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Manganese in PDB 1p8p: 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: 1p8p 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) 14.89 / 2.50
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 89.000, 89.000, 115.400, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 26.3

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 1p8p). 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: 1p8p:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1p8p

Go back to Manganese Binding Sites List in 1p8p
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:59.6
occ:1.00
 OD2 A:ASP124 1.9 19.4 1.0
OD1 A:ASN101 2.0 37.6 0.0
OD2 A:ASP128 2.1 36.1 1.0
OD2 A:ASP232 2.5 34.0 1.0
CG A:ASN101 3.0 38.2 0.0
CG A:ASP124 3.1 24.6 1.0
MN A:MN501 3.1 36.5 1.0
CG A:ASP128 3.2 34.1 1.0
CG A:ASP232 3.4 30.6 1.0
OD1 A:ASP128 3.5 33.8 1.0
OD1 A:ASP124 3.6 23.5 1.0
CB A:ASN101 3.7 36.0 0.0
CB A:ASP232 3.7 29.4 1.0
ND2 A:ASN101 4.1 38.5 0.0
NE1 A:TRP122 4.2 29.3 1.0
CB A:ASP124 4.3 26.8 1.0
CZ2 A:TRP122 4.3 28.9 1.0
CB A:ASP128 4.4 35.2 1.0
OD1 A:ASP232 4.5 32.9 1.0
O A:HOH809 4.5 30.0 1.0
CE2 A:TRP122 4.6 26.1 1.0
O A:HIS126 4.6 25.2 1.0
O A:HIS141 4.7 36.0 1.0
OE2 A:GLU277 4.8 35.3 1.0
O A:HOH800 4.9 15.1 1.0
CG A:GLU277 4.9 35.1 1.0
ND1 A:HIS126 4.9 25.0 1.0
CB A:HIS126 4.9 26.6 1.0
OD2 A:ASP234 4.9 34.3 1.0

Manganese binding site 2 out of 6 in 1p8p

Go back to Manganese Binding Sites List in 1p8p
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:36.5
occ:1.00
 OD1 A:ASP124 2.2 23.5 1.0
ND1 A:HIS126 2.2 25.0 1.0
OD2 A:ASP232 2.2 34.0 1.0
OD2 A:ASP234 2.5 34.3 1.0
OD1 A:ASP234 2.7 35.0 1.0
CG A:ASP124 2.9 24.6 1.0
CG A:ASP234 2.9 34.7 1.0
OD2 A:ASP124 3.0 19.4 1.0
CE1 A:HIS126 3.1 24.8 1.0
MN A:MN500 3.1 59.6 1.0
CG A:HIS126 3.2 27.1 1.0
CG A:ASP232 3.3 30.6 1.0
CB A:HIS126 3.6 26.6 1.0
O A:HOH809 3.8 30.0 1.0
N A:HIS126 3.9 28.7 1.0
OD1 A:ASP232 4.0 32.9 1.0
N A:ALA125 4.2 26.9 1.0
NE2 A:HIS126 4.2 26.7 1.0
CB A:ASP232 4.3 29.4 1.0
CD2 A:HIS126 4.3 26.3 1.0
CA A:HIS126 4.3 27.0 1.0
CB A:ASP124 4.4 26.8 1.0
OD2 A:ASP128 4.4 36.1 1.0
CB A:ASP234 4.5 31.6 1.0
OD1 A:ASP128 4.5 33.8 1.0
C A:ALA125 4.8 28.3 1.0
O A:HIS126 4.8 25.2 1.0
CB A:ALA125 4.8 26.0 1.0
CA A:ALA125 4.9 28.1 1.0
CG A:ASP128 4.9 34.1 1.0
OD1 A:ASN101 4.9 37.6 0.0
CA A:ASP124 4.9 28.3 1.0
C A:HIS126 5.0 27.4 1.0

Manganese binding site 3 out of 6 in 1p8p

Go back to Manganese Binding Sites List in 1p8p
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:67.6
occ:1.00
 OD1 B:ASN101 2.1 39.3 0.0
OD2 B:ASP232 2.2 32.8 1.0
OD2 B:ASP124 2.5 21.3 1.0
OD2 B:ASP128 2.6 37.6 1.0
MN B:MN503 3.0 35.2 1.0
CG B:ASN101 3.0 36.9 0.0
CG B:ASP232 3.2 32.1 1.0
O B:HOH824 3.3 51.1 1.0
CB B:ASN101 3.4 36.8 0.0
CG B:ASP124 3.5 25.4 1.0
CG B:ASP128 3.5 35.1 1.0
OD1 B:ASP128 3.7 36.3 1.0
CB B:ASP232 3.8 30.7 1.0
OD1 B:ASP124 3.8 23.1 1.0
OE2 B:GLU277 4.1 39.7 1.0
OD1 B:ASP232 4.2 32.4 1.0
ND2 B:ASN101 4.2 37.9 0.0
CG B:GLU277 4.3 34.6 1.0
OD2 B:ASP234 4.5 36.0 1.0
O B:HIS141 4.6 39.2 1.0
CD B:GLU277 4.7 37.8 1.0
CB B:ASP124 4.8 27.9 1.0
ND1 B:HIS126 4.8 29.5 1.0
CB B:ASP128 4.9 35.3 1.0
CA B:ASN101 4.9 36.5 0.0
CZ2 B:TRP122 4.9 29.8 1.0
NE1 B:TRP122 5.0 31.0 1.0

Manganese binding site 4 out of 6 in 1p8p

Go back to Manganese Binding Sites List in 1p8p
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:35.2
occ:1.00
 OD2 B:ASP232 2.2 32.8 1.0
OD1 B:ASP124 2.2 23.1 1.0
ND1 B:HIS126 2.3 29.5 1.0
OD2 B:ASP234 2.3 36.0 1.0
OD1 B:ASP234 2.5 33.1 1.0
CG B:ASP234 2.7 34.5 1.0
MN B:MN502 3.0 67.6 1.0
CG B:ASP124 3.0 25.4 1.0
CE1 B:HIS126 3.1 26.6 1.0
OD2 B:ASP124 3.2 21.3 1.0
CG B:ASP232 3.2 32.1 1.0
CG B:HIS126 3.4 28.4 1.0
O B:HOH824 3.7 51.1 1.0
CB B:HIS126 3.8 27.5 1.0
OD1 B:ASP232 3.8 32.4 1.0
N B:HIS126 4.0 29.0 1.0
N B:ALA125 4.2 27.2 1.0
CB B:ASP232 4.2 30.7 1.0
CB B:ASP234 4.3 32.9 1.0
NE2 B:HIS126 4.3 30.4 1.0
CD2 B:HIS126 4.4 26.9 1.0
CB B:ASP124 4.5 27.9 1.0
CA B:HIS126 4.5 28.7 1.0
OD2 B:ASP128 4.6 37.6 1.0
OD1 B:ASP128 4.7 36.3 1.0
C B:ALA125 4.8 29.3 1.0
CB B:ALA125 4.8 24.9 1.0
CA B:ALA125 4.9 27.2 1.0
CA B:ASP124 4.9 30.7 1.0
OD1 B:ASN101 4.9 39.3 0.0
O B:HIS126 5.0 29.0 1.0

Manganese binding site 5 out of 6 in 1p8p

Go back to Manganese Binding Sites List in 1p8p
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:56.6
occ:1.00
 OD2 C:ASP128 2.1 35.2 1.0
OD2 C:ASP124 2.1 23.5 1.0
OD1 C:ASN101 2.1 38.3 0.0
OD2 C:ASP232 2.6 30.8 1.0
CG C:ASP128 3.1 34.2 1.0
CG C:ASN101 3.1 37.4 0.0
CG C:ASP124 3.1 27.9 1.0
MN C:MN505 3.2 31.0 1.0
OD1 C:ASP128 3.5 33.6 1.0
CG C:ASP232 3.5 30.7 1.0
OD1 C:ASP124 3.6 22.2 1.0
CB C:ASN101 3.6 36.8 0.0
CB C:ASP232 3.8 31.1 1.0
ND2 C:ASN101 4.1 38.0 0.0
O C:HOH840 4.2 49.5 1.0
NE1 C:TRP122 4.3 28.4 1.0
CB C:ASP128 4.3 36.4 1.0
CZ2 C:TRP122 4.4 30.2 1.0
CB C:ASP124 4.4 29.0 1.0
O C:HIS141 4.5 31.8 1.0
OD1 C:ASP232 4.6 31.1 1.0
CE2 C:TRP122 4.7 28.0 1.0
OE2 C:GLU277 4.7 37.8 1.0
O C:HIS126 4.7 23.8 1.0
ND1 C:HIS126 4.8 20.4 1.0
CB C:HIS126 4.8 24.3 1.0
OD2 C:ASP234 4.9 36.8 1.0
CG C:GLU277 4.9 34.8 1.0

Manganese binding site 6 out of 6 in 1p8p

Go back to Manganese Binding Sites List in 1p8p
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:31.0
occ:1.00
 OD1 C:ASP124 2.0 22.2 1.0
ND1 C:HIS126 2.2 20.4 1.0
OD2 C:ASP232 2.2 30.8 1.0
OD2 C:ASP234 2.4 36.8 1.0
OD1 C:ASP234 2.5 36.0 1.0
CG C:ASP234 2.8 36.5 1.0
CG C:ASP124 2.9 27.9 1.0
CE1 C:HIS126 3.0 18.9 1.0
OD2 C:ASP124 3.2 23.5 1.0
MN C:MN504 3.2 56.6 1.0
CG C:HIS126 3.3 20.9 1.0
CG C:ASP232 3.3 30.7 1.0
CB C:HIS126 3.7 24.3 1.0
O C:HOH840 3.8 49.5 1.0
N C:HIS126 3.8 28.5 1.0
OD1 C:ASP232 4.0 31.1 1.0
N C:ALA125 4.0 28.4 1.0
NE2 C:HIS126 4.2 23.5 1.0
CB C:ASP232 4.2 31.1 1.0
CB C:ASP234 4.3 34.5 1.0
CD2 C:HIS126 4.3 21.0 1.0
CB C:ASP124 4.3 29.0 1.0
CA C:HIS126 4.4 26.4 1.0
OD2 C:ASP128 4.5 35.2 1.0
C C:ALA125 4.6 29.5 1.0
CB C:ALA125 4.7 28.3 1.0
CA C:ALA125 4.7 29.1 1.0
OD1 C:ASP128 4.8 33.6 1.0
CA C:ASP124 4.8 30.3 1.0
C C:ASP124 4.9 30.4 1.0
O C:HIS126 4.9 23.8 1.0
OD1 C:ASN101 5.0 38.3 0.0

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 12:02:54 2024

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