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Manganese in PDB 3e8z: X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex

Enzymatic activity of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex

All present enzymatic activity of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex:
3.5.3.1;

Protein crystallography data

The structure of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex, PDB code: 3e8z was solved by E.Y.Shishova, L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.77 / 2.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 87.500, 87.500, 100.110, 90.00, 90.00, 120.00
R / Rfree (%) 23.6 / 28

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex (pdb code 3e8z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex, PDB code: 3e8z:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3e8z

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Manganese binding site 1 out of 6 in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:16.0
occ:1.00
 OD2 A:ASP124 2.1 10.6 1.0
OD2 A:ASP128 2.2 21.2 1.0
OD2 A:ASP232 2.2 13.9 1.0
ND1 A:HIS101 2.4 15.9 1.0
O A:HOH599 2.6 26.4 1.0
CG A:ASP128 3.1 19.1 1.0
CG A:ASP124 3.2 15.8 1.0
CG A:ASP232 3.3 15.0 1.0
CG A:HIS101 3.3 14.6 1.0
MN A:MN501 3.3 16.4 1.0
OD1 A:ASP128 3.4 20.2 1.0
CE1 A:HIS101 3.4 14.6 1.0
CB A:HIS101 3.4 13.7 1.0
OD1 A:ASP124 3.5 12.3 1.0
CB A:ASP232 3.6 13.2 1.0
NE1 A:TRP122 4.3 16.1 1.0
OD1 A:ASP232 4.4 12.6 1.0
CD2 A:HIS101 4.5 14.0 1.0
O A:HIS141 4.5 15.7 1.0
CB A:ASP124 4.5 12.8 1.0
CB A:ASP128 4.5 17.6 1.0
NE2 A:HIS101 4.5 15.4 1.0
CZ2 A:TRP122 4.5 14.7 1.0
CG A:GLU277 4.7 17.9 1.0
CE2 A:TRP122 4.8 15.9 1.0
OE2 A:GLU277 4.8 17.6 1.0
CA A:HIS101 4.9 15.4 1.0
CA A:ASP232 5.0 14.7 1.0

Manganese binding site 2 out of 6 in 3e8z

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Manganese binding site 2 out of 6 in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:16.4
occ:1.00
 OD2 A:ASP234 2.2 11.6 1.0
OD1 A:ASP124 2.2 12.3 1.0
O A:HOH599 2.3 26.4 1.0
ND1 A:HIS126 2.4 19.4 1.0
OD1 A:ASP234 2.6 15.3 1.0
OD2 A:ASP232 2.7 13.9 1.0
CG A:ASP234 2.7 14.6 1.0
CG A:ASP124 3.2 15.8 1.0
CE1 A:HIS126 3.2 16.4 1.0
CG A:ASP232 3.2 15.0 1.0
CG A:HIS126 3.3 16.4 1.0
MN A:MN500 3.3 16.0 1.0
OD2 A:ASP124 3.4 10.6 1.0
OD1 A:ASP232 3.6 12.6 1.0
CB A:HIS126 3.7 16.3 1.0
N A:HIS126 4.0 14.1 1.0
CB A:ASP232 4.2 13.2 1.0
CB A:ASP234 4.2 14.7 1.0
NE2 A:HIS126 4.3 17.3 1.0
N A:ALA125 4.3 10.8 1.0
CD2 A:HIS126 4.3 17.9 1.0
CA A:HIS126 4.5 15.7 1.0
O A:HOH537 4.5 16.2 1.0
OD1 A:ASP128 4.6 20.2 1.0
CB A:ASP124 4.6 12.8 1.0
CB A:ALA125 4.7 14.0 1.0
C A:ALA125 4.9 13.1 1.0
OD2 A:ASP128 4.9 21.2 1.0
CA A:ALA125 4.9 11.7 1.0
CA A:ASP124 5.0 13.2 1.0

Manganese binding site 3 out of 6 in 3e8z

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Manganese binding site 3 out of 6 in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:16.7
occ:1.00
 OD2 B:ASP124 2.1 17.0 1.0
OD2 B:ASP128 2.2 12.2 1.0
ND1 B:HIS101 2.2 18.3 1.0
O B:HOH587 2.3 15.7 1.0
OD2 B:ASP232 2.3 18.6 1.0
CG B:ASP128 3.2 12.8 1.0
CG B:HIS101 3.2 17.0 1.0
CG B:ASP124 3.2 13.7 1.0
CE1 B:HIS101 3.3 17.5 1.0
MN B:MN501 3.3 14.9 1.0
CG B:ASP232 3.3 17.7 1.0
CB B:HIS101 3.4 15.8 1.0
OD1 B:ASP128 3.4 13.2 1.0
CB B:ASP232 3.6 14.3 1.0
OD1 B:ASP124 3.6 11.0 1.0
CD2 B:HIS101 4.3 17.2 1.0
NE2 B:HIS101 4.3 18.8 1.0
NE1 B:TRP122 4.4 14.9 1.0
OD1 B:ASP232 4.4 14.0 1.0
CB B:ASP124 4.5 11.6 1.0
CB B:ASP128 4.5 14.5 1.0
O B:HIS141 4.6 19.0 1.0
CZ2 B:TRP122 4.6 16.0 1.0
CG B:GLU277 4.8 17.4 1.0
CE2 B:TRP122 4.8 14.7 1.0
CA B:HIS101 4.9 19.3 1.0
CA B:ASP232 4.9 14.4 1.0

Manganese binding site 4 out of 6 in 3e8z

Go back to Manganese Binding Sites List in 3e8z
Manganese binding site 4 out of 6 in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:14.9
occ:1.00
 OD1 B:ASP124 2.3 11.0 1.0
OD2 B:ASP234 2.3 14.0 1.0
ND1 B:HIS126 2.3 14.3 1.0
O B:HOH587 2.3 15.7 1.0
OD2 B:ASP232 2.4 18.6 1.0
OD1 B:ASP234 2.7 13.4 1.0
CG B:ASP234 2.8 13.3 1.0
CG B:ASP124 3.1 13.7 1.0
CE1 B:HIS126 3.1 13.4 1.0
CG B:ASP232 3.2 17.7 1.0
MN B:MN500 3.3 16.7 1.0
OD2 B:ASP124 3.3 17.0 1.0
CG B:HIS126 3.4 13.1 1.0
OD1 B:ASP232 3.8 14.0 1.0
CB B:HIS126 3.8 12.1 1.0
N B:HIS126 4.1 12.5 1.0
CB B:ASP232 4.2 14.3 1.0
CB B:ASP234 4.3 10.9 1.0
NE2 B:HIS126 4.3 12.3 1.0
N B:ALA125 4.4 12.5 1.0
OD1 B:ASP128 4.4 13.2 1.0
CD2 B:HIS126 4.5 13.9 1.0
CB B:ASP124 4.5 11.6 1.0
O B:HOH531 4.6 5.7 1.0
CA B:HIS126 4.6 13.8 1.0
OD2 B:ASP128 4.7 12.2 1.0
O B:HOH555 4.8 24.3 1.0
CA B:ASP124 5.0 12.6 1.0
C B:ALA125 5.0 12.7 1.0
CG B:ASP128 5.0 12.8 1.0

Manganese binding site 5 out of 6 in 3e8z

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Manganese binding site 5 out of 6 in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn500

b:24.1
occ:1.00
 OD2 C:ASP124 2.2 20.4 1.0
OD2 C:ASP128 2.3 25.2 1.0
OD2 C:ASP232 2.3 21.4 1.0
ND1 C:HIS101 2.4 23.6 1.0
O C:HOH555 2.5 26.8 1.0
CG C:HIS101 3.2 22.8 1.0
CG C:ASP232 3.3 20.7 1.0
CG C:ASP124 3.3 19.5 1.0
CG C:ASP128 3.3 25.9 1.0
MN C:MN501 3.3 18.2 1.0
CB C:HIS101 3.4 25.1 1.0
CE1 C:HIS101 3.4 23.4 1.0
CB C:ASP232 3.6 19.5 1.0
OD1 C:ASP128 3.6 26.8 1.0
OD1 C:ASP124 3.7 17.0 1.0
OD1 C:ASP232 4.4 21.6 1.0
CD2 C:HIS101 4.4 22.4 1.0
NE1 C:TRP122 4.5 18.1 1.0
NE2 C:HIS101 4.5 23.2 1.0
CB C:ASP124 4.5 16.2 1.0
CG C:GLU277 4.5 23.4 1.0
O C:HIS141 4.5 30.7 1.0
CB C:ASP128 4.6 24.7 1.0
CZ2 C:TRP122 4.8 19.1 1.0
OD2 C:ASP234 4.8 20.4 1.0
CA C:HIS101 4.9 27.6 1.0
OE2 C:GLU277 4.9 18.6 1.0
CA C:ASP232 4.9 17.6 1.0
ND1 C:HIS126 4.9 21.5 1.0
CE2 C:TRP122 5.0 18.3 1.0

Manganese binding site 6 out of 6 in 3e8z

Go back to Manganese Binding Sites List in 3e8z
Manganese binding site 6 out of 6 in the X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Structure of Rat Arginase I-N130A Mutant: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:18.2
occ:1.00
 OD2 C:ASP234 2.0 20.4 1.0
ND1 C:HIS126 2.2 21.5 1.0
OD1 C:ASP124 2.3 17.0 1.0
OD1 C:ASP234 2.5 19.2 1.0
O C:HOH555 2.5 26.8 1.0
OD2 C:ASP232 2.5 21.4 1.0
CG C:ASP234 2.6 20.4 1.0
CE1 C:HIS126 2.8 20.2 1.0
CG C:ASP124 3.1 19.5 1.0
CG C:ASP232 3.2 20.7 1.0
CG C:HIS126 3.3 21.9 1.0
MN C:MN500 3.3 24.1 1.0
OD2 C:ASP124 3.3 20.4 1.0
OD1 C:ASP232 3.8 21.6 1.0
CB C:HIS126 3.9 20.1 1.0
N C:HIS126 4.0 21.0 1.0
NE2 C:HIS126 4.1 19.5 1.0
CB C:ASP234 4.1 18.0 1.0
N C:ALA125 4.2 17.6 1.0
CB C:ASP232 4.2 19.5 1.0
CD2 C:HIS126 4.3 22.5 1.0
O C:HOH525 4.5 25.1 1.0
CB C:ASP124 4.5 16.2 1.0
OD1 C:ASP128 4.5 26.8 1.0
CA C:HIS126 4.6 21.6 1.0
CB C:ALA125 4.7 19.6 1.0
OD2 C:ASP128 4.8 25.2 1.0
C C:ALA125 4.8 21.2 1.0
CA C:ALA125 4.9 19.5 1.0
CA C:ASP124 4.9 17.7 1.0
CA C:ASP234 5.0 16.1 1.0

Reference:

E.Y.Shishova, L.Di Costanzo, F.A.Emig, D.E.Ash, D.W.Christianson. Probing the Specificity Determinants of Amino Acid Recognition By Arginase. Biochemistry V. 48 121 2009.
ISSN: ISSN 0006-2960
PubMed: 19093830
DOI: 10.1021/BI801911V
Page generated: Sat Oct 5 16:10:11 2024

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