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Manganese in PDB 1p8q: Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Cluster of Arginase I.

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

All present enzymatic activity of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear 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 Cluster of Arginase I., PDB code: 1p8q 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) 30.00 / 2.95
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 88.326, 88.326, 111.853, 90.00, 90.00, 120.00
R / Rfree (%) 26.2 / 28.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Cluster of Arginase I. (pdb code 1p8q). 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 Cluster of Arginase I., PDB code: 1p8q:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1p8q

Go back to Manganese Binding Sites List in 1p8q
Manganese binding site 1 out of 6 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear 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 Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:64.4
occ:1.00
 OD1 A:ASP124 2.0 52.6 1.0
ND1 A:HIS101 2.1 56.0 1.0
OD1 A:ASP128 2.2 61.5 1.0
OD1 A:ASP232 2.4 55.1 1.0
O A:HOH845 2.5 28.6 1.0
CE1 A:HIS101 3.1 55.1 1.0
CG A:ASP128 3.1 60.8 1.0
CG A:HIS101 3.1 56.1 1.0
CG A:ASP124 3.2 52.1 1.0
MN A:MN501 3.3 97.8 1.0
CG A:ASP232 3.3 54.4 1.0
CB A:HIS101 3.5 56.6 1.0
OD2 A:ASP128 3.5 58.2 1.0
CB A:ASP232 3.7 55.0 1.0
OD2 A:ASP124 3.7 49.9 1.0
NE2 A:HIS101 4.2 55.9 1.0
NE1 A:TRP122 4.2 51.5 1.0
CB A:ASP128 4.2 60.7 1.0
CD2 A:HIS101 4.2 56.1 1.0
CZ2 A:TRP122 4.3 52.4 1.0
OD2 A:ASP232 4.4 53.2 1.0
CB A:ASP124 4.4 54.1 1.0
CE2 A:TRP122 4.6 51.7 1.0
O A:HIS141 4.6 66.0 1.0
OE2 A:GLU277 4.7 55.4 1.0
O A:HIS126 4.9 58.8 1.0
CG A:GLU277 5.0 57.7 1.0

Manganese binding site 2 out of 6 in 1p8q

Go back to Manganese Binding Sites List in 1p8q
Manganese binding site 2 out of 6 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear 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 Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:97.8
occ:1.00
 ND1 A:HIS126 2.4 64.2 1.0
OD2 A:ASP124 2.4 49.9 1.0
OD1 A:ASP232 2.5 55.1 1.0
OE1 A:GLU234 2.9 54.8 1.0
OD1 A:ASP124 3.1 52.6 1.0
CG A:ASP124 3.1 52.1 1.0
MN A:MN500 3.3 64.4 1.0
CE1 A:HIS126 3.3 63.5 1.0
CG A:HIS126 3.3 63.6 1.0
O A:HOH845 3.4 28.6 1.0
CG A:ASP232 3.6 54.4 1.0
CB A:HIS126 3.6 60.9 1.0
N A:HIS126 3.7 58.7 1.0
CD A:GLU234 4.0 53.8 1.0
CB A:GLU234 4.1 50.1 1.0
OD2 A:ASP128 4.1 58.2 1.0
CA A:HIS126 4.2 59.0 1.0
N A:ALA125 4.3 57.1 1.0
OD2 A:ASP232 4.3 53.2 1.0
NE2 A:HIS126 4.4 64.1 1.0
CD2 A:HIS126 4.4 64.0 1.0
OD1 A:ASP128 4.4 61.5 1.0
CB A:ASP232 4.5 55.0 1.0
CB A:ALA125 4.5 54.7 1.0
CG A:GLU234 4.5 52.3 1.0
CB A:ASP124 4.6 54.1 1.0
CG A:ASP128 4.7 60.8 1.0
C A:ALA125 4.7 58.4 1.0
CA A:ALA125 4.8 57.1 1.0
O A:HIS126 4.8 58.8 1.0
C A:HIS126 4.9 59.0 1.0
OE2 A:GLU234 4.9 54.4 1.0

Manganese binding site 3 out of 6 in 1p8q

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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 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 Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:57.6
occ:1.00
 ND1 B:HIS101 2.0 52.5 1.0
OD1 B:ASP128 2.0 64.1 1.0
OD1 B:ASP124 2.2 54.2 1.0
O B:HOH838 2.4 27.5 1.0
OD1 B:ASP232 2.5 56.4 1.0
CG B:HIS101 2.9 53.6 1.0
CE1 B:HIS101 3.0 52.6 1.0
CG B:ASP128 3.0 63.4 1.0
CB B:HIS101 3.2 55.7 1.0
MN B:MN503 3.3 98.5 1.0
CG B:ASP124 3.4 53.3 1.0
CG B:ASP232 3.5 55.8 1.0
OD2 B:ASP128 3.6 63.7 1.0
CB B:ASP232 3.9 54.9 1.0
OD2 B:ASP124 3.9 51.8 1.0
CD2 B:HIS101 4.1 54.4 1.0
NE2 B:HIS101 4.1 54.0 1.0
CB B:ASP128 4.2 61.8 1.0
NE1 B:TRP122 4.3 55.7 1.0
CZ2 B:TRP122 4.3 54.2 1.0
O B:HIS141 4.4 66.3 1.0
OD2 B:ASP232 4.5 55.1 1.0
OE2 B:GLU277 4.5 55.3 1.0
CB B:ASP124 4.6 53.3 1.0
CE2 B:TRP122 4.7 55.5 1.0
CA B:HIS101 4.8 58.2 1.0
CG B:GLU277 4.9 55.2 1.0

Manganese binding site 4 out of 6 in 1p8q

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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 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 Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:98.5
occ:1.00
 OD2 B:ASP124 2.4 51.8 1.0
ND1 B:HIS126 2.5 59.4 1.0
OD1 B:ASP232 2.5 56.4 1.0
OE1 B:GLU234 2.8 51.2 1.0
OD1 B:ASP124 3.0 54.2 1.0
CG B:ASP124 3.1 53.3 1.0
O B:HOH838 3.3 27.5 1.0
MN B:MN502 3.3 57.6 1.0
CE1 B:HIS126 3.3 59.9 1.0
CG B:HIS126 3.4 58.7 1.0
CG B:ASP232 3.5 55.8 1.0
CB B:HIS126 3.7 58.3 1.0
N B:HIS126 3.8 57.2 1.0
CD B:GLU234 3.8 52.7 1.0
CB B:GLU234 4.0 51.4 1.0
OD2 B:ASP232 4.1 55.1 1.0
OD2 B:ASP128 4.2 63.7 1.0
N B:ALA125 4.3 52.8 1.0
CB B:ALA125 4.3 52.9 1.0
CA B:HIS126 4.3 57.7 1.0
OD1 B:ASP128 4.4 64.1 1.0
CB B:ASP232 4.4 54.9 1.0
CG B:GLU234 4.4 51.0 1.0
NE2 B:HIS126 4.5 60.4 1.0
CD2 B:HIS126 4.5 59.1 1.0
C B:ALA125 4.6 54.8 1.0
CB B:ASP124 4.6 53.3 1.0
CG B:ASP128 4.7 63.4 1.0
CA B:ALA125 4.7 53.8 1.0
OE2 B:GLU234 4.8 55.0 1.0
O B:HIS126 5.0 57.1 1.0
O B:HOH810 5.0 13.8 1.0

Manganese binding site 5 out of 6 in 1p8q

Go back to Manganese Binding Sites List in 1p8q
Manganese binding site 5 out of 6 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear 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 Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:41.5
occ:1.00
 OD1 C:ASP124 2.0 57.0 1.0
OD1 C:ASP128 2.0 56.6 1.0
ND1 C:HIS101 2.2 55.0 1.0
O C:HOH846 2.4 28.9 1.0
OD1 C:ASP232 2.5 50.8 1.0
CG C:ASP128 3.0 57.8 1.0
CE1 C:HIS101 3.1 54.8 1.0
CG C:ASP124 3.1 52.9 1.0
CG C:HIS101 3.2 54.5 1.0
MN C:MN505 3.3 99.3 1.0
CG C:ASP232 3.4 50.1 1.0
OD2 C:ASP128 3.6 56.3 1.0
CB C:HIS101 3.6 55.9 1.0
OD2 C:ASP124 3.7 51.6 1.0
CB C:ASP232 3.8 51.1 1.0
CB C:ASP128 4.1 59.0 1.0
NE1 C:TRP122 4.2 50.1 1.0
NE2 C:HIS101 4.2 53.6 1.0
CD2 C:HIS101 4.3 53.2 1.0
CZ2 C:TRP122 4.3 50.4 1.0
CB C:ASP124 4.4 51.6 1.0
OD2 C:ASP232 4.4 47.6 1.0
CE2 C:TRP122 4.6 50.2 1.0
O C:HIS141 4.6 67.4 1.0
O C:HIS126 4.8 55.3 1.0
OE2 C:GLU277 4.8 53.7 1.0

Manganese binding site 6 out of 6 in 1p8q

Go back to Manganese Binding Sites List in 1p8q
Manganese binding site 6 out of 6 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear 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 Cluster of Arginase I. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:99.3
occ:1.00
 ND1 C:HIS126 2.3 57.5 1.0
OD2 C:ASP124 2.4 51.6 1.0
OD1 C:ASP232 2.5 50.8 1.0
OE1 C:GLU234 2.9 55.2 1.0
CG C:ASP124 3.2 52.9 1.0
CE1 C:HIS126 3.2 58.9 1.0
OD1 C:ASP124 3.2 57.0 1.0
CG C:HIS126 3.3 57.7 1.0
MN C:MN504 3.3 41.5 1.0
O C:HOH846 3.4 28.9 1.0
CG C:ASP232 3.6 50.1 1.0
CB C:HIS126 3.6 56.6 1.0
N C:HIS126 3.7 55.5 1.0
CD C:GLU234 4.0 54.5 1.0
CB C:GLU234 4.1 48.1 1.0
OD2 C:ASP128 4.2 56.3 1.0
CA C:HIS126 4.2 55.9 1.0
N C:ALA125 4.2 52.9 1.0
NE2 C:HIS126 4.3 61.1 1.0
OD1 C:ASP128 4.3 56.6 1.0
OD2 C:ASP232 4.3 47.6 1.0
CD2 C:HIS126 4.4 58.5 1.0
CB C:ALA125 4.5 54.5 1.0
CB C:ASP232 4.5 51.1 1.0
CG C:GLU234 4.5 50.9 1.0
CB C:ASP124 4.6 51.6 1.0
CG C:ASP128 4.6 57.8 1.0
C C:ALA125 4.7 53.9 1.0
CA C:ALA125 4.7 53.5 1.0
O C:HIS126 4.8 55.3 1.0
C C:HIS126 4.9 55.7 1.0
OE2 C:GLU234 4.9 56.8 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 12:03:22 2024

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