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Chlorine 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:

Iron (Fe) 4 atoms
Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5trx

Go back to Chlorine Binding Sites List in 5trx
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl402

b:36.9
occ:1.00
CE1 A:HIS248 3.1 30.9 1.0
NH2 A:ARG243 3.2 36.1 1.0
ND1 A:HIS248 3.4 30.8 1.0
NH1 A:ARG293 3.4 41.4 1.0
CG A:ARG293 3.4 33.6 1.0
NH1 A:ARG243 3.4 36.9 1.0
CB A:ARG293 3.4 33.0 1.0
CD A:ARG293 3.5 34.3 1.0
CZ A:ARG243 3.8 35.5 1.0
O A:ARG293 3.9 32.9 1.0
CA A:ARG293 3.9 32.7 1.0
OH A:TYR257 4.0 36.9 1.0
NE2 A:HIS248 4.2 31.7 1.0
C A:ARG293 4.2 34.3 1.0
CZ A:ARG293 4.3 37.7 1.0
NE A:ARG293 4.3 37.6 1.0
O A:HOH564 4.3 40.6 1.0
CH2 A:TRP304 4.3 36.7 1.0
CZ2 A:TRP304 4.3 37.4 1.0
CG A:HIS248 4.6 31.2 1.0
CZ A:TYR257 4.9 37.6 1.0
CZ3 A:TRP304 5.0 37.0 1.0
CD2 A:HIS248 5.0 31.9 1.0
CE2 A:TYR257 5.0 36.5 1.0

Chlorine binding site 2 out of 4 in 5trx

Go back to Chlorine Binding Sites List in 5trx
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl403

b:35.3
occ:1.00
NH1 B:ARG293 3.2 33.2 1.0
NH2 B:ARG243 3.2 36.6 1.0
NH1 B:ARG243 3.3 32.8 1.0
CE1 B:HIS248 3.3 31.8 1.0
ND1 B:HIS248 3.4 32.3 1.0
CB B:ARG293 3.4 31.9 1.0
CD B:ARG293 3.6 32.9 1.0
CG B:ARG293 3.6 32.4 1.0
CZ B:ARG243 3.7 34.8 1.0
O B:ARG293 3.9 31.0 1.0
CA B:ARG293 3.9 32.6 1.0
CH2 B:TRP304 3.9 42.6 1.0
OH B:TYR257 4.0 35.2 1.0
CZ2 B:TRP304 4.0 40.0 1.0
CZ B:ARG293 4.2 32.4 1.0
C B:ARG293 4.2 33.3 1.0
NE B:ARG293 4.3 32.5 1.0
NE2 B:HIS248 4.6 33.9 1.0
CZ3 B:TRP304 4.6 43.2 1.0
CG B:HIS248 4.7 33.6 1.0
CE2 B:TRP304 4.8 38.0 1.0
O B:HOH511 4.8 39.4 1.0
CZ B:TYR257 4.9 34.7 1.0
CE2 B:TYR257 5.0 37.0 1.0

Chlorine binding site 3 out of 4 in 5trx

Go back to Chlorine Binding Sites List in 5trx
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl402

b:36.9
occ:1.00
NH2 C:ARG243 3.0 41.5 1.0
CB C:ARG293 3.2 39.9 1.0
CE1 C:HIS248 3.2 47.6 1.0
NH1 C:ARG243 3.2 42.1 1.0
ND1 C:HIS248 3.3 46.5 1.0
NH1 C:ARG293 3.4 42.4 1.0
CG C:ARG293 3.4 40.0 1.0
CZ C:ARG243 3.6 42.3 1.0
CD C:ARG293 3.7 40.9 1.0
CA C:ARG293 3.7 38.8 1.0
O C:ARG293 3.8 37.4 1.0
OH C:TYR257 3.9 39.9 1.0
C C:ARG293 4.1 38.6 1.0
CH2 C:TRP304 4.1 43.0 1.0
NE2 C:HIS248 4.2 47.7 1.0
CZ2 C:TRP304 4.3 42.5 1.0
CZ C:ARG293 4.4 42.3 1.0
CG C:HIS248 4.4 45.0 1.0
NE C:ARG293 4.5 42.7 1.0
O C:HOH526 4.7 32.7 1.0
CZ3 C:TRP304 4.7 43.3 1.0
CZ C:TYR257 4.9 38.1 1.0
CD2 C:HIS248 4.9 45.2 1.0
NE C:ARG243 4.9 42.2 1.0
CE1 C:TYR257 4.9 38.6 1.0

Chlorine binding site 4 out of 4 in 5trx

Go back to Chlorine Binding Sites List in 5trx
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl402

b:36.7
occ:1.00
NH1 D:ARG293 3.2 43.7 1.0
CE1 D:HIS248 3.2 36.6 1.0
CB D:ARG293 3.4 37.8 1.0
NH1 D:ARG243 3.4 40.5 1.0
ND1 D:HIS248 3.5 35.4 1.0
NH2 D:ARG243 3.5 36.2 1.0
CG D:ARG293 3.6 39.6 1.0
O D:ARG293 3.7 30.8 1.0
CD D:ARG293 3.8 41.5 1.0
CA D:ARG293 3.8 35.7 1.0
CZ D:ARG243 3.9 39.1 1.0
OH D:TYR257 4.0 35.2 1.0
CH2 D:TRP304 4.1 44.6 1.0
C D:ARG293 4.1 35.5 1.0
CZ2 D:TRP304 4.2 43.4 1.0
CZ D:ARG293 4.3 44.0 1.0
NE2 D:HIS248 4.4 36.0 1.0
O D:HOH506 4.5 30.7 1.0
NE D:ARG293 4.5 43.0 1.0
CZ3 D:TRP304 4.7 44.1 1.0
CG D:HIS248 4.7 33.9 1.0
CE2 D:TRP304 4.9 41.8 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: Fri Jul 26 17:40:00 2024

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