Atomistry » Manganese » PDB 3cev-3ea3 » 3e8z
Atomistry »
  Manganese »
    PDB 3cev-3ea3 »
      3e8z »

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

Go back to Manganese Binding Sites List in 3e8z
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

Go back to Manganese Binding Sites List in 3e8z
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

Go back to Manganese Binding Sites List in 3e8z
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

Go back to Manganese Binding Sites List in 3e8z
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy