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Manganese in PDB 3rla: Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function

Enzymatic activity of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function

All present enzymatic activity of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function:
3.5.3.1;

Protein crystallography data

The structure of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function, PDB code: 3rla was solved by L.R.Scolnick, Z.F.Kanyo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.54
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 (%) 19.4 / 28.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function (pdb code 3rla). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function, PDB code: 3rla:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3rla

Go back to Manganese Binding Sites List in 3rla
Manganese binding site 1 out of 6 in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:34.3
occ:0.60
 OD2 A:ASP124 1.9 31.7 1.0
OD2 A:ASP128 2.1 31.4 1.0
OD2 A:ASP232 2.3 41.3 1.0
CG A:ASP124 3.0 35.5 1.0
CG A:ASP128 3.3 32.6 1.0
CG A:ASP232 3.3 30.3 1.0
MN A:MN501 3.4 36.2 1.0
OD1 A:ASP124 3.4 46.1 1.0
CB A:ASP232 3.7 27.1 1.0
CZ2 A:TRP122 3.8 31.7 1.0
OD1 A:ASP128 3.9 26.6 1.0
NE1 A:TRP122 4.0 37.7 1.0
CE2 A:TRP122 4.2 25.8 1.0
CB A:ASP124 4.2 32.4 1.0
OD1 A:ASP232 4.4 35.9 1.0
CB A:ASP128 4.4 35.3 1.0
O A:HIS126 4.5 25.4 1.0
CH2 A:TRP122 4.8 40.1 1.0
CB A:HIS126 5.0 28.7 1.0
OE2 A:GLU277 5.0 29.9 1.0
CA A:ASP232 5.0 24.3 1.0

Manganese binding site 2 out of 6 in 3rla

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Manganese binding site 2 out of 6 in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:36.2
occ:1.00
 OD1 A:ASP124 2.1 46.1 1.0
OD2 A:ASP234 2.2 26.7 1.0
OD2 A:ASP232 2.3 41.3 1.0
ND1 A:HIS126 2.5 22.3 1.0
OD1 A:ASP234 2.6 35.0 1.0
CG A:ASP234 2.8 27.6 1.0
CG A:ASP124 3.1 35.5 1.0
CG A:ASP232 3.2 30.3 1.0
OD2 A:ASP124 3.3 31.7 1.0
MN A:MN500 3.4 34.3 0.6
CG A:HIS126 3.4 24.2 1.0
CE1 A:HIS126 3.5 21.1 1.0
CB A:HIS126 3.6 28.7 1.0
OD1 A:ASP232 3.7 35.9 1.0
N A:HIS126 4.0 33.2 1.0
CB A:ASP232 4.2 27.1 1.0
N A:ALA125 4.2 21.2 1.0
CB A:ASP234 4.3 26.8 1.0
OD2 A:ASP128 4.4 31.4 1.0
CA A:HIS126 4.4 30.1 1.0
CB A:ASP124 4.4 32.4 1.0
O A:HOH507 4.5 25.9 1.0
NE2 A:HIS126 4.6 25.0 1.0
CD2 A:HIS126 4.6 17.2 1.0
OD1 A:ASP128 4.7 26.6 1.0
O A:HIS126 4.8 25.4 1.0
CA A:ASP124 4.9 29.3 1.0
CB A:ALA125 4.9 22.7 1.0
C A:ALA125 4.9 31.6 1.0
CA A:ALA125 4.9 25.4 1.0

Manganese binding site 3 out of 6 in 3rla

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Manganese binding site 3 out of 6 in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:48.9
occ:0.60
 OD2 B:ASP124 2.0 29.8 1.0
OD2 B:ASP128 2.2 38.0 1.0
OD2 B:ASP232 2.5 39.7 1.0
CG B:ASP124 3.1 38.8 1.0
CG B:ASP128 3.3 33.8 1.0
CG B:ASP232 3.3 32.4 1.0
CB B:ASP232 3.6 27.0 1.0
CZ2 B:TRP122 3.7 43.1 1.0
OD1 B:ASP124 3.7 31.4 1.0
O B:HOH504 3.7 38.8 1.0
MN B:MN503 3.8 44.8 1.0
OD1 B:ASP128 3.9 38.3 1.0
NE1 B:TRP122 4.0 42.5 1.0
CE2 B:TRP122 4.1 43.1 1.0
CB B:ASP124 4.3 35.3 1.0
OD1 B:ASP232 4.5 31.1 1.0
CB B:ASP128 4.5 31.9 1.0
CH2 B:TRP122 4.7 41.3 1.0
O B:HIS126 4.7 36.0 1.0
CA B:ASP232 4.9 32.4 1.0
CA B:ASN101 5.0 42.5 1.0

Manganese binding site 4 out of 6 in 3rla

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Manganese binding site 4 out of 6 in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:44.8
occ:1.00
 OD2 B:ASP234 2.1 38.5 1.0
OD2 B:ASP232 2.3 39.7 1.0
OD1 B:ASP124 2.3 31.4 1.0
ND1 B:HIS126 2.4 28.6 1.0
OD1 B:ASP234 2.5 33.8 1.0
O B:HOH504 2.6 38.8 1.0
CG B:ASP234 2.6 38.0 1.0
CE1 B:HIS126 3.2 27.2 1.0
CG B:ASP124 3.2 38.8 1.0
CG B:ASP232 3.3 32.4 1.0
CG B:HIS126 3.4 28.5 1.0
OD2 B:ASP124 3.5 29.8 1.0
MN B:MN502 3.8 48.9 0.6
CB B:HIS126 3.8 27.2 1.0
OD1 B:ASP232 3.8 31.1 1.0
CB B:ASP234 4.1 26.9 1.0
N B:HIS126 4.2 35.5 1.0
CB B:ASP232 4.3 27.0 1.0
NE2 B:HIS126 4.4 31.5 1.0
N B:ALA125 4.4 27.0 1.0
CD2 B:HIS126 4.5 28.8 1.0
CA B:HIS126 4.6 29.6 1.0
OD2 B:ASP128 4.7 38.0 1.0
CB B:ASP124 4.7 35.3 1.0
OD1 B:ASP128 4.8 38.3 1.0
O B:HIS126 5.0 36.0 1.0

Manganese binding site 5 out of 6 in 3rla

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Manganese binding site 5 out of 6 in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:30.2
occ:0.60
 OD2 C:ASP128 2.1 31.0 1.0
OD2 C:ASP124 2.2 43.5 1.0
OD2 C:ASP232 2.8 47.1 1.0
CG C:ASP124 3.3 45.3 1.0
CG C:ASP128 3.3 34.1 1.0
CZ2 C:TRP122 3.5 41.2 1.0
CG C:ASP232 3.6 32.7 1.0
CB C:ASP232 3.7 30.4 1.0
OD1 C:ASP124 3.9 34.3 1.0
MN C:MN505 4.0 32.5 1.0
NE1 C:TRP122 4.0 40.5 1.0
CE2 C:TRP122 4.0 33.4 1.0
OD1 C:ASP128 4.1 30.5 1.0
CB C:ASP128 4.3 40.7 1.0
CB C:ASP124 4.4 35.3 1.0
CH2 C:TRP122 4.5 45.0 1.0
OD1 C:ASP232 4.8 26.1 1.0
O C:HIS126 4.8 22.9 1.0
O C:HIS141 4.9 30.7 1.0
OE2 C:GLU277 4.9 30.7 1.0
CA C:ASN101 5.0 39.1 1.0

Manganese binding site 6 out of 6 in 3rla

Go back to Manganese Binding Sites List in 3rla
Manganese binding site 6 out of 6 in the Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:32.5
occ:1.00
 ND1 C:HIS126 2.3 20.9 1.0
OD2 C:ASP234 2.3 35.6 1.0
OD1 C:ASP124 2.3 34.3 1.0
OD1 C:ASP234 2.6 28.6 1.0
OD2 C:ASP232 2.6 47.1 1.0
CG C:ASP234 2.8 31.8 1.0
CG C:ASP124 3.2 45.3 1.0
CE1 C:HIS126 3.2 21.5 1.0
CG C:HIS126 3.2 26.5 1.0
OD2 C:ASP124 3.5 43.5 1.0
CB C:HIS126 3.5 29.2 1.0
CG C:ASP232 3.5 32.7 1.0
MN C:MN504 4.0 30.2 0.6
N C:HIS126 4.0 28.4 1.0
OD1 C:ASP232 4.1 26.1 1.0
CB C:ASP234 4.3 29.4 1.0
N C:ALA125 4.3 22.4 1.0
NE2 C:HIS126 4.4 30.9 1.0
CD2 C:HIS126 4.4 22.8 1.0
CA C:HIS126 4.4 26.8 1.0
CB C:ASP232 4.4 30.4 1.0
OD2 C:ASP128 4.6 31.0 1.0
CB C:ASP124 4.7 35.3 1.0
OD1 C:ASP128 4.8 30.5 1.0
C C:ALA125 4.9 28.9 1.0
CB C:ALA125 5.0 19.7 1.0
CA C:ALA125 5.0 27.0 1.0

Reference:

L.R.Scolnick, Z.F.Kanyo, R.C.Cavalli, D.E.Ash, D.W.Christianson. Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function. Biochemistry V. 36 10558 1997.
ISSN: ISSN 0006-2960
PubMed: 9265637
DOI: 10.1021/BI970800V
Page generated: Tue Dec 15 04:14:53 2020

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