Iron in PDB 5trx: Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography

The structure of Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography, PDB code: 5trx was solved by E.G.Kovaleva, D.Oberthuer, A.Tolstikova, V.Mariani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.38
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.570, 154.860, 101.800, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.2

The structure of Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography (pdb code 5trx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography, PDB code: 5trx:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:39.8 occ:1.00 OE1 A:GLU267 2.1 34.9 1.0 O A:HOH571 2.1 34.8 1.0 O A:HOH555 2.3 30.8 1.0 NE2 A:HIS214 2.4 37.0 1.0 NE2 A:HIS155 2.4 28.9 1.0 O A:HOH564 2.5 40.6 1.0 CE1 A:HIS214 3.0 36.7 1.0 CD A:GLU267 3.1 35.3 1.0 CE1 A:HIS155 3.3 30.8 1.0 CD2 A:HIS155 3.5 30.9 1.0 CD2 A:HIS214 3.5 37.1 1.0 OE2 A:GLU267 3.6 34.8 1.0 OH A:TYR257 3.9 36.9 1.0 NE2 A:HIS200 4.1 39.4 1.0 ND1 A:HIS214 4.2 36.8 1.0 O A:HOH594 4.4 31.0 1.0 ND1 A:HIS155 4.4 30.9 1.0 CG A:GLU267 4.4 35.3 1.0 CG A:HIS214 4.5 37.0 1.0 ND2 A:ASN157 4.5 36.0 1.0 CE1 A:TYR257 4.5 37.3 1.0 CG A:HIS155 4.6 31.1 1.0 CE1 A:HIS200 4.6 38.2 1.0 CB A:GLU267 4.7 34.3 1.0 CZ A:TYR257 4.7 37.6 1.0 CB A:ALA216 4.9 30.1 1.0 CB A:ASN157 4.9 34.9 1.0

Iron binding site 2 out of 4 in the Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:40.2 occ:1.00 O B:HOH511 2.1 39.4 1.0 OE1 B:GLU267 2.1 34.7 1.0 O B:HOH558 2.1 29.2 1.0 NE2 B:HIS214 2.4 37.2 1.0 NE2 B:HIS155 2.5 31.5 1.0 CD B:GLU267 3.1 34.0 1.0 CE1 B:HIS214 3.1 38.0 1.0 OE2 B:GLU267 3.4 35.3 1.0 CE1 B:HIS155 3.4 29.8 1.0 CD2 B:HIS155 3.5 31.6 1.0 CD2 B:HIS214 3.6 37.2 1.0 NE2 B:HIS200 3.9 38.2 1.0 OH B:TYR257 4.0 35.2 1.0 ND1 B:HIS214 4.4 36.2 1.0 CG B:GLU267 4.4 34.8 1.0 ND2 B:ASN157 4.5 34.7 1.0 ND1 B:HIS155 4.5 30.8 1.0 CG B:HIS155 4.6 31.3 1.0 CE1 B:HIS200 4.6 37.7 1.0 CG B:HIS214 4.6 37.0 1.0 CE1 B:TYR257 4.6 33.2 1.0 CB B:GLU267 4.7 34.9 1.0 CZ B:TYR257 4.8 34.7 1.0 CB B:ASN157 4.9 32.8 1.0 NE2 B:HIS248 4.9 33.9 1.0 CB B:ALA216 4.9 35.8 1.0

Iron binding site 3 out of 4 in the Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:45.2 occ:1.00 O C:HOH572 2.1 24.3 1.0 OE1 C:GLU267 2.2 43.9 1.0 O C:HOH526 2.3 32.7 1.0 NE2 C:HIS214 2.4 42.3 1.0 NE2 C:HIS155 2.5 38.8 1.0 CE1 C:HIS214 3.0 43.0 1.0 CD C:GLU267 3.2 39.1 1.0 CE1 C:HIS155 3.3 39.8 1.0 CD2 C:HIS155 3.5 39.5 1.0 CD2 C:HIS214 3.5 43.0 1.0 OE2 C:GLU267 3.7 36.7 1.0 NE2 C:HIS200 3.7 50.3 1.0 OH C:TYR257 4.0 39.9 1.0 ND1 C:HIS214 4.2 42.4 1.0 CG C:HIS214 4.4 42.1 1.0 CG C:GLU267 4.4 39.7 1.0 CE1 C:HIS200 4.5 50.2 1.0 ND1 C:HIS155 4.5 37.8 1.0 ND2 C:ASN157 4.5 37.8 1.0 CG C:HIS155 4.6 38.5 1.0 CE2 C:TYR257 4.6 39.9 1.0 CB C:GLU267 4.6 41.3 1.0 CZ C:TYR257 4.7 38.1 1.0 CB C:ASN157 4.8 38.7 1.0 CD2 C:HIS200 4.8 50.8 1.0 CB C:ALA216 4.9 38.0 1.0

Iron binding site 4 out of 4 in the Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Room Temperature Structure of An Extradiol Ring-Cleaving Dioxygenase From B.Fuscum Determined Using Serial Femtosecond Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:44.6 occ:1.00 OE1 D:GLU267 2.1 41.2 1.0 O D:HOH565 2.2 11.2 0.5 O D:HOH558 2.3 38.3 1.0 O D:HOH506 2.3 30.7 1.0 NE2 D:HIS214 2.3 39.1 1.0 NE2 D:HIS155 2.5 35.7 1.0 CE1 D:HIS214 3.1 38.4 1.0 CD D:GLU267 3.1 41.3 1.0 CE1 D:HIS155 3.3 35.8 1.0 CD2 D:HIS214 3.4 38.5 1.0 OE2 D:GLU267 3.5 38.8 1.0 CD2 D:HIS155 3.6 35.5 1.0 OH D:TYR257 4.0 35.2 1.0 NE2 D:HIS200 4.0 49.3 1.0 ND1 D:HIS214 4.2 38.6 1.0 O D:HOH579 4.3 11.6 0.5 ND2 D:ASN157 4.4 38.5 1.0 CG D:GLU267 4.4 41.1 1.0 CG D:HIS214 4.5 38.7 1.0 ND1 D:HIS155 4.5 35.9 1.0 CE1 D:HIS200 4.6 48.2 1.0 CG D:HIS155 4.6 36.1 1.0 CE1 D:TYR257 4.7 33.5 1.0 CB D:GLU267 4.7 42.2 1.0 CZ D:TYR257 4.8 34.8 1.0 CB D:ASN157 4.8 38.4 1.0 CB D:ALA216 4.9 34.6 1.0

D.Oberthuer, J.Knoska, M.O.Wiedorn, K.R.Beyerlein, D.A.Bushnell, E.G.Kovaleva, M.Heymann, L.Gumprecht, R.A.Kirian, A.Barty, V.Mariani, A.Tolstikova, L.Adriano, S.Awel, M.Barthelmess, K.Dorner, P.L.Xavier, O.Yefanov, D.R.James, G.Nelson, D.Wang, G.Calvey, Y.Chen, A.Schmidt, M.Szczepek, S.Frielingsdorf, O.Lenz, E.Snell, P.J.Robinson, B.Sarler, G.Belsak, M.Macek, F.Wilde, A.Aquila, S.Boutet, M.Liang, M.S.Hunter, P.Scheerer, J.D.Lipscomb, U.Weierstall, R.D.Kornberg, J.C.H.Spence, L.Pollack, H.N.Chapman, S.Bajt. Double-Flow Focused Liquid Injector For Efficient Serial Femtosecond Crystallography Sci. Rep. V. 7 44628 2017.
ISSN: ESSN 2045-2322
DOI: 10.1038/SREP44628