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Manganese in PDB 1p8s: 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: 1p8s 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) 29.77 / 3.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 90.940, 90.940, 105.690, 90.00, 90.00, 120.00
R / Rfree (%) 28.6 / 31.5

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 1p8s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 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: 1p8s:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1p8s

Go back to Manganese Binding Sites List in 1p8s
Manganese binding site 1 out of 6 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:59.2
occ:1.00
 OD2 A:ASP124 2.3 83.5 1.0
ND1 A:HIS126 2.4 63.2 1.0
OD2 A:ASP234 2.5 55.2 1.0
OD1 A:ASP124 2.8 83.6 1.0
CG A:ASP124 2.9 81.4 1.0
MN A:MN501 2.9 75.2 1.0
SG A:CYS232 3.1 52.6 1.0
CG A:ASP234 3.2 58.4 1.0
OD1 A:ASP234 3.2 62.7 1.0
CE1 A:HIS126 3.3 62.7 1.0
CG A:HIS126 3.4 63.7 1.0
OD2 A:ASP128 3.7 50.5 1.0
CB A:HIS126 3.7 65.9 1.0
CB A:CYS232 4.0 58.9 1.0
N A:HIS126 4.0 68.3 1.0
OD1 A:ASP128 4.1 49.1 1.0
CG A:ASP128 4.3 53.8 1.0
CB A:ASP124 4.4 77.7 1.0
NE2 A:HIS126 4.4 62.0 1.0
CA A:HIS126 4.5 67.8 1.0
CD2 A:HIS126 4.5 62.6 1.0
N A:ALA125 4.5 73.7 1.0
CB A:ASP234 4.7 58.1 1.0
C A:ALA125 4.9 69.5 1.0
ND1 A:HIS101 5.0 83.1 1.0

Manganese binding site 2 out of 6 in 1p8s

Go back to Manganese Binding Sites List in 1p8s
Manganese binding site 2 out of 6 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:75.2
occ:1.00
 OD1 A:ASP124 2.1 83.6 1.0
ND1 A:HIS101 2.1 83.1 1.0
OD1 A:ASP128 2.1 49.1 1.0
MN A:MN500 2.9 59.2 1.0
CG A:HIS101 3.1 82.9 1.0
CE1 A:HIS101 3.1 83.7 1.0
CG A:ASP128 3.1 53.8 1.0
SG A:CYS232 3.2 52.6 1.0
CG A:ASP124 3.3 81.4 1.0
CB A:HIS101 3.4 82.7 1.0
OD2 A:ASP128 3.4 50.5 1.0
CB A:CYS232 3.5 58.9 1.0
OD2 A:ASP124 3.8 83.5 1.0
NE2 A:HIS101 4.2 83.9 1.0
CD2 A:HIS101 4.2 83.1 1.0
O A:HIS141 4.4 89.8 1.0
CB A:ASP124 4.5 77.7 1.0
CB A:ASP128 4.5 60.2 1.0
CA A:CYS232 4.7 60.2 1.0
OD2 A:ASP234 4.7 55.2 1.0
CA A:HIS101 4.8 82.3 1.0
NE1 A:TRP122 4.9 75.5 1.0

Manganese binding site 3 out of 6 in 1p8s

Go back to Manganese Binding Sites List in 1p8s
Manganese binding site 3 out of 6 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:71.6
occ:1.00
 OD2 B:ASP234 2.3 64.5 1.0
OD2 B:ASP124 2.4 74.8 1.0
ND1 B:HIS126 2.5 86.6 1.0
OD1 B:ASP124 2.8 75.5 1.0
CG B:ASP124 2.9 75.1 1.0
MN B:MN503 2.9 77.8 1.0
SG B:CYS232 3.1 55.0 1.0
CG B:ASP234 3.2 66.4 1.0
OD1 B:ASP234 3.3 67.0 1.0
CG B:HIS126 3.4 84.8 1.0
CE1 B:HIS126 3.4 86.5 1.0
OD2 B:ASP128 3.6 82.2 1.0
CB B:HIS126 3.7 83.2 1.0
N B:HIS126 3.9 78.5 1.0
OD1 B:ASP128 3.9 81.3 1.0
CB B:CYS232 4.0 61.8 1.0
CG B:ASP128 4.2 81.4 1.0
N B:ALA125 4.2 75.2 1.0
CA B:HIS126 4.4 81.1 1.0
CB B:ASP124 4.4 74.8 1.0
NE2 B:HIS126 4.4 86.0 1.0
CD2 B:HIS126 4.4 84.5 1.0
CB B:ASP234 4.6 67.4 1.0
C B:ALA125 4.7 76.8 1.0
CB B:ALA125 4.8 74.7 1.0
CA B:ALA125 4.8 76.3 1.0

Manganese binding site 4 out of 6 in 1p8s

Go back to Manganese Binding Sites List in 1p8s
Manganese binding site 4 out of 6 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:77.8
occ:1.00
 OD1 B:ASP124 2.1 75.5 1.0
ND1 B:HIS101 2.3 85.0 1.0
OD1 B:ASP128 2.4 81.3 1.0
MN B:MN502 2.9 71.6 1.0
CG B:HIS101 3.2 84.1 1.0
CG B:ASP128 3.2 81.4 1.0
SG B:CYS232 3.2 55.0 1.0
CE1 B:HIS101 3.2 85.8 1.0
CG B:ASP124 3.3 75.1 1.0
CB B:HIS101 3.4 83.1 1.0
CB B:CYS232 3.5 61.8 1.0
OD2 B:ASP128 3.5 82.2 1.0
OD2 B:ASP124 3.8 74.8 1.0
CD2 B:HIS101 4.3 83.9 1.0
NE2 B:HIS101 4.3 84.5 1.0
O B:HIS141 4.4 92.7 1.0
CB B:ASP128 4.4 79.9 1.0
OD2 B:ASP234 4.5 64.5 1.0
CB B:ASP124 4.5 74.8 1.0
CG B:GLU277 4.7 85.1 1.0
CA B:CYS232 4.7 62.9 1.0
NE1 B:TRP122 4.8 72.1 1.0
CA B:HIS101 4.9 81.6 1.0

Manganese binding site 5 out of 6 in 1p8s

Go back to Manganese Binding Sites List in 1p8s
Manganese binding site 5 out of 6 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 5 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
C:Mn504

b:49.6
occ:1.00
 OD2 C:ASP124 2.2 55.1 1.0
ND1 C:HIS126 2.3 50.0 1.0
OD2 C:ASP234 2.4 59.6 1.0
OD1 C:ASP128 2.8 61.5 1.0
OD1 C:ASP124 2.9 58.3 1.0
CG C:ASP124 2.9 56.0 1.0
MN C:MN505 2.9 45.7 1.0
CE1 C:HIS126 3.0 48.9 1.0
SG C:CYS232 3.1 40.5 1.0
OD1 C:ASP234 3.1 63.9 1.0
CG C:ASP234 3.2 60.5 1.0
CG C:HIS126 3.2 50.0 1.0
CG C:ASP128 3.6 59.5 1.0
OD2 C:ASP128 3.7 56.5 1.0
CB C:HIS126 3.7 50.4 1.0
CB C:CYS232 4.0 50.4 1.0
NE2 C:HIS126 4.1 49.6 1.0
CD2 C:HIS126 4.2 50.3 1.0
N C:HIS126 4.2 51.7 1.0
CB C:ASP124 4.4 54.2 1.0
N C:ALA125 4.5 53.8 1.0
CA C:HIS126 4.5 51.4 1.0
CB C:ASP234 4.6 59.1 1.0

Manganese binding site 6 out of 6 in 1p8s

Go back to Manganese Binding Sites List in 1p8s
Manganese binding site 6 out of 6 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 6 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
C:Mn505

b:45.7
occ:1.00
 OD1 C:ASP128 2.1 61.5 1.0
OD1 C:ASP124 2.2 58.3 1.0
ND1 C:HIS101 2.2 70.8 1.0
CG C:ASP128 2.9 59.5 1.0
MN C:MN504 2.9 49.6 1.0
CG C:HIS101 3.1 71.4 1.0
CE1 C:HIS101 3.2 70.4 1.0
CG C:ASP124 3.3 56.0 1.0
CB C:HIS101 3.3 72.2 1.0
SG C:CYS232 3.3 40.5 1.0
CB C:CYS232 3.5 50.4 1.0
OD2 C:ASP128 3.5 56.5 1.0
OD2 C:ASP124 3.7 55.1 1.0
CB C:ASP128 3.9 58.9 1.0
CD2 C:HIS101 4.3 70.9 1.0
NE2 C:HIS101 4.3 70.2 1.0
O C:HIS141 4.4 75.4 1.0
CB C:ASP124 4.5 54.2 1.0
OD2 C:ASP234 4.6 59.6 1.0
CG C:GLU277 4.7 68.9 1.0
CA C:HIS101 4.8 74.3 1.0
CA C:CYS232 4.8 53.1 1.0
NE1 C:TRP122 4.9 57.4 1.0
OE2 C:GLU277 5.0 69.3 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 12:04:37 2024

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