Atomistry » Manganese » PDB 1ss9-1uvi » 1t5g
Atomistry »
  Manganese »
    PDB 1ss9-1uvi »
      1t5g »

Manganese in PDB 1t5g: Arginase-F2-L-Arginine Complex

Enzymatic activity of Arginase-F2-L-Arginine Complex

All present enzymatic activity of Arginase-F2-L-Arginine Complex:
3.5.3.1;

Protein crystallography data

The structure of Arginase-F2-L-Arginine Complex, PDB code: 1t5g was solved by E.Cama, S.Pethe, J.-L.Boucher, S.Han, F.A.Emig, D.E.Ash, R.E.Viola, D.Mansuy, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.69 / 2.40
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 87.720, 87.720, 104.520, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 25.4

Other elements in 1t5g:

The structure of Arginase-F2-L-Arginine Complex also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Arginase-F2-L-Arginine Complex (pdb code 1t5g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Arginase-F2-L-Arginine Complex, PDB code: 1t5g:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1t5g

Go back to Manganese Binding Sites List in 1t5g
Manganese binding site 1 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:26.8
occ:1.00
 OD2 A:ASP234 2.1 24.8 1.0
OD2 A:ASP232 2.2 22.6 1.0
F A:F602 2.2 30.8 1.0
OD1 A:ASP124 2.3 27.8 1.0
ND1 A:HIS126 2.3 32.4 1.0
OD1 A:ASP234 2.4 20.7 1.0
CG A:ASP234 2.5 22.6 1.0
NH2 A:ARG1000 2.8 44.3 1.0
CE1 A:HIS126 2.8 33.6 1.0
CG A:ASP232 3.2 23.6 1.0
CG A:ASP124 3.3 27.2 1.0
MN A:MN501 3.3 29.5 1.0
CG A:HIS126 3.5 33.0 1.0
OD2 A:ASP124 3.5 27.4 1.0
OD1 A:ASP232 3.8 24.7 1.0
F A:F603 3.8 64.9 1.0
CZ A:ARG1000 4.0 45.7 1.0
NE2 A:HIS126 4.0 34.3 1.0
CB A:ASP234 4.1 20.5 1.0
CB A:HIS126 4.2 32.6 1.0
N A:HIS126 4.2 29.7 1.0
N A:ALA125 4.2 31.6 1.0
CB A:ASP232 4.3 23.7 1.0
CD A:ARG1000 4.3 44.6 1.0
CD2 A:HIS126 4.4 34.1 1.0
OD1 A:ASP128 4.5 34.0 1.0
NE A:ARG1000 4.5 45.3 1.0
CB A:ASP124 4.6 28.8 1.0
CB A:ALA125 4.7 31.6 1.0
OD2 A:ASP128 4.7 35.0 1.0
CA A:HIS126 4.8 31.1 1.0
CA A:ALA125 4.9 30.7 1.0
C A:ALA125 4.9 30.2 1.0
O A:ASP234 4.9 20.4 1.0
NH1 A:ARG1000 5.0 47.5 1.0
CA A:ASP234 5.0 20.7 1.0

Manganese binding site 2 out of 6 in 1t5g

Go back to Manganese Binding Sites List in 1t5g
Manganese binding site 2 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:29.5
occ:1.00
 OD2 A:ASP124 2.0 27.4 1.0
ND1 A:HIS101 2.3 29.7 1.0
OD2 A:ASP232 2.3 22.6 1.0
OD2 A:ASP128 2.3 35.0 1.0
F A:F603 2.3 64.9 1.0
F A:F602 2.4 30.8 1.0
NH2 A:ARG1000 2.9 44.3 1.0
CG A:ASP124 3.0 27.2 1.0
CG A:ASP232 3.2 23.6 1.0
CG A:HIS101 3.2 29.1 1.0
CE1 A:HIS101 3.3 28.0 1.0
MN A:MN500 3.3 26.8 1.0
CG A:ASP128 3.3 35.6 1.0
OD1 A:ASP124 3.4 27.8 1.0
CB A:HIS101 3.4 28.7 1.0
CB A:ASP232 3.5 23.7 1.0
OD1 A:ASP128 3.7 34.0 1.0
CZ A:ARG1000 4.1 45.7 1.0
OD1 A:ASP232 4.3 24.7 1.0
CD2 A:HIS101 4.3 27.7 1.0
NE2 A:HIS101 4.3 26.3 1.0
CB A:ASP124 4.3 28.8 1.0
NE1 A:TRP122 4.5 29.9 1.0
NH1 A:ARG1000 4.5 47.5 1.0
CG A:GLU277 4.6 32.4 1.0
CB A:ASP128 4.7 36.0 1.0
O A:ALA141 4.7 37.7 1.0
CZ2 A:TRP122 4.8 31.9 1.0
OD2 A:ASP234 4.8 24.8 1.0
CA A:ASP232 4.8 23.1 1.0
CA A:HIS101 4.9 30.0 1.0
OE2 A:GLU277 4.9 33.6 1.0
OD1 A:ASP234 4.9 20.7 1.0
CE2 A:TRP122 5.0 31.0 1.0

Manganese binding site 3 out of 6 in 1t5g

Go back to Manganese Binding Sites List in 1t5g
Manganese binding site 3 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:26.8
occ:1.00
 OD2 B:ASP234 2.0 21.2 1.0
OD2 B:ASP232 2.2 23.4 1.0
F B:F604 2.2 30.8 1.0
OD1 B:ASP124 2.3 28.9 1.0
ND1 B:HIS126 2.3 31.6 1.0
OD1 B:ASP234 2.4 24.2 1.0
CG B:ASP234 2.5 21.2 1.0
NH2 B:ARG1001 2.8 44.3 1.0
CE1 B:HIS126 2.8 33.1 1.0
CG B:ASP232 3.2 25.4 1.0
CG B:ASP124 3.3 28.3 1.0
MN B:MN503 3.3 29.5 1.0
CG B:HIS126 3.5 33.2 1.0
OD2 B:ASP124 3.6 30.3 1.0
OD1 B:ASP232 3.8 25.4 1.0
F B:F605 3.8 64.9 1.0
CB B:ASP234 3.9 20.1 1.0
CZ B:ARG1001 4.0 45.7 1.0
NE2 B:HIS126 4.1 33.1 1.0
CB B:HIS126 4.1 31.2 1.0
N B:HIS126 4.2 29.0 1.0
N B:ALA125 4.2 30.6 1.0
CB B:ASP232 4.3 24.8 1.0
CD B:ARG1001 4.3 44.6 1.0
CD2 B:HIS126 4.4 34.2 1.0
OD1 B:ASP128 4.5 38.3 1.0
NE B:ARG1001 4.5 45.3 1.0
CB B:ASP124 4.6 28.5 1.0
OD2 B:ASP128 4.7 39.6 1.0
CB B:ALA125 4.7 30.4 1.0
O B:ASP234 4.7 19.5 1.0
CA B:HIS126 4.8 30.8 1.0
CA B:ALA125 4.9 29.9 1.0
C B:ALA125 4.9 29.3 1.0
CA B:ASP234 4.9 19.5 1.0
NH1 B:ARG1001 5.0 47.5 1.0

Manganese binding site 4 out of 6 in 1t5g

Go back to Manganese Binding Sites List in 1t5g
Manganese binding site 4 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:29.5
occ:1.00
 OD2 B:ASP124 2.1 30.3 1.0
ND1 B:HIS101 2.3 28.9 1.0
OD2 B:ASP232 2.3 23.4 1.0
OD2 B:ASP128 2.3 39.6 1.0
F B:F605 2.3 64.9 1.0
F B:F604 2.4 30.8 1.0
NH2 B:ARG1001 2.9 44.3 1.0
CG B:ASP124 3.0 28.3 1.0
CG B:HIS101 3.2 30.0 1.0
CG B:ASP232 3.2 25.4 1.0
CE1 B:HIS101 3.3 28.5 1.0
MN B:MN502 3.3 26.8 1.0
OD1 B:ASP124 3.3 28.9 1.0
CG B:ASP128 3.3 38.2 1.0
CB B:HIS101 3.4 28.7 1.0
CB B:ASP232 3.5 24.8 1.0
OD1 B:ASP128 3.7 38.3 1.0
CZ B:ARG1001 4.1 45.7 1.0
OD1 B:ASP232 4.3 25.4 1.0
CD2 B:HIS101 4.3 27.9 1.0
NE2 B:HIS101 4.3 26.5 1.0
CB B:ASP124 4.4 28.5 1.0
NE1 B:TRP122 4.5 31.1 1.0
NH1 B:ARG1001 4.5 47.5 1.0
CG B:GLU277 4.5 33.2 1.0
CB B:ASP128 4.6 36.5 1.0
OD1 B:ASP234 4.7 24.2 1.0
O B:ALA141 4.7 37.3 1.0
CZ2 B:TRP122 4.8 33.3 1.0
CA B:ASP232 4.9 25.4 1.0
CA B:HIS101 4.9 30.3 1.0
OE2 B:GLU277 4.9 33.6 1.0
OD2 B:ASP234 4.9 21.2 1.0
CE2 B:TRP122 5.0 32.7 1.0

Manganese binding site 5 out of 6 in 1t5g

Go back to Manganese Binding Sites List in 1t5g
Manganese binding site 5 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:26.8
occ:1.00
 OD2 C:ASP234 2.1 25.4 1.0
OD2 C:ASP232 2.2 19.0 1.0
F C:F600 2.2 30.8 1.0
ND1 C:HIS126 2.3 30.2 1.0
OD1 C:ASP124 2.3 32.8 1.0
OD1 C:ASP234 2.5 26.3 1.0
CG C:ASP234 2.6 23.8 1.0
NH2 C:ARG1002 2.8 44.3 1.0
CE1 C:HIS126 2.8 30.5 1.0
CG C:ASP232 3.2 22.3 1.0
CG C:ASP124 3.2 30.8 1.0
MN C:MN505 3.3 29.5 1.0
OD2 C:ASP124 3.5 31.5 1.0
CG C:HIS126 3.5 31.0 1.0
OD1 C:ASP232 3.8 22.8 1.0
F C:F601 3.8 64.9 1.0
CZ C:ARG1002 4.0 45.7 1.0
NE2 C:HIS126 4.1 30.1 1.0
CB C:ASP234 4.1 22.3 1.0
CB C:HIS126 4.2 31.6 1.0
N C:HIS126 4.2 30.7 1.0
N C:ALA125 4.2 30.0 1.0
CB C:ASP232 4.3 22.5 1.0
CD C:ARG1002 4.3 44.6 1.0
CD2 C:HIS126 4.4 30.6 1.0
OD1 C:ASP128 4.5 36.1 1.0
NE C:ARG1002 4.5 45.3 1.0
CB C:ASP124 4.6 29.5 1.0
CB C:ALA125 4.7 28.4 1.0
OD2 C:ASP128 4.7 36.8 1.0
CA C:HIS126 4.8 31.9 1.0
CA C:ALA125 4.9 30.0 1.0
NH1 C:ARG1002 4.9 47.5 1.0
C C:ALA125 4.9 30.0 1.0
O C:ASP234 5.0 21.9 1.0

Manganese binding site 6 out of 6 in 1t5g

Go back to Manganese Binding Sites List in 1t5g
Manganese binding site 6 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:29.5
occ:1.00
 OD2 C:ASP124 2.0 31.5 1.0
ND1 C:HIS101 2.3 29.0 1.0
OD2 C:ASP232 2.3 19.0 1.0
F C:F601 2.3 64.9 1.0
OD2 C:ASP128 2.3 36.8 1.0
F C:F600 2.4 30.8 1.0
NH2 C:ARG1002 2.9 44.3 1.0
CG C:ASP124 3.0 30.8 1.0
CG C:HIS101 3.2 29.7 1.0
CG C:ASP232 3.2 22.3 1.0
CE1 C:HIS101 3.3 28.1 1.0
MN C:MN504 3.3 26.8 1.0
CG C:ASP128 3.4 35.5 1.0
CB C:HIS101 3.4 29.9 1.0
OD1 C:ASP124 3.4 32.8 1.0
CB C:ASP232 3.5 22.5 1.0
OD1 C:ASP128 3.7 36.1 1.0
CZ C:ARG1002 4.1 45.7 1.0
CD2 C:HIS101 4.3 27.8 1.0
OD1 C:ASP232 4.3 22.8 1.0
NE2 C:HIS101 4.3 27.6 1.0
CB C:ASP124 4.3 29.5 1.0
NH1 C:ARG1002 4.5 47.5 1.0
NE1 C:TRP122 4.5 30.6 1.0
CG C:GLU277 4.6 30.9 1.0
CB C:ASP128 4.7 34.6 1.0
O C:ALA141 4.7 37.1 1.0
CZ2 C:TRP122 4.8 30.6 1.0
CA C:ASP232 4.8 22.9 1.0
CA C:HIS101 4.9 32.2 1.0
OE2 C:GLU277 4.9 31.1 1.0
OD1 C:ASP234 4.9 26.3 1.0
OD2 C:ASP234 5.0 25.4 1.0
CE2 C:TRP122 5.0 31.1 1.0

Reference:

E.Cama, S.Pethe, J.-L.Boucher, S.Han, F.A.Emig, D.E.Ash, R.E.Viola, D.Mansuy, D.W.Christianson. Inhibitor Coordination Interactions in the Binuclear Manganese Cluster of Arginase Biochemistry V. 43 8987 2004.
ISSN: ISSN 0006-2960
PubMed: 15248756
DOI: 10.1021/BI0491705
Page generated: Sat Oct 5 12:31:04 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