 A:ASP128 4.9 8.6 1.0
CA A:ASP124 4.9 8.9 1.0

Manganese binding site 2 out of 4 in 1p8r

Go back to Manganese Binding Sites List in 1p8r
Manganese binding site 2 out of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:23.2
occ:1.00
 OD1 A:ASP128 2.1 8.6 1.0
O1 A:S2C551 2.1 40.5 1.0
OD1 A:ASP124 2.3 10.5 1.0
OE1 A:GLU101 2.3 18.3 1.0
OD2 A:ASP232 2.4 17.6 1.0
O2 A:S2C551 2.5 40.8 1.0
B A:S2C551 2.7 42.3 1.0
CG A:ASP128 3.1 7.5 1.0
O3 A:S2C551 3.2 43.0 1.0
CG A:ASP124 3.4 10.3 1.0
OD2 A:ASP128 3.4 10.8 1.0
CD A:GLU101 3.4 18.6 1.0
CG A:ASP232 3.5 15.7 1.0
MN A:MN500 3.6 18.2 1.0
CB A:GLU101 3.8 18.0 1.0
OD2 A:ASP124 3.9 11.9 1.0
CB A:ASP232 3.9 14.6 1.0
CG A:GLU101 4.0 16.6 1.0
O A:HIS141 4.1 19.6 1.0
CE A:S2C551 4.2 43.6 1.0
CZ2 A:TRP122 4.2 12.9 1.0
NE1 A:TRP122 4.2 12.3 1.0
CB A:ASP128 4.4 8.2 1.0
OE2 A:GLU101 4.4 17.7 1.0
OD1 A:ASP232 4.5 14.5 1.0
CE2 A:TRP122 4.6 12.4 1.0
CD A:S2C551 4.6 46.7 1.0
CB A:ASP124 4.6 8.5 1.0
CG A:GLU277 4.7 17.1 1.0
OD2 A:ASP234 5.0 22.4 1.0

Manganese binding site 3 out of 4 in 1p8r

Go back to Manganese Binding Sites List in 1p8r
Manganese binding site 3 out of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:15.6
occ:1.00
 O1 B:S2C552 2.2 29.1 1.0
ND1 B:HIS126 2.2 12.5 1.0
OD1 B:ASP234 2.3 8.9 1.0
OD2 B:ASP234 2.3 9.7 1.0
OD2 B:ASP124 2.3 18.2 1.0
OD2 B:ASP232 2.5 16.0 1.0
CG B:ASP234 2.6 7.1 1.0
CE1 B:HIS126 2.9 13.1 1.0
CG B:ASP124 3.1 16.6 1.0
B B:S2C552 3.2 29.4 1.0
O3 B:S2C552 3.2 30.6 1.0
OD1 B:ASP124 3.2 15.9 1.0
CG B:ASP232 3.3 15.1 1.0
CG B:HIS126 3.4 14.3 1.0
MN B:MN503 3.7 22.7 1.0
OD1 B:ASP232 3.8 16.9 1.0
CE B:S2C552 3.9 29.1 1.0
CB B:HIS126 4.0 13.8 1.0
N B:HIS126 4.0 13.8 1.0
N B:ALA125 4.0 12.3 1.0
CB B:ASP234 4.1 6.4 1.0
NE2 B:HIS126 4.2 14.8 1.0
CB B:ASP232 4.2 12.7 1.0
O2 B:S2C552 4.4 29.5 1.0
CD2 B:HIS126 4.4 14.6 1.0
CB B:ASP124 4.5 13.2 1.0
CB B:ALA125 4.6 10.0 1.0
CA B:HIS126 4.6 13.3 1.0
CD B:S2C552 4.6 29.7 1.0
CA B:ALA125 4.7 11.6 1.0
C B:ALA125 4.7 13.1 1.0
O B:THR246 4.8 18.4 1.0
CA B:ASP124 4.8 12.8 1.0
OD2 B:ASP128 4.8 11.2 1.0
C B:ASP234 4.9 8.8 1.0
C B:ASP124 4.9 12.9 1.0
CA B:ASP234 4.9 9.0 1.0
O B:ASP234 4.9 10.1 1.0
OD1 B:ASP128 5.0 8.3 1.0

Manganese binding site 4 out of 4 in 1p8r

Go back to Manganese Binding Sites List in 1p8r
Manganese binding site 4 out of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:22.7
occ:1.00
 OD1 B:ASP128 2.2 8.3 1.0
O1 B:S2C552 2.2 29.1 1.0
OE1 B:GLU101 2.2 18.9 1.0
OD1 B:ASP124 2.3 15.9 1.0
OD2 B:ASP232 2.4 16.0 1.0
O2 B:S2C552 2.5 29.5 1.0
B B:S2C552 2.8 29.4 1.0
CG B:ASP128 3.2 10.4 1.0
CD B:GLU101 3.4 19.6 1.0
CG B:ASP232 3.4 15.1 1.0
O3 B:S2C552 3.4 30.6 1.0
CG B:ASP124 3.4 16.6 1.0
OD2 B:ASP128 3.5 11.2 1.0
MN B:MN502 3.7 15.6 1.0
CB B:GLU101 3.8 18.9 1.0
CB B:ASP232 3.9 12.7 1.0
OD2 B:ASP124 3.9 18.2 1.0
CG B:GLU101 3.9 18.6 1.0
O B:HIS141 4.1 4.2 1.0
CZ2 B:TRP122 4.2 11.2 1.0
NE1 B:TRP122 4.2 11.7 1.0
CE B:S2C552 4.3 29.1 1.0
OE2 B:GLU101 4.4 19.3 1.0
OD1 B:ASP232 4.4 16.9 1.0
CB B:ASP128 4.5 13.7 1.0
CE2 B:TRP122 4.6 10.3 1.0
CG B:GLU277 4.6 20.7 1.0
CB B:ASP124 4.6 13.2 1.0
CD B:S2C552 4.7 29.7 1.0
OD2 B:ASP234 5.0 9.7 1.0

Reference:

E.Cama, F.A.Emig, D.E.Ash, D.W.Christianson. Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I Biochemistry V. 42 7748 2003.
ISSN: ISSN 0006-2960
PubMed: 12820884
DOI: 10.1021/BI030074Y
Page generated: Sat Oct 5 12:03:39 2024

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