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Iron in PDB 2phd: Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans

Enzymatic activity of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans

All present enzymatic activity of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans:
1.13.11.4;

Protein crystallography data

The structure of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans, PDB code: 2phd was solved by I.Matera, M.Ferraroni, F.Briganti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.016, 133.016, 190.748, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 26.2

Other elements in 2phd:

The structure of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans (pdb code 2phd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans, PDB code: 2phd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2phd

Go back to Iron Binding Sites List in 2phd
Iron binding site 1 out of 4 in the Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe370

b:40.6
occ:1.00
 NE2 A:HIS119 1.9 43.6 1.0
NE2 A:HIS160 2.2 39.8 1.0
NE2 A:HIS121 2.2 38.4 1.0
CE1 A:HIS119 2.8 43.1 1.0
O A:ACT371 2.9 43.1 1.0
CD2 A:HIS119 3.0 43.6 1.0
CE1 A:HIS121 3.1 38.2 1.0
CD2 A:HIS160 3.1 41.1 1.0
CE1 A:HIS160 3.2 40.3 1.0
CD2 A:HIS121 3.3 40.3 1.0
OXT A:ACT371 3.4 42.3 1.0
C A:ACT371 3.6 43.0 1.0
ND1 A:HIS119 4.0 41.5 1.0
CG A:HIS119 4.1 42.2 1.0
ND1 A:HIS121 4.3 39.4 1.0
ND1 A:HIS160 4.3 39.2 1.0
CG A:HIS160 4.3 40.5 1.0
CG A:HIS121 4.4 39.5 1.0
NH2 A:ARG127 4.5 40.3 1.0

Iron binding site 2 out of 4 in 2phd

Go back to Iron Binding Sites List in 2phd
Iron binding site 2 out of 4 in the Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe370

b:41.1
occ:1.00
 NE2 B:HIS119 1.8 40.6 1.0
NE2 B:HIS160 2.0 39.5 1.0
O B:HOH419 2.2 15.1 1.0
NE2 B:HIS121 2.3 36.8 1.0
O D:ACT1 2.5 53.6 1.0
CE1 B:HIS160 2.7 40.4 1.0
CE1 B:HIS119 2.8 42.0 1.0
CD2 B:HIS119 2.8 41.2 1.0
CD2 B:HIS160 3.2 40.0 1.0
CD2 B:HIS121 3.3 39.3 1.0
CE1 B:HIS121 3.3 37.3 1.0
OXT D:ACT1 3.4 54.6 1.0
C D:ACT1 3.4 54.4 1.0
ND1 B:HIS119 3.9 42.0 1.0
ND1 B:HIS160 3.9 39.6 1.0
CG B:HIS119 3.9 41.9 1.0
O B:HOH371 4.1 32.7 1.0
CG B:HIS160 4.2 40.3 1.0
ND1 B:HIS121 4.4 37.6 1.0
CG B:HIS121 4.4 37.9 1.0
NH2 B:ARG127 4.5 45.0 1.0
O B:HOH378 4.7 26.9 1.0
CH3 D:ACT1 4.9 53.5 1.0

Iron binding site 3 out of 4 in 2phd

Go back to Iron Binding Sites List in 2phd
Iron binding site 3 out of 4 in the Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe370

b:35.0
occ:1.00
 NE2 C:HIS160 1.9 38.6 1.0
O C:HOH432 1.9 28.5 1.0
NE2 C:HIS121 2.1 37.3 1.0
NE2 C:HIS119 2.2 43.4 1.0
CE1 C:HIS160 2.9 39.6 1.0
CD2 C:HIS160 2.9 40.2 1.0
CE1 C:HIS121 3.0 36.7 1.0
O C:HOH382 3.0 22.3 1.0
CD2 C:HIS119 3.1 41.5 1.0
CD2 C:HIS121 3.2 38.4 1.0
CE1 C:HIS119 3.3 43.5 1.0
O C:HOH371 3.8 26.4 1.0
ND1 C:HIS160 4.0 39.2 1.0
CG C:HIS160 4.1 40.5 1.0
ND1 C:HIS121 4.2 35.5 1.0
O C:HOH372 4.2 31.6 1.0
CG C:HIS119 4.3 40.1 1.0
CG C:HIS121 4.3 38.3 1.0
ND1 C:HIS119 4.3 40.8 1.0
NH2 C:ARG127 4.6 39.2 1.0
CE A:MET46 4.8 54.1 1.0

Iron binding site 4 out of 4 in 2phd

Go back to Iron Binding Sites List in 2phd
Iron binding site 4 out of 4 in the Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Determination of A Salicylate 1,2- Dioxygenase From Pseudaminobacter Salicylatoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe370

b:31.2
occ:1.00
 NE2 D:HIS119 2.0 42.3 1.0
NE2 D:HIS121 2.1 38.7 1.0
NE2 D:HIS160 2.2 40.2 1.0
O D:HOH374 2.5 23.1 1.0
CE1 D:HIS119 2.9 43.2 1.0
CE1 D:HIS121 3.0 39.0 1.0
CD2 D:HIS119 3.1 40.9 1.0
CE1 D:HIS160 3.1 39.8 1.0
CD2 D:HIS160 3.2 41.3 1.0
CD2 D:HIS121 3.2 39.5 1.0
ND1 D:HIS119 4.1 40.4 1.0
CG D:HIS119 4.2 40.0 1.0
ND1 D:HIS121 4.2 38.0 1.0
ND1 D:HIS160 4.2 39.1 1.0
O D:HOH375 4.3 30.6 1.0
CG D:HIS160 4.3 40.0 1.0
CG D:HIS121 4.3 38.3 1.0
O D:HOH388 4.4 17.5 1.0
NH2 D:ARG127 4.7 39.6 1.0

Reference:

M.Ferraroni, I.Matera, F.Briganti, A.Stolz, S.Burger. Crystal Structure Determination of A Salicylate 1,2-Dioxygenase From Pseudaminobacter Salicylatoxidans To Be Published.
Page generated: Thu Jul 17 03:28:26 2025

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