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Manganese in PDB 1p8m: 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: 1p8m was solved by E.Cama, F.A.Emig, E.-D.Ash, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.97 / 2.84
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 88.492, 88.492, 113.902, 90.00, 90.00, 120.00
R / Rfree (%) 28.6 / 29.8

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 1p8m). 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: 1p8m:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1p8m

Go back to Manganese Binding Sites List in 1p8m
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:73.5
occ:1.00
 ND1 A:HIS126 2.1 70.1 1.0
OD2 A:ASP234 2.3 84.6 1.0
OE2 A:GLU128 2.3 86.5 0.0
OD1 A:ASP232 2.4 79.7 1.0
O A:HOH844 2.5 65.1 1.0
OD2 A:ASP124 2.5 77.0 1.0
CE1 A:HIS126 2.8 70.2 1.0
CG A:ASP234 3.0 80.7 1.0
OD1 A:ASP234 3.0 84.1 1.0
CG A:HIS126 3.3 70.0 1.0
CG A:ASP232 3.4 79.0 1.0
CG A:ASP124 3.4 74.2 1.0
MN A:MN501 3.4 76.3 1.0
CD A:GLU128 3.5 86.3 0.0
OD1 A:ASP124 3.6 73.2 1.0
CB A:HIS126 3.9 70.9 1.0
NE2 A:HIS126 4.0 70.2 1.0
OD2 A:ASP232 4.0 79.7 1.0
OE1 A:GLU128 4.0 86.3 0.0
CD2 A:HIS126 4.2 69.4 1.0
N A:HIS126 4.3 70.1 1.0
CB A:ASP232 4.4 76.8 1.0
CB A:ASP234 4.5 74.1 1.0
CG A:GLU128 4.7 78.8 0.0
N A:ALA125 4.7 70.6 1.0
CA A:HIS126 4.7 70.6 1.0
CB A:ASP124 4.8 71.8 1.0
CB A:THR246 4.8 75.3 1.0

Manganese binding site 2 out of 6 in 1p8m

Go back to Manganese Binding Sites List in 1p8m
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:76.3
occ:1.00
 ND1 A:HIS101 2.0 65.8 1.0
OD1 A:ASP124 2.1 73.2 1.0
OE1 A:GLU128 2.2 86.3 0.0
OD1 A:ASP232 2.5 79.7 1.0
O A:HOH844 2.8 65.1 1.0
CD A:GLU128 2.8 86.3 0.0
OE2 A:GLU128 2.9 86.5 0.0
CG A:HIS101 2.9 67.6 1.0
CE1 A:HIS101 3.0 66.5 1.0
CG A:ASP124 3.1 74.2 1.0
CB A:HIS101 3.3 69.0 1.0
CG A:ASP232 3.3 79.0 1.0
MN A:MN500 3.4 73.5 1.0
CB A:ASP232 3.4 76.8 1.0
OD2 A:ASP124 3.5 77.0 1.0
NE2 A:HIS101 4.1 67.8 1.0
CD2 A:HIS101 4.1 67.0 1.0
CG A:GLU128 4.1 78.8 0.0
CZ2 A:TRP122 4.1 73.2 1.0
NE1 A:TRP122 4.3 72.6 1.0
CB A:ASP124 4.4 71.8 1.0
OD2 A:ASP232 4.5 79.7 1.0
CE2 A:TRP122 4.5 72.7 1.0
OE2 A:GLU277 4.6 95.7 1.0
O A:HIS141 4.6 73.3 1.0
CB A:GLU128 4.6 70.9 0.0
CG A:GLU277 4.7 92.0 1.0
CA A:ASP232 4.8 74.4 1.0
CA A:HIS101 4.8 72.3 1.0

Manganese binding site 3 out of 6 in 1p8m

Go back to Manganese Binding Sites List in 1p8m
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:61.1
occ:1.00
 OD1 B:ASP232 2.1 58.7 1.0
ND1 B:HIS126 2.2 52.8 1.0
OD2 B:ASP234 2.2 69.3 1.0
OE2 B:GLU128 2.4 89.9 0.0
O B:HOH845 2.5 55.1 1.0
OD2 B:ASP124 2.5 72.0 1.0
CE1 B:HIS126 2.8 55.5 1.0
OD1 B:ASP234 2.9 67.8 1.0
CG B:ASP234 2.9 66.0 1.0
CG B:ASP232 3.0 56.9 1.0
CG B:ASP124 3.3 68.9 1.0
MN B:MN503 3.3 68.5 1.0
CG B:HIS126 3.3 53.6 1.0
OD1 B:ASP124 3.3 72.8 1.0
CD B:GLU128 3.6 96.2 0.0
OD2 B:ASP232 3.6 58.5 1.0
CB B:HIS126 3.9 53.7 1.0
NE2 B:HIS126 4.0 57.4 1.0
OE1 B:GLU128 4.1 89.9 0.0
CB B:ASP232 4.1 53.5 1.0
CD2 B:HIS126 4.2 54.4 1.0
CB B:ASP234 4.4 61.5 1.0
N B:HIS126 4.4 52.0 1.0
N B:ALA125 4.7 57.0 1.0
CG B:GLU128 4.7 92.9 0.0
CB B:ASP124 4.7 62.7 1.0
CA B:HIS126 4.8 53.4 1.0
CB B:THR246 4.9 55.4 1.0

Manganese binding site 4 out of 6 in 1p8m

Go back to Manganese Binding Sites List in 1p8m
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:68.5
occ:1.00
 OD1 B:ASP124 2.0 72.8 1.0
ND1 B:HIS101 2.1 54.8 1.0
OE1 B:GLU128 2.2 89.9 0.0
OD1 B:ASP232 2.4 58.7 1.0
CD B:GLU128 2.7 96.2 0.0
O B:HOH845 2.7 55.1 1.0
OE2 B:GLU128 2.7 89.9 0.0
CG B:HIS101 3.1 57.3 1.0
CG B:ASP124 3.1 68.9 1.0
CE1 B:HIS101 3.1 53.0 1.0
CG B:ASP232 3.2 56.9 1.0
MN B:MN502 3.3 61.1 1.0
CB B:ASP232 3.3 53.5 1.0
CB B:HIS101 3.4 62.4 1.0
OD2 B:ASP124 3.6 72.0 1.0
CG B:GLU128 3.9 92.9 0.0
NE2 B:HIS101 4.2 53.5 1.0
CD2 B:HIS101 4.2 53.6 1.0
NE1 B:TRP122 4.2 80.5 1.0
CZ2 B:TRP122 4.3 81.0 1.0
CB B:ASP124 4.3 62.7 1.0
OD2 B:ASP232 4.4 58.5 1.0
CB B:GLU128 4.6 93.8 0.0
CE2 B:TRP122 4.6 80.4 1.0
O B:HIS141 4.6 60.4 1.0
CA B:ASP232 4.7 48.4 1.0
OE2 B:GLU277 4.7 70.5 1.0
CG B:GLU277 4.8 66.4 1.0
CA B:HIS101 4.9 68.2 1.0
OD2 B:ASP234 5.0 69.3 1.0
ND1 B:HIS126 5.0 52.8 1.0

Manganese binding site 5 out of 6 in 1p8m

Go back to Manganese Binding Sites List in 1p8m
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:51.5
occ:1.00
 ND1 C:HIS126 2.1 47.0 1.0
OD2 C:ASP234 2.2 58.0 1.0
OD1 C:ASP232 2.4 57.6 1.0
OE2 C:GLU128 2.4 84.8 0.0
O C:HOH841 2.4 65.1 1.0
OD2 C:ASP124 2.5 94.3 1.0
CE1 C:HIS126 2.7 48.7 1.0
CG C:ASP234 2.9 56.1 1.0
OD1 C:ASP234 2.9 57.6 1.0
CG C:ASP232 3.2 57.1 1.0
CG C:ASP124 3.3 88.8 1.0
OD1 C:ASP124 3.3 93.0 1.0
CG C:HIS126 3.4 51.2 1.0
MN C:MN505 3.4 62.4 1.0
CD C:GLU128 3.6 84.8 0.0
OG1 C:THR246 3.6 69.1 1.0
OD2 C:ASP232 3.8 56.1 1.0
NE2 C:HIS126 3.9 48.6 1.0
CB C:HIS126 4.0 58.2 1.0
OE1 C:GLU128 4.1 85.8 0.0
CD2 C:HIS126 4.3 49.5 1.0
CB C:ASP232 4.3 54.3 1.0
N C:HIS126 4.4 67.0 1.0
CB C:ASP234 4.4 54.0 1.0
N C:ALA125 4.6 70.2 1.0
CB C:ASP124 4.7 78.3 1.0
CG C:GLU128 4.7 83.8 0.0
CB C:THR246 4.8 66.0 1.0
CA C:HIS126 4.8 64.8 1.0

Manganese binding site 6 out of 6 in 1p8m

Go back to Manganese Binding Sites List in 1p8m
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:62.4
occ:1.00
 ND1 C:HIS101 2.1 48.0 1.0
OD1 C:ASP124 2.1 93.0 1.0
OE1 C:GLU128 2.2 85.8 0.0
OD1 C:ASP232 2.4 57.6 1.0
CD C:GLU128 2.7 84.8 0.0
O C:HOH841 2.8 65.1 1.0
OE2 C:GLU128 2.8 84.8 0.0
CG C:HIS101 3.1 50.2 1.0
CE1 C:HIS101 3.1 48.8 1.0
CG C:ASP124 3.1 88.8 1.0
CG C:ASP232 3.3 57.1 1.0
CB C:HIS101 3.4 55.4 1.0
MN C:MN504 3.4 51.5 1.0
CB C:ASP232 3.5 54.3 1.0
OD2 C:ASP124 3.5 94.3 1.0
CG C:GLU128 4.0 83.8 0.0
NE2 C:HIS101 4.2 47.3 1.0
NE1 C:TRP122 4.2 58.6 1.0
CD2 C:HIS101 4.2 47.2 1.0
CZ2 C:TRP122 4.2 60.8 1.0
CB C:ASP124 4.3 78.3 1.0
OD2 C:ASP232 4.5 56.1 1.0
CE2 C:TRP122 4.5 59.5 1.0
CB C:GLU128 4.6 84.7 0.0
O C:HIS141 4.7 63.2 1.0
OE2 C:GLU277 4.7 63.7 1.0
CG C:GLU277 4.8 63.8 1.0
CA C:ASP232 4.8 51.6 1.0
CA C:HIS101 4.9 60.5 1.0
ND1 C:HIS126 5.0 47.0 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 12:02:21 2024

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