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Manganese in PDB 3e9b: X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec

Enzymatic activity of X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec

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

Protein crystallography data

The structure of X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec, PDB code: 3e9b 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) 50.00 / 2.15
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 87.505, 87.505, 100.696, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 27.4

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec (pdb code 3e9b). 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 Mutant: the Complex with Bec, PDB code: 3e9b:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3e9b

Go back to Manganese Binding Sites List in 3e9b
Manganese binding site 1 out of 6 in the X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec


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 Mutant: the Complex with Bec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:15.0
occ:1.00
 OD2 A:ASP124 2.2 4.4 1.0
OD2 A:ASP128 2.2 12.4 1.0
OD2 A:ASP232 2.4 11.5 1.0
O1 A:S2C502 2.4 21.8 1.0
ND1 A:HIS101 2.4 15.9 1.0
O2 A:S2C502 2.5 20.4 1.0
B A:S2C502 3.0 24.2 1.0
CG A:ASP128 3.1 11.5 1.0
CG A:ASP124 3.2 9.9 1.0
OD1 A:ASP128 3.3 14.9 1.0
CG A:HIS101 3.3 11.7 1.0
MN A:MN501 3.4 12.2 1.0
CG A:ASP232 3.4 13.8 1.0
CE1 A:HIS101 3.4 16.2 1.0
CB A:HIS101 3.5 11.0 1.0
OD1 A:ASP124 3.6 8.0 1.0
CB A:ASP232 3.7 12.4 1.0
O3 A:S2C502 3.7 19.9 1.0
NE1 A:TRP122 4.3 10.0 1.0
CE A:S2C502 4.3 24.2 1.0
CD2 A:HIS101 4.5 12.2 1.0
O A:HIS141 4.5 9.4 1.0
NE2 A:HIS101 4.5 13.6 1.0
CB A:ASP124 4.5 8.0 1.0
CZ2 A:TRP122 4.5 8.1 1.0
CB A:ASP128 4.5 10.6 1.0
OD1 A:ASP232 4.5 15.4 1.0
CE2 A:TRP122 4.8 8.4 1.0
CG A:GLU277 4.8 10.8 1.0
OD2 A:ASP234 4.9 6.7 1.0
CA A:ASP232 5.0 12.1 1.0
OE2 A:GLU277 5.0 8.7 1.0

Manganese binding site 2 out of 6 in 3e9b

Go back to Manganese Binding Sites List in 3e9b
Manganese binding site 2 out of 6 in the X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec


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 Mutant: the Complex with Bec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:12.2
occ:1.00
 OD2 A:ASP234 2.1 6.7 1.0
O1 A:S2C502 2.2 21.8 1.0
ND1 A:HIS126 2.2 10.5 1.0
OD1 A:ASP124 2.3 8.0 1.0
OD1 A:ASP234 2.6 11.0 1.0
OD2 A:ASP232 2.7 11.5 1.0
CG A:ASP234 2.7 10.5 1.0
O3 A:S2C502 2.8 19.9 1.0
B A:S2C502 3.1 24.2 1.0
CE1 A:HIS126 3.1 10.0 1.0
CG A:ASP124 3.2 9.9 1.0
CG A:ASP232 3.3 13.8 1.0
CG A:HIS126 3.3 11.5 1.0
MN A:MN500 3.4 15.0 1.0
OD2 A:ASP124 3.5 4.4 1.0
CB A:HIS126 3.7 12.1 1.0
OD1 A:ASP232 3.7 15.4 1.0
O2 A:S2C502 4.0 20.4 1.0
N A:HIS126 4.0 11.5 1.0
CB A:ASP234 4.2 9.3 1.0
CE A:S2C502 4.2 24.2 1.0
NE2 A:HIS126 4.3 10.6 1.0
CB A:ASP232 4.3 12.4 1.0
N A:ALA125 4.3 8.3 1.0
O A:HOH533 4.3 6.2 1.0
CD2 A:HIS126 4.4 12.6 1.0
CD A:S2C502 4.4 26.6 1.0
OD1 A:ASP128 4.4 14.9 1.0
CA A:HIS126 4.5 11.2 1.0
CB A:ASP124 4.6 8.0 1.0
CB A:ALA125 4.8 12.5 1.0
C A:ALA125 4.9 12.0 1.0
O A:HOH512 4.9 8.0 1.0
OD2 A:ASP128 4.9 12.4 1.0
CA A:ALA125 5.0 10.1 1.0
CA A:ASP124 5.0 7.5 1.0

Manganese binding site 3 out of 6 in 3e9b

Go back to Manganese Binding Sites List in 3e9b
Manganese binding site 3 out of 6 in the X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec


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 Mutant: the Complex with Bec within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:13.8
occ:1.00
 OD2 B:ASP124 2.1 8.5 1.0
OD2 B:ASP128 2.1 10.1 1.0
O1 B:S2C502 2.3 15.4 1.0
ND1 B:HIS101 2.3 14.5 1.0
OD2 B:ASP232 2.4 15.3 1.0
O2 B:S2C502 2.6 16.2 1.0
B B:S2C502 2.9 18.8 1.0
CG B:ASP128 3.1 13.7 1.0
CG B:ASP124 3.2 8.4 1.0
CG B:HIS101 3.2 13.4 1.0
MN B:MN501 3.3 12.2 1.0
OD1 B:ASP128 3.3 13.1 1.0
CE1 B:HIS101 3.3 12.9 1.0
CG B:ASP232 3.4 14.7 1.0
CB B:HIS101 3.4 14.5 1.0
O3 B:S2C502 3.4 15.2 1.0
OD1 B:ASP124 3.6 5.6 1.0
CB B:ASP232 3.7 13.1 1.0
CE B:S2C502 4.3 18.5 1.0
O B:HIS141 4.3 16.9 1.0
NE1 B:TRP122 4.3 8.5 1.0
CD2 B:HIS101 4.4 13.0 1.0
NE2 B:HIS101 4.4 13.9 1.0
CB B:ASP124 4.4 11.0 1.0
CB B:ASP128 4.4 13.0 1.0
OD1 B:ASP232 4.5 11.0 1.0
CZ2 B:TRP122 4.6 5.5 1.0
CE2 B:TRP122 4.8 5.8 1.0
CG B:GLU277 4.8 13.8 1.0
CA B:HIS101 4.9 17.0 1.0
OD2 B:ASP234 5.0 14.8 1.0
ND1 B:HIS126 5.0 10.6 1.0
CA B:ASP232 5.0 14.1 1.0

Manganese binding site 4 out of 6 in 3e9b

Go back to Manganese Binding Sites List in 3e9b
Manganese binding site 4 out of 6 in the X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec


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 Mutant: the Complex with Bec within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:12.2
occ:1.00
 ND1 B:HIS126 2.2 10.6 1.0
OD2 B:ASP234 2.2 14.8 1.0
OD1 B:ASP124 2.3 5.6 1.0
O1 B:S2C502 2.4 15.4 1.0
OD2 B:ASP232 2.4 15.3 1.0
O3 B:S2C502 2.6 15.2 1.0
OD1 B:ASP234 2.7 12.7 1.0
CG B:ASP234 2.8 14.1 1.0
CE1 B:HIS126 3.0 13.0 1.0
B B:S2C502 3.1 18.8 1.0
CG B:ASP124 3.2 8.4 1.0
CG B:ASP232 3.2 14.7 1.0
MN B:MN500 3.3 13.8 1.0
OD2 B:ASP124 3.3 8.5 1.0
CG B:HIS126 3.3 13.8 1.0
CB B:HIS126 3.8 10.7 1.0
OD1 B:ASP232 3.8 11.0 1.0
O2 B:S2C502 4.1 16.2 1.0
N B:HIS126 4.1 12.3 1.0
CB B:ASP232 4.1 13.1 1.0
CD B:S2C502 4.2 23.6 1.0
CE B:S2C502 4.2 18.5 1.0
NE2 B:HIS126 4.2 11.5 1.0
N B:ALA125 4.2 12.9 1.0
CB B:ASP234 4.3 10.9 1.0
OD1 B:ASP128 4.4 13.1 1.0
CD2 B:HIS126 4.4 12.9 1.0
CB B:ASP124 4.5 11.0 1.0
O B:HOH510 4.6 16.0 1.0
CA B:HIS126 4.6 12.3 1.0
OD2 B:ASP128 4.8 10.1 1.0
CB B:ALA125 4.8 14.6 1.0
C B:ALA125 4.8 13.6 1.0
O B:HOH505 4.9 11.5 1.0
CA B:ALA125 4.9 15.3 1.0
CA B:ASP124 5.0 12.4 1.0

Manganese binding site 5 out of 6 in 3e9b

Go back to Manganese Binding Sites List in 3e9b
Manganese binding site 5 out of 6 in the X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec


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 Mutant: the Complex with Bec within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn500

b:22.7
occ:1.00
 OD2 C:ASP124 2.1 11.9 1.0
OD2 C:ASP128 2.1 16.4 1.0
OD2 C:ASP232 2.2 8.2 1.0
ND1 C:HIS101 2.4 15.6 1.0
O1 C:S2C502 2.5 29.7 1.0
O2 C:S2C502 2.5 31.4 1.0
B C:S2C502 3.0 31.6 1.0
CG C:ASP128 3.1 18.0 1.0
CG C:ASP124 3.2 13.6 1.0
CG C:HIS101 3.2 16.4 1.0
CG C:ASP232 3.3 10.1 1.0
OD1 C:ASP128 3.3 16.5 1.0
CB C:HIS101 3.4 17.7 1.0
CE1 C:HIS101 3.4 16.6 1.0
MN C:MN501 3.4 13.9 1.0
CB C:ASP232 3.6 11.5 1.0
OD1 C:ASP124 3.6 14.0 1.0
O3 C:S2C502 3.7 31.0 1.0
NE1 C:TRP122 4.3 12.8 1.0
O C:HIS141 4.3 22.9 1.0
CE C:S2C502 4.4 30.0 1.0
OD1 C:ASP232 4.4 8.5 1.0
CB C:ASP128 4.4 18.2 1.0
CZ2 C:TRP122 4.4 10.1 1.0
CD2 C:HIS101 4.4 15.7 1.0
CB C:ASP124 4.5 13.5 1.0
NE2 C:HIS101 4.5 17.5 1.0
CE2 C:TRP122 4.7 12.1 1.0
CG C:GLU277 4.8 15.2 1.0
CA C:ASP232 4.9 11.9 1.0
CA C:HIS101 4.9 18.7 1.0
OD2 C:ASP234 5.0 11.8 1.0

Manganese binding site 6 out of 6 in 3e9b

Go back to Manganese Binding Sites List in 3e9b
Manganese binding site 6 out of 6 in the X-Ray Structure of Rat Arginase I-T135A Mutant: the Complex with Bec


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 Mutant: the Complex with Bec within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:13.9
occ:1.00
 OD2 C:ASP234 2.1 11.8 1.0
O1 C:S2C502 2.3 29.7 1.0
OD1 C:ASP124 2.5 14.0 1.0
ND1 C:HIS126 2.5 16.8 1.0
OD2 C:ASP232 2.5 8.2 1.0
OD1 C:ASP234 2.5 12.8 1.0
CG C:ASP234 2.6 13.4 1.0
O3 C:S2C502 2.9 31.0 1.0
B C:S2C502 3.1 31.6 1.0
CG C:ASP232 3.2 10.1 1.0
CE1 C:HIS126 3.2 14.4 1.0
CG C:ASP124 3.2 13.6 1.0
OD2 C:ASP124 3.4 11.9 1.0
MN C:MN500 3.4 22.7 1.0
CG C:HIS126 3.6 16.9 1.0
OD1 C:ASP232 3.6 8.5 1.0
CB C:HIS126 4.0 17.9 1.0
O2 C:S2C502 4.1 31.4 1.0
CB C:ASP234 4.1 12.7 1.0
CB C:ASP232 4.1 11.5 1.0
N C:HIS126 4.1 16.0 1.0
N C:ALA125 4.3 15.1 1.0
CE C:S2C502 4.3 30.0 1.0
CD C:S2C502 4.3 30.0 1.0
OD1 C:ASP128 4.4 16.5 1.0
NE2 C:HIS126 4.4 19.0 1.0
O C:HOH540 4.6 16.1 1.0
CB C:ASP124 4.6 13.5 1.0
CD2 C:HIS126 4.6 16.1 1.0
CA C:HIS126 4.7 17.5 1.0
CB C:ALA125 4.8 15.2 1.0
OD2 C:ASP128 4.9 16.4 1.0
C C:ALA125 4.9 15.8 1.0
CA C:ALA125 4.9 15.6 1.0
O C:THR246 4.9 18.0 1.0
CA C:ASP124 4.9 13.9 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: Tue Dec 15 04:09:04 2020

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