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

Ca in 5W0R
Ca in 5VYG
Ca in 5VT8
Ca in 5VYF
Ca in 5VYB
Ca in 5VXZ
Ca in 5VTM
Ca in 5VWM
Ca in 5VTD
Ca in 5VUG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy