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Manganese in PDB 3e8q: X-Ray Structure of Rat Arginase I-T135A: the Unliganded Complex

Enzymatic activity of X-Ray Structure of Rat Arginase I-T135A: the Unliganded Complex

All present enzymatic activity of X-Ray Structure of Rat Arginase I-T135A: the Unliganded Complex:
3.5.3.1;

Protein crystallography data

The structure of X-Ray Structure of Rat Arginase I-T135A: the Unliganded Complex, PDB code: 3e8q was solved by E.Y.Shishova, L.Di Costanzo, 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) 25.13 / 2.90
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 87.398, 87.398, 100.818, 90.00, 90.00, 120.00
R / Rfree (%) 26.3 / 29.6

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of Rat Arginase I-T135A: the Unliganded Complex (pdb code 3e8q). 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-T135A: the Unliganded Complex, PDB code: 3e8q:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3e8q

Go back to Manganese Binding Sites List in 3e8q
Manganese binding site 1 out of 6 in the X-Ray Structure of Rat Arginase I-T135A: 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-T135A: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:33.4
occ:1.00
 OD2 A:ASP232 2.1 27.7 1.0
OD2 A:ASP128 2.2 42.5 1.0
ND1 A:HIS101 2.3 32.1 1.0
O A:HOH514 2.5 41.6 1.0
OD2 A:ASP124 3.0 31.2 1.0
CG A:ASP128 3.1 42.2 1.0
CG A:HIS101 3.1 31.4 1.0
CB A:HIS101 3.2 31.8 1.0
CG A:ASP232 3.3 28.3 1.0
OD1 A:ASP128 3.4 42.9 1.0
CE1 A:HIS101 3.4 32.5 1.0
MN A:MN501 3.5 36.9 1.0
CG A:ASP124 3.6 29.8 1.0
CB A:ASP232 3.9 27.1 1.0
CZ2 A:TRP122 4.1 24.6 1.0
OD1 A:ASP124 4.2 31.0 1.0
OD1 A:ASP232 4.3 29.3 1.0
CB A:ASP124 4.3 29.2 1.0
CD2 A:HIS101 4.3 31.2 1.0
O A:HIS141 4.4 40.1 1.0
NE1 A:TRP122 4.4 22.8 1.0
NE2 A:HIS101 4.4 31.0 1.0
CB A:ASP128 4.5 38.9 1.0
CE2 A:TRP122 4.5 23.7 1.0
CA A:HIS101 4.8 32.5 1.0
CG A:GLU277 4.9 34.8 1.0

Manganese binding site 2 out of 6 in 3e8q

Go back to Manganese Binding Sites List in 3e8q
Manganese binding site 2 out of 6 in the X-Ray Structure of Rat Arginase I-T135A: 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-T135A: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:36.9
occ:1.00
 ND1 A:HIS126 2.2 29.3 1.0
OD1 A:ASP124 2.2 31.0 1.0
OD2 A:ASP234 2.3 24.5 1.0
OD1 A:ASP234 2.6 25.7 1.0
O A:HOH514 2.6 41.6 1.0
CG A:ASP234 2.8 25.7 1.0
OD2 A:ASP232 2.9 27.7 1.0
CG A:ASP124 2.9 29.8 1.0
OD2 A:ASP124 2.9 31.2 1.0
CE1 A:HIS126 3.1 28.6 1.0
CG A:HIS126 3.3 29.7 1.0
CG A:ASP232 3.3 28.3 1.0
OD1 A:ASP232 3.5 29.3 1.0
MN A:MN500 3.5 33.4 1.0
CB A:HIS126 3.6 30.4 1.0
N A:HIS126 4.2 30.6 1.0
NE2 A:HIS126 4.2 28.3 1.0
CB A:ASP124 4.3 29.2 1.0
CB A:ASP234 4.3 25.6 1.0
N A:ALA125 4.3 28.4 1.0
CD2 A:HIS126 4.3 29.2 1.0
CB A:ASP232 4.4 27.1 1.0
OD1 A:ASP128 4.5 42.9 1.0
CA A:HIS126 4.5 31.8 1.0
C A:ALA125 4.9 29.6 1.0
OD2 A:ASP128 5.0 42.5 1.0
CA A:ASP124 5.0 28.7 1.0

Manganese binding site 3 out of 6 in 3e8q

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Manganese binding site 3 out of 6 in the X-Ray Structure of Rat Arginase I-T135A: 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-T135A: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:26.3
occ:1.00
 OD2 B:ASP232 2.1 26.0 1.0
OD2 B:ASP128 2.2 39.8 1.0
ND1 B:HIS101 2.5 31.3 1.0
O B:HOH511 2.6 4.7 1.0
OD2 B:ASP124 2.9 25.7 1.0
CG B:ASP128 3.0 39.6 1.0
MN B:MN503 3.2 39.1 1.0
OD1 B:ASP128 3.2 39.0 1.0
CG B:HIS101 3.3 31.4 1.0
CG B:ASP232 3.3 26.2 1.0
CB B:HIS101 3.4 32.6 1.0
CG B:ASP124 3.5 26.5 1.0
CE1 B:HIS101 3.5 30.0 1.0
CB B:ASP232 4.0 26.1 1.0
OD1 B:ASP124 4.1 27.8 1.0
CZ2 B:TRP122 4.1 23.6 1.0
CB B:ASP124 4.3 27.4 1.0
OD1 B:ASP232 4.3 26.6 1.0
O B:HIS141 4.4 41.5 1.0
NE1 B:TRP122 4.4 24.7 1.0
CB B:ASP128 4.4 39.5 1.0
CD2 B:HIS101 4.5 30.1 1.0
CE2 B:TRP122 4.6 23.2 1.0
NE2 B:HIS101 4.6 31.3 1.0
CA B:HIS101 4.9 33.8 1.0
CG B:GLU277 5.0 34.0 1.0
CB B:HIS126 5.0 31.6 1.0
ND1 B:HIS126 5.0 29.0 1.0

Manganese binding site 4 out of 6 in 3e8q

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Manganese binding site 4 out of 6 in the X-Ray Structure of Rat Arginase I-T135A: 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-T135A: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:39.1
occ:1.00
 ND1 B:HIS126 2.2 29.0 1.0
OD1 B:ASP124 2.2 27.8 1.0
OD2 B:ASP234 2.4 25.5 1.0
O B:HOH511 2.5 4.7 1.0
OD1 B:ASP234 2.8 23.6 1.0
OD2 B:ASP232 2.8 26.0 1.0
OD2 B:ASP124 2.8 25.7 1.0
CG B:ASP124 2.8 26.5 1.0
CG B:ASP234 2.9 24.6 1.0
CE1 B:HIS126 3.1 28.9 1.0
CG B:HIS126 3.2 30.7 1.0
MN B:MN502 3.2 26.3 1.0
CG B:ASP232 3.3 26.2 1.0
CB B:HIS126 3.6 31.6 1.0
OD1 B:ASP232 3.6 26.6 1.0
N B:HIS126 4.1 30.7 1.0
CB B:ASP124 4.2 27.4 1.0
NE2 B:HIS126 4.3 29.1 1.0
OD1 B:ASP128 4.3 39.0 1.0
CD2 B:HIS126 4.3 30.2 1.0
N B:ALA125 4.4 30.1 1.0
CB B:ASP232 4.4 26.1 1.0
CB B:ASP234 4.5 24.5 1.0
CA B:HIS126 4.5 32.0 1.0
OD2 B:ASP128 4.8 39.8 1.0
C B:ALA125 4.9 30.7 1.0
CA B:ASP124 5.0 27.8 1.0

Manganese binding site 5 out of 6 in 3e8q

Go back to Manganese Binding Sites List in 3e8q
Manganese binding site 5 out of 6 in the X-Ray Structure of Rat Arginase I-T135A: 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-T135A: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:36.5
occ:1.00
 OD2 C:ASP232 2.0 28.1 1.0
ND1 C:HIS101 2.2 31.7 1.0
OD2 C:ASP128 2.4 40.9 1.0
OD2 C:ASP124 3.0 27.0 1.0
CG C:HIS101 3.0 32.5 1.0
CB C:HIS101 3.2 32.8 1.0
CG C:ASP232 3.2 28.8 1.0
CG C:ASP128 3.3 40.5 1.0
CE1 C:HIS101 3.3 31.4 1.0
MN C:MN505 3.5 39.0 1.0
OD1 C:ASP128 3.5 40.5 1.0
CG C:ASP124 3.6 27.8 1.0
CB C:ASP232 3.8 28.8 1.0
CZ2 C:TRP122 4.1 25.1 1.0
OD1 C:ASP124 4.2 27.1 1.0
OD1 C:ASP232 4.2 26.9 1.0
CD2 C:HIS101 4.3 32.0 1.0
CB C:ASP124 4.3 27.5 1.0
NE2 C:HIS101 4.4 31.9 1.0
O C:HIS141 4.5 42.1 1.0
NE1 C:TRP122 4.5 27.7 1.0
CB C:ASP128 4.6 40.6 1.0
CE2 C:TRP122 4.6 25.8 1.0
CA C:HIS101 4.7 34.1 1.0
CG C:GLU277 4.8 35.6 1.0
OE2 C:GLU277 5.0 34.1 1.0

Manganese binding site 6 out of 6 in 3e8q

Go back to Manganese Binding Sites List in 3e8q
Manganese binding site 6 out of 6 in the X-Ray Structure of Rat Arginase I-T135A: 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-T135A: the Unliganded Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:39.0
occ:1.00
 ND1 C:HIS126 2.2 31.0 1.0
OD1 C:ASP124 2.2 27.1 1.0
OD2 C:ASP234 2.3 23.4 1.0
OD1 C:ASP234 2.6 22.6 1.0
CG C:ASP234 2.8 24.6 1.0
CG C:ASP124 2.8 27.8 1.0
OD2 C:ASP232 2.9 28.1 1.0
OD2 C:ASP124 2.9 27.0 1.0
CE1 C:HIS126 3.1 31.1 1.0
CG C:HIS126 3.3 32.2 1.0
CG C:ASP232 3.3 28.8 1.0
MN C:MN504 3.5 36.5 1.0
OD1 C:ASP232 3.5 26.9 1.0
CB C:HIS126 3.6 33.4 1.0
N C:HIS126 4.2 33.0 1.0
CB C:ASP124 4.2 27.5 1.0
NE2 C:HIS126 4.2 30.6 1.0
N C:ALA125 4.3 29.8 1.0
CB C:ASP234 4.3 24.7 1.0
CD2 C:HIS126 4.3 31.1 1.0
CB C:ASP232 4.4 28.8 1.0
OD1 C:ASP128 4.4 40.5 1.0
CA C:HIS126 4.5 33.8 1.0
C C:ALA125 4.8 32.3 1.0
OD2 C:ASP128 4.9 40.9 1.0
CA C:ASP124 5.0 28.6 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 16:09:40 2024

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