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Manganese in PDB 1rla: Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle

Enzymatic activity of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle

All present enzymatic activity of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle:
3.5.3.1;

Protein crystallography data

The structure of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle, PDB code: 1rla was solved by Z.Kanyo, L.Scolnick, D.Ash, D.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 88.500, 88.500, 106.200, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 22.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle (pdb code 1rla). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle, PDB code: 1rla:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1rla

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Manganese binding site 1 out of 6 in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:31.4
occ:1.00
 OD2 A:ASP124 2.0 16.0 1.0
OD2 A:ASP128 2.1 30.7 1.0
ND1 A:HIS101 2.3 38.6 1.0
OD2 A:ASP232 2.3 33.2 1.0
O A:HOH502 2.4 25.7 1.0
CG A:ASP124 3.0 19.7 1.0
CG A:ASP128 3.1 30.5 1.0
CG A:HIS101 3.2 36.1 1.0
CG A:ASP232 3.2 26.2 1.0
CE1 A:HIS101 3.3 31.8 1.0
MN A:MN501 3.3 28.4 1.0
OD1 A:ASP124 3.3 17.3 1.0
CB A:HIS101 3.4 30.0 1.0
CB A:ASP232 3.5 26.5 1.0
OD1 A:ASP128 3.5 29.9 1.0
HE1 A:TRP122 3.7 32.0 1.0
CB A:ASP124 4.3 15.3 1.0
CD2 A:HIS101 4.4 35.9 1.0
NE1 A:TRP122 4.4 23.1 1.0
OD1 A:ASP232 4.4 28.0 1.0
NE2 A:HIS101 4.4 34.7 1.0
CB A:ASP128 4.4 31.1 1.0
CZ2 A:TRP122 4.6 24.0 1.0
OE2 A:GLU277 4.6 28.1 1.0
O A:HIS141 4.7 39.2 1.0
CG A:GLU277 4.7 25.7 1.0
CE2 A:TRP122 4.8 21.1 1.0
ND1 A:HIS126 4.8 36.3 1.0
OD2 A:ASP234 4.9 20.8 1.0
CA A:ASP232 4.9 24.6 1.0
CA A:HIS101 4.9 31.1 1.0
O A:HIS126 5.0 35.4 1.0

Manganese binding site 2 out of 6 in 1rla

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Manganese binding site 2 out of 6 in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:28.4
occ:1.00
 OD1 A:ASP124 2.1 17.3 1.0
ND1 A:HIS126 2.1 36.3 1.0
OD2 A:ASP234 2.1 20.8 1.0
OD1 A:ASP234 2.4 18.2 1.0
O A:HOH502 2.4 25.7 1.0
OD2 A:ASP232 2.5 33.2 1.0
CG A:ASP234 2.6 14.3 1.0
CE1 A:HIS126 2.9 33.4 1.0
CG A:ASP124 3.1 19.7 1.0
CG A:ASP232 3.2 26.2 1.0
CG A:HIS126 3.3 27.9 1.0
MN A:MN500 3.3 31.4 1.0
H A:HIS126 3.4 32.0 1.0
OD2 A:ASP124 3.4 16.0 1.0
H A:ALA125 3.5 32.0 1.0
CB A:HIS126 3.8 26.4 1.0
OD1 A:ASP232 3.8 28.0 1.0
N A:HIS126 4.0 27.8 1.0
CB A:ASP234 4.1 14.6 1.0
NE2 A:HIS126 4.1 30.4 1.0
CB A:ASP232 4.2 26.5 1.0
N A:ALA125 4.2 25.9 1.0
CD2 A:HIS126 4.3 31.7 1.0
CB A:ASP124 4.4 15.3 1.0
CA A:HIS126 4.5 27.5 1.0
OD1 A:ASP128 4.6 29.9 1.0
CB A:ALA125 4.6 19.0 1.0
O A:HOH510 4.6 30.0 1.0
OD2 A:ASP128 4.7 30.7 1.0
CA A:ASP124 4.8 19.0 1.0
H A:ASP234 4.8 32.0 1.0
CA A:ALA125 4.8 22.6 1.0
C A:ALA125 4.9 24.7 1.0
C A:ASP124 4.9 23.8 1.0
HE2 A:HIS126 5.0 32.0 1.0

Manganese binding site 3 out of 6 in 1rla

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Manganese binding site 3 out of 6 in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:32.9
occ:1.00
 OD2 B:ASP128 2.0 31.7 1.0
OD2 B:ASP124 2.1 30.3 1.0
ND1 B:HIS101 2.1 19.7 1.0
OD2 B:ASP232 2.4 33.0 1.0
O B:HOH551 2.5 33.9 1.0
CG B:HIS101 3.1 19.9 1.0
CG B:ASP128 3.1 29.8 1.0
CG B:ASP124 3.1 20.3 1.0
CE1 B:HIS101 3.1 22.5 1.0
CG B:ASP232 3.3 25.9 1.0
CB B:HIS101 3.3 19.2 1.0
MN B:MN503 3.4 28.4 1.0
OD1 B:ASP124 3.4 19.8 1.0
OD1 B:ASP128 3.5 30.0 1.0
CB B:ASP232 3.6 19.8 1.0
HE1 B:TRP122 3.7 32.0 1.0
CD2 B:HIS101 4.2 23.6 1.0
NE2 B:HIS101 4.2 22.9 1.0
NE1 B:TRP122 4.3 29.8 1.0
CB B:ASP128 4.3 29.0 1.0
CB B:ASP124 4.4 20.4 1.0
OD1 B:ASP232 4.5 28.6 1.0
CZ2 B:TRP122 4.5 28.4 1.0
O B:HIS141 4.5 45.3 1.0
OE2 B:GLU277 4.7 31.3 1.0
CE2 B:TRP122 4.7 27.4 1.0
CG B:GLU277 4.9 30.5 1.0
CA B:HIS101 4.9 28.6 1.0
ND1 B:HIS126 4.9 31.4 1.0
CA B:ASP232 4.9 23.3 1.0
O B:HIS126 5.0 26.0 1.0

Manganese binding site 4 out of 6 in 1rla

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Manganese binding site 4 out of 6 in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:28.4
occ:1.00
 OD1 B:ASP124 2.1 19.8 1.0
ND1 B:HIS126 2.1 31.4 1.0
OD2 B:ASP234 2.1 24.7 1.0
OD2 B:ASP232 2.4 33.0 1.0
OD1 B:ASP234 2.4 25.6 1.0
O B:HOH551 2.6 33.9 1.0
CG B:ASP234 2.6 24.6 1.0
CE1 B:HIS126 2.9 27.4 1.0
CG B:ASP124 3.1 20.3 1.0
CG B:ASP232 3.1 25.9 1.0
CG B:HIS126 3.3 26.2 1.0
MN B:MN502 3.4 32.9 1.0
OD2 B:ASP124 3.4 30.3 1.0
H B:ALA125 3.5 32.0 1.0
H B:HIS126 3.5 32.0 1.0
OD1 B:ASP232 3.7 28.6 1.0
CB B:HIS126 3.8 19.9 1.0
N B:HIS126 4.0 24.7 1.0
CB B:ASP232 4.1 19.8 1.0
CB B:ASP234 4.1 24.0 1.0
NE2 B:HIS126 4.2 30.7 1.0
N B:ALA125 4.2 21.1 1.0
CD2 B:HIS126 4.3 27.4 1.0
CB B:ASP124 4.5 20.4 1.0
OD1 B:ASP128 4.5 30.0 1.0
O B:HOH505 4.5 33.2 1.0
CA B:HIS126 4.5 26.1 1.0
H B:ASP234 4.7 32.0 1.0
CB B:ALA125 4.7 13.3 1.0
OD2 B:ASP128 4.7 31.7 1.0
CA B:ASP124 4.8 20.3 1.0
C B:ALA125 4.9 20.8 1.0
CA B:ALA125 4.9 18.0 1.0
C B:ASP124 5.0 22.7 1.0
O B:HOH544 5.0 38.8 1.0
HE2 B:HIS126 5.0 32.0 1.0

Manganese binding site 5 out of 6 in 1rla

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Manganese binding site 5 out of 6 in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:31.6
occ:1.00
 OD2 C:ASP128 2.1 29.7 1.0
OD2 C:ASP124 2.2 27.4 1.0
ND1 C:HIS101 2.2 37.9 1.0
O C:HOH573 2.4 43.5 1.0
OD2 C:ASP232 2.4 27.2 1.0
CG C:HIS101 3.1 32.5 1.0
CG C:ASP124 3.1 27.6 1.0
CG C:ASP128 3.1 23.6 1.0
CE1 C:HIS101 3.3 32.2 1.0
CB C:HIS101 3.3 31.8 1.0
CG C:ASP232 3.3 22.2 1.0
MN C:MN505 3.4 26.6 1.0
OD1 C:ASP124 3.5 17.9 1.0
CB C:ASP232 3.5 19.1 1.0
OD1 C:ASP128 3.6 25.8 1.0
HE1 C:TRP122 3.7 32.0 1.0
CD2 C:HIS101 4.3 34.6 1.0
NE1 C:TRP122 4.3 23.9 1.0
OE2 C:GLU277 4.4 30.1 1.0
NE2 C:HIS101 4.4 31.1 1.0
CB C:ASP128 4.4 20.8 1.0
CB C:ASP124 4.4 22.0 1.0
OD1 C:ASP232 4.5 21.0 1.0
O C:HIS141 4.5 35.3 1.0
CZ2 C:TRP122 4.5 22.0 1.0
CG C:GLU277 4.7 26.1 1.0
CE2 C:TRP122 4.8 23.8 1.0
CA C:HIS101 4.8 35.4 1.0
CA C:ASP232 4.9 20.4 1.0
ND1 C:HIS126 4.9 23.9 1.0
OD2 C:ASP234 5.0 22.8 1.0

Manganese binding site 6 out of 6 in 1rla

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Manganese binding site 6 out of 6 in the Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Three-Dimensional Structure of Rat Liver Arginase, the Binuclear Manganese Metalloenzyme of the Urea Cycle within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:26.6
occ:1.00
 OD1 C:ASP124 2.0 17.9 1.0
ND1 C:HIS126 2.1 23.9 1.0
OD2 C:ASP234 2.2 22.8 1.0
O C:HOH573 2.2 43.5 1.0
OD2 C:ASP232 2.3 27.2 1.0
OD1 C:ASP234 2.4 21.6 1.0
CG C:ASP234 2.7 24.6 1.0
CE1 C:HIS126 2.9 21.7 1.0
CG C:ASP124 3.0 27.6 1.0
CG C:ASP232 3.2 22.2 1.0
CG C:HIS126 3.3 20.8 1.0
MN C:MN504 3.4 31.6 1.0
OD2 C:ASP124 3.4 27.4 1.0
H C:ALA125 3.5 32.0 1.0
H C:HIS126 3.5 32.0 1.0
CB C:HIS126 3.8 24.3 1.0
OD1 C:ASP232 3.8 21.0 1.0
CB C:ASP232 4.1 19.1 1.0
N C:HIS126 4.1 27.4 1.0
NE2 C:HIS126 4.2 20.5 1.0
CB C:ASP234 4.2 24.3 1.0
N C:ALA125 4.2 20.0 1.0
CD2 C:HIS126 4.3 21.1 1.0
CB C:ASP124 4.4 22.0 1.0
OD1 C:ASP128 4.5 25.8 1.0
CA C:HIS126 4.6 26.1 1.0
OD2 C:ASP128 4.6 29.7 1.0
O C:HOH511 4.6 29.8 1.0
CA C:ASP124 4.8 23.4 1.0
H C:ASP234 4.8 32.0 1.0
CB C:ALA125 4.8 19.0 1.0
C C:ALA125 4.9 25.0 1.0
CA C:ALA125 4.9 22.2 1.0
C C:ASP124 4.9 23.0 1.0
CG C:ASP128 4.9 23.6 1.0

Reference:

Z.F.Kanyo, L.R.Scolnick, D.E.Ash, D.W.Christianson. Structure of A Unique Binuclear Manganese Cluster in Arginase. Nature V. 383 554 1996.
ISSN: ISSN 0028-0836
PubMed: 8849731
DOI: 10.1038/383554A0
Page generated: Sat Oct 5 12:20:04 2024

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