Atomistry » Iron » PDB 8ca4-8csp » 8ch4
Atomistry »
  Iron »
    PDB 8ca4-8csp »
      8ch4 »

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: Fri Aug 9 21:15:40 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy