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Manganese in PDB 1p8o: 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: 1p8o 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) 30.07 / 2.96
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 88.550, 88.550, 111.548, 90.00, 90.00, 120.00
R / Rfree (%) 29.3 / 29.7

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 1p8o). 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: 1p8o:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1p8o

Go back to Manganese Binding Sites List in 1p8o
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:57.7
occ:1.00
 ND1 A:HIS126 2.1 71.6 1.0
OD1 A:ASP232 2.2 47.1 1.0
OD2 A:ASP124 2.3 76.1 1.0
O A:HOH817 2.4 64.8 1.0
OD2 A:ASP234 2.4 52.3 1.0
OD1 A:ASP234 2.5 52.3 1.0
CG A:ASP234 2.8 54.3 1.0
CE1 A:HIS126 2.9 73.0 1.0
CG A:ASP232 3.1 45.1 1.0
CG A:ASP124 3.1 74.5 1.0
OD1 A:ASP124 3.1 77.8 1.0
CG A:HIS126 3.3 74.2 1.0
MN A:MN501 3.4 68.0 1.0
OD2 A:ASP232 3.6 42.7 1.0
CB A:HIS126 3.9 76.4 1.0
CB A:ASP232 4.1 45.4 1.0
NE2 A:HIS126 4.1 74.3 1.0
N A:HIS126 4.2 73.1 1.0
N A:ALA125 4.3 70.7 1.0
CD2 A:HIS126 4.3 73.7 1.0
CB A:ASP234 4.3 55.3 1.0
CB A:ASP124 4.5 70.3 1.0
OD1 A:ASN128 4.5 56.2 0.0
CA A:HIS126 4.6 73.3 1.0
CA A:ASP124 4.9 61.9 1.0
CB A:ALA125 5.0 72.7 1.0
C A:ALA125 5.0 74.7 1.0

Manganese binding site 2 out of 6 in 1p8o

Go back to Manganese Binding Sites List in 1p8o
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:68.0
occ:1.00
 ND1 A:HIS101 2.0 57.0 1.0
OD1 A:ASP124 2.1 77.8 1.0
OD1 A:ASP232 2.4 47.1 1.0
CG A:HIS101 3.0 60.8 1.0
CE1 A:HIS101 3.0 55.3 1.0
OD1 A:ASN128 3.1 56.2 0.0
CG A:ASP124 3.2 74.5 1.0
CG A:ASP232 3.3 45.1 1.0
O A:HOH817 3.3 64.8 1.0
CB A:HIS101 3.3 67.5 1.0
MN A:MN500 3.4 57.7 1.0
CB A:ASP232 3.4 45.4 1.0
OD2 A:ASP124 3.8 76.1 1.0
NE2 A:HIS101 4.1 55.2 1.0
CD2 A:HIS101 4.1 57.0 1.0
NE1 A:TRP122 4.2 92.0 1.0
CG A:ASN128 4.2 58.7 0.0
CZ2 A:TRP122 4.4 93.7 1.0
CB A:ASP124 4.4 70.3 1.0
OD2 A:ASP232 4.4 42.7 1.0
CA A:ASP232 4.6 35.7 1.0
CG A:GLU277 4.6 81.5 1.0
OE2 A:GLU277 4.6 82.0 1.0
CE2 A:TRP122 4.6 92.1 1.0
O A:HIS141 4.7 64.8 1.0
CA A:HIS101 4.8 75.8 1.0
OD2 A:ASP234 5.0 52.3 1.0

Manganese binding site 3 out of 6 in 1p8o

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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:43.7
occ:1.00
 ND1 B:HIS126 2.0 72.1 1.0
OD2 B:ASP234 2.2 40.6 1.0
OD1 B:ASP232 2.3 32.5 1.0
OD2 B:ASP124 2.4 71.7 1.0
O B:HOH800 2.4 24.6 1.0
OD1 B:ASP234 2.5 31.9 1.0
CE1 B:HIS126 2.6 70.8 1.0
CG B:ASP234 2.7 39.2 1.0
CG B:ASP232 3.1 33.0 1.0
CG B:ASP124 3.1 69.4 1.0
OD1 B:ASP124 3.2 74.2 1.0
CG B:HIS126 3.3 74.2 1.0
MN B:MN503 3.5 67.4 1.0
OD2 B:ASP232 3.6 27.1 1.0
NE2 B:HIS126 3.8 72.0 1.0
CB B:HIS126 3.9 76.4 1.0
CB B:ASP232 4.1 34.7 1.0
CD2 B:HIS126 4.2 73.2 1.0
N B:HIS126 4.2 79.8 1.0
CB B:ASP234 4.2 40.0 1.0
N B:ALA125 4.3 64.6 1.0
CB B:ASP124 4.5 63.4 1.0
OD1 B:ASN128 4.6 49.7 0.0
CA B:HIS126 4.7 81.1 1.0
CB B:ALA125 5.0 72.7 1.0

Manganese binding site 4 out of 6 in 1p8o

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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:67.4
occ:1.00
 ND1 B:HIS101 2.0 38.9 1.0
OD1 B:ASP124 2.2 74.2 1.0
OD1 B:ASP232 2.4 32.5 1.0
CG B:HIS101 2.9 44.1 1.0
CE1 B:HIS101 3.0 38.0 1.0
OD1 B:ASN128 3.1 49.7 0.0
CB B:HIS101 3.2 53.1 1.0
CG B:ASP232 3.2 33.0 1.0
O B:HOH800 3.3 24.6 1.0
CG B:ASP124 3.4 69.4 1.0
CB B:ASP232 3.4 34.7 1.0
MN B:MN502 3.5 43.7 1.0
OD2 B:ASP124 3.9 71.7 1.0
CD2 B:HIS101 4.1 39.3 1.0
NE2 B:HIS101 4.1 36.4 1.0
CG B:ASN128 4.2 52.2 0.0
NE1 B:TRP122 4.3 62.4 1.0
OD2 B:ASP232 4.4 27.1 1.0
CZ2 B:TRP122 4.4 64.3 1.0
CB B:ASP124 4.5 63.4 1.0
CG B:GLU277 4.5 82.7 1.0
OE2 B:GLU277 4.6 82.9 1.0
CA B:ASP232 4.6 38.4 1.0
CE2 B:TRP122 4.7 62.6 1.0
CA B:HIS101 4.7 71.5 1.0
O B:HIS141 4.8 65.3 1.0
OD2 B:ASP234 5.0 40.6 1.0
ND1 B:HIS126 5.0 72.1 1.0

Manganese binding site 5 out of 6 in 1p8o

Go back to Manganese Binding Sites List in 1p8o
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:69.0
occ:1.00
 ND1 C:HIS126 2.2 79.2 1.0
OD2 C:ASP234 2.3 54.7 1.0
OD1 C:ASP232 2.3 45.5 1.0
O C:HOH816 2.4 46.8 1.0
OD2 C:ASP124 2.5 74.7 1.0
OD1 C:ASP234 2.5 54.5 1.0
CG C:ASP234 2.7 54.6 1.0
CE1 C:HIS126 2.9 78.1 1.0
CG C:ASP232 3.1 49.0 1.0
CG C:ASP124 3.2 71.2 1.0
OD1 C:ASP124 3.2 70.2 1.0
CG C:HIS126 3.4 79.5 1.0
MN C:MN505 3.5 79.0 1.0
OD2 C:ASP232 3.6 45.7 1.0
CB C:HIS126 3.9 79.2 1.0
NE2 C:HIS126 4.1 77.4 1.0
CB C:ASP232 4.1 51.8 1.0
N C:HIS126 4.2 71.7 1.0
CB C:ASP234 4.2 53.8 1.0
N C:ALA125 4.3 63.6 1.0
CD2 C:HIS126 4.4 77.9 1.0
CB C:ASP124 4.6 70.1 1.0
OD1 C:ASN128 4.6 66.1 0.0
CA C:HIS126 4.7 75.4 1.0
CB C:ALA125 4.9 73.5 1.0
C C:ALA125 5.0 65.3 1.0

Manganese binding site 6 out of 6 in 1p8o

Go back to Manganese Binding Sites List in 1p8o
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:79.0
occ:1.00
 ND1 C:HIS101 2.0 69.9 1.0
OD1 C:ASP124 2.1 70.2 1.0
OD1 C:ASP232 2.4 45.5 1.0
CE1 C:HIS101 3.0 69.3 1.0
CG C:HIS101 3.0 72.7 1.0
OD1 C:ASN128 3.1 66.1 0.0
CG C:ASP124 3.3 71.2 1.0
CG C:ASP232 3.3 49.0 1.0
O C:HOH816 3.3 46.8 1.0
CB C:HIS101 3.3 77.7 1.0
CB C:ASP232 3.3 51.8 1.0
MN C:MN504 3.5 69.0 1.0
OD2 C:ASP124 3.9 74.7 1.0
NE2 C:HIS101 4.1 70.2 1.0
CD2 C:HIS101 4.1 70.4 1.0
NE1 C:TRP122 4.2 80.0 1.0
CG C:ASN128 4.2 71.0 0.0
CB C:ASP124 4.4 70.1 1.0
CZ2 C:TRP122 4.4 80.0 1.0
OD2 C:ASP232 4.4 45.7 1.0
CA C:ASP232 4.6 60.1 1.0
CE2 C:TRP122 4.6 80.0 1.0
OE2 C:GLU277 4.6 86.9 1.0
CG C:GLU277 4.6 88.9 1.0
O C:HIS141 4.8 82.5 1.0
CA C:HIS101 4.9 82.4 1.0
OD2 C:ASP234 4.9 54.7 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 12:02:41 2024

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