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Iron in PDB 2vc5: Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities

Enzymatic activity of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities

All present enzymatic activity of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities:
3.1.8.1;

Protein crystallography data

The structure of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities, PDB code: 2vc5 was solved by M.Elias, J.Dupuy, L.Merone, L.Mandrich, S.Moniot, C.Lecomte, M.Rossi, P.Masson, G.Manco, E.Chabriere, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.90 / 2.6
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.160, 104.820, 155.360, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 28.2

Other elements in 2vc5:

The structure of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities also contains other interesting chemical elements:

Cobalt (Co) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities (pdb code 2vc5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities, PDB code: 2vc5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2vc5

Go back to Iron Binding Sites List in 2vc5
Iron binding site 1 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1315

b:20.6
occ:1.00
 O A:HOH2064 2.0 41.9 1.0
OQ2 A:KCX137 2.0 25.3 1.0
OD2 A:ASP256 2.1 33.0 1.0
NE2 A:HIS24 2.2 24.2 1.0
NE2 A:HIS22 2.2 26.6 1.0
CX A:KCX137 3.0 25.2 1.0
CD2 A:HIS24 3.0 24.5 1.0
CD2 A:HIS22 3.0 26.5 1.0
CG A:ASP256 3.1 33.4 1.0
OQ1 A:KCX137 3.2 24.9 1.0
CE1 A:HIS24 3.3 24.2 1.0
CE1 A:HIS22 3.3 26.7 1.0
OD1 A:ASP256 3.4 33.2 1.0
CO A:CO1316 3.4 28.3 1.0
NZ A:KCX137 4.1 25.5 1.0
CG A:HIS24 4.2 24.9 1.0
CG A:HIS22 4.2 26.6 1.0
O A:HOH2012 4.3 26.8 1.0
CE1 A:HIS199 4.3 28.4 1.0
ND1 A:HIS24 4.3 24.5 1.0
ND1 A:HIS22 4.4 26.7 1.0
CB A:ASP256 4.4 33.5 1.0
NE2 A:HIS199 4.5 28.2 1.0
CG A:PRO67 4.6 27.0 1.0
O A:HOH2045 4.8 31.5 1.0
CA A:ASP256 4.8 33.6 1.0
O A:ASP256 4.9 33.9 1.0

Iron binding site 2 out of 4 in 2vc5

Go back to Iron Binding Sites List in 2vc5
Iron binding site 2 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1315

b:19.5
occ:1.00
 O B:HOH2062 2.0 37.5 1.0
NE2 B:HIS22 2.1 26.6 1.0
OQ2 B:KCX137 2.1 27.5 1.0
NE2 B:HIS24 2.1 24.2 1.0
OD1 B:ASP256 2.2 32.1 1.0
CX B:KCX137 3.0 27.8 1.0
CD2 B:HIS22 3.1 26.6 1.0
CE1 B:HIS24 3.1 24.2 1.0
CD2 B:HIS24 3.1 24.2 1.0
CG B:ASP256 3.1 32.1 1.0
CE1 B:HIS22 3.1 26.8 1.0
OQ1 B:KCX137 3.2 27.2 1.0
CO B:CO1316 3.3 29.7 1.0
OD2 B:ASP256 3.5 32.0 1.0
O B:HOH2020 3.9 17.0 1.0
NZ B:KCX137 4.2 28.4 1.0
ND1 B:HIS24 4.2 24.4 1.0
CG B:HIS22 4.2 26.9 1.0
ND1 B:HIS22 4.2 26.7 1.0
CG B:HIS24 4.3 24.7 1.0
CE1 B:HIS199 4.4 32.7 1.0
CB B:ASP256 4.4 32.2 1.0
CG B:PRO67 4.5 28.4 1.0
NE2 B:HIS199 4.6 32.8 1.0
CA B:ASP256 4.8 32.3 1.0
O B:ASP256 4.9 32.4 1.0

Iron binding site 3 out of 4 in 2vc5

Go back to Iron Binding Sites List in 2vc5
Iron binding site 3 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1315

b:25.3
occ:1.00
 O C:HOH2056 1.9 23.3 1.0
NE2 C:HIS22 2.1 31.6 1.0
OQ2 C:KCX137 2.1 26.2 1.0
NE2 C:HIS24 2.1 29.8 1.0
OD1 C:ASP256 2.3 37.6 1.0
CX C:KCX137 3.0 26.4 1.0
CD2 C:HIS22 3.0 31.8 1.0
CE1 C:HIS24 3.1 29.7 1.0
CE1 C:HIS22 3.1 31.7 1.0
CG C:ASP256 3.1 37.9 1.0
CD2 C:HIS24 3.1 29.9 1.0
OQ1 C:KCX137 3.3 26.1 1.0
OD2 C:ASP256 3.4 37.7 1.0
CO C:CO1316 3.4 28.1 1.0
O C:HOH2013 3.9 11.8 1.0
NZ C:KCX137 4.1 26.8 1.0
CG C:HIS22 4.2 31.8 1.0
ND1 C:HIS22 4.2 31.8 1.0
ND1 C:HIS24 4.2 29.7 1.0
CG C:HIS24 4.3 30.2 1.0
CG C:PRO67 4.3 29.7 1.0
CE1 C:HIS199 4.4 35.8 1.0
CB C:ASP256 4.5 38.0 1.0
NE2 C:HIS199 4.8 35.7 1.0
CA C:ASP256 4.9 38.1 1.0

Iron binding site 4 out of 4 in 2vc5

Go back to Iron Binding Sites List in 2vc5
Iron binding site 4 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1315

b:34.5
occ:1.00
 O D:HOH2061 1.9 29.5 1.0
OQ2 D:KCX137 2.1 39.8 1.0
NE2 D:HIS24 2.1 30.3 1.0
OD1 D:ASP256 2.2 41.9 1.0
NE2 D:HIS22 2.2 33.7 1.0
CX D:KCX137 3.0 39.9 1.0
CE1 D:HIS24 3.1 30.4 1.0
CG D:ASP256 3.1 41.9 1.0
CD2 D:HIS22 3.1 33.6 1.0
CD2 D:HIS24 3.1 30.5 1.0
CE1 D:HIS22 3.2 33.8 1.0
OQ1 D:KCX137 3.2 39.7 1.0
CO D:CO1316 3.2 33.4 1.0
OD2 D:ASP256 3.4 41.7 1.0
O D:HOH2040 4.0 32.9 1.0
NZ D:KCX137 4.1 40.2 1.0
CE1 D:HIS199 4.1 50.8 1.0
ND1 D:HIS24 4.2 30.5 1.0
CG D:HIS24 4.3 30.9 1.0
NE2 D:HIS199 4.3 50.7 1.0
ND1 D:HIS22 4.3 33.8 1.0
CG D:HIS22 4.3 33.7 1.0
CB D:ASP256 4.4 42.0 1.0
CG D:PRO67 4.6 29.8 1.0
CA D:ASP256 4.8 42.0 1.0
O D:ASP256 5.0 41.9 1.0

Reference:

M.Elias, J.Dupuy, L.Merone, L.Mandrich, E.Porzio, S.Moniot, D.Rochu, C.Lecomte, M.Rossi, P.Masson, G.Manco, E.Chabriere. Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities. J.Mol.Biol. V. 379 1017 2008.
ISSN: ISSN 0022-2836
PubMed: 18486146
DOI: 10.1016/J.JMB.2008.04.022
Page generated: Sun Aug 4 02:35:42 2024

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