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

Protein crystallography data

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

Other elements in 5trx:

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

Iron Binding Sites:

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 5trx

Go back to Iron Binding Sites List in 5trx
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 5trx

Go back to Iron Binding Sites List in 5trx
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 5trx

Go back to Iron Binding Sites List in 5trx
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 5trx

Go back to Iron Binding Sites List in 5trx
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

Reference:

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
Page generated: Sun Dec 13 16:12:49 2020

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