Iron in PDB 8ch4: Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp.

Enzymatic activity of Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp.

All present enzymatic activity of Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp.:
1.13.11.64;

Protein crystallography data

The structure of Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp., PDB code: 8ch4 was solved by M.Ferraroni, A.Stolz, E.Eppinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.427, 143.173, 60.076, 90, 107.33, 90
R / Rfree (%) 21.6 / 27.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp. (pdb code 8ch4). 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 of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp., PDB code: 8ch4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8ch4

Go back to Iron Binding Sites List in 8ch4
Iron binding site 1 out of 4 in the Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:32.4
occ:1.00
 O A:HOH410 2.0 39.2 1.0
NE2 A:HIS136 2.1 27.2 1.0
NE2 A:HIS96 2.1 53.9 1.0
O A:HOH415 2.2 42.5 1.0
O A:HOH432 2.2 24.9 1.0
NE2 A:HIS98 2.3 37.9 1.0
CE1 A:HIS136 3.0 29.4 1.0
CE1 A:HIS96 3.0 51.9 1.0
CE1 A:HIS98 3.1 37.3 1.0
CD2 A:HIS136 3.1 29.3 1.0
CD2 A:HIS96 3.2 53.3 1.0
CD2 A:HIS98 3.3 38.6 1.0
O A:HOH436 3.5 40.8 1.0
OH A:TYR104 3.7 61.2 1.0
ND1 A:HIS136 4.1 31.8 1.0
ND1 A:HIS96 4.1 54.0 1.0
CG A:HIS136 4.2 31.7 1.0
CG A:HIS96 4.3 49.4 1.0
ND1 A:HIS98 4.3 40.2 1.0
CG A:HIS98 4.4 40.0 1.0
O A:HOH403 4.5 41.6 1.0

Iron binding site 2 out of 4 in 8ch4

Go back to Iron Binding Sites List in 8ch4
Iron binding site 2 out of 4 in the Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:32.9
occ:1.00
 O B:HOH403 1.8 30.4 1.0
NE2 B:HIS96 2.1 51.8 1.0
NE2 B:HIS136 2.1 27.1 1.0
O B:HOH416 2.2 36.2 1.0
NE2 B:HIS98 2.3 49.9 1.0
O B:HOH425 2.3 26.9 1.0
CE1 B:HIS96 2.9 53.8 1.0
CE1 B:HIS136 2.9 29.2 1.0
CE1 B:HIS98 3.0 50.0 1.0
CD2 B:HIS96 3.1 52.9 1.0
CD2 B:HIS136 3.2 33.1 1.0
CD2 B:HIS98 3.4 53.5 1.0
O B:HOH435 3.6 52.2 1.0
OH B:TYR104 3.8 73.0 1.0
ND1 B:HIS96 4.0 54.1 1.0
ND1 B:HIS136 4.1 29.9 1.0
CG B:HIS96 4.2 48.8 1.0
ND1 B:HIS98 4.2 46.5 1.0
CG B:HIS136 4.2 31.4 1.0
O B:HOH406 4.3 54.3 1.0
CG B:HIS98 4.4 47.4 1.0
CZ2 B:TRP165 4.8 53.1 1.0

Iron binding site 3 out of 4 in 8ch4

Go back to Iron Binding Sites List in 8ch4
Iron binding site 3 out of 4 in the Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:34.0
occ:1.00
 O C:HOH404 1.9 30.1 1.0
NE2 C:HIS96 2.0 50.7 1.0
NE2 C:HIS136 2.1 30.5 1.0
O C:HOH407 2.1 40.4 1.0
NE2 C:HIS98 2.1 39.8 1.0
O C:HOH430 2.4 25.9 1.0
CE1 C:HIS96 2.6 48.0 1.0
CE1 C:HIS136 2.9 33.8 1.0
CE1 C:HIS98 3.0 40.0 1.0
CD2 C:HIS96 3.1 48.9 1.0
CD2 C:HIS136 3.1 30.5 1.0
CD2 C:HIS98 3.2 42.0 1.0
O C:HOH433 3.4 49.9 1.0
ND1 C:HIS96 3.7 50.7 1.0
CG C:HIS96 4.0 47.7 1.0
OH C:TYR104 4.1 52.2 1.0
ND1 C:HIS136 4.1 32.9 1.0
ND1 C:HIS98 4.2 39.2 1.0
CG C:HIS136 4.2 33.4 1.0
CG C:HIS98 4.3 39.2 1.0
CZ2 C:TRP165 5.0 53.0 1.0

Iron binding site 4 out of 4 in 8ch4

Go back to Iron Binding Sites List in 8ch4
Iron binding site 4 out of 4 in the Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Ring Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:35.1
occ:1.00
 NE2 D:HIS96 1.9 50.4 1.0
O D:HOH406 2.0 37.2 1.0
NE2 D:HIS136 2.1 31.3 1.0
O D:HOH431 2.2 33.5 1.0
NE2 D:HIS98 2.2 42.6 1.0
CE1 D:HIS96 2.8 51.2 1.0
CD2 D:HIS96 3.0 53.4 1.0
CE1 D:HIS136 3.1 30.5 1.0
CE1 D:HIS98 3.1 40.3 1.0
CD2 D:HIS136 3.1 31.8 1.0
CD2 D:HIS98 3.3 42.3 1.0
O D:HOH443 3.4 42.6 1.0
OH D:TYR104 3.9 56.3 1.0
ND1 D:HIS96 3.9 53.1 1.0
CG D:HIS96 4.0 49.6 1.0
ND1 D:HIS136 4.2 31.3 1.0
CG D:HIS136 4.3 33.6 1.0
ND1 D:HIS98 4.3 47.1 1.0
CG D:HIS98 4.4 42.2 1.0
O D:HOH407 4.4 44.1 1.0
O D:HOH445 4.4 67.2 1.0
CZ2 D:TRP165 4.9 53.3 1.0

Reference:

E.Eppinger, A.Stolz, M.Ferraroni. Crystal Structure of the Monocupin Ring-Cleaving Dioxygenase 5-Nitrosalicylate 1,2-Dioxygenase From Bradyrhizobium Sp. Acta Crystallogr D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37326584
DOI: 10.1107/S2059798323004199
Page generated: Thu Jul 27 16:07:51 2023

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