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Strontium in PDB 6nhh: Rhodobacter Sphaeroides BC1 with Azoxystrobin

Enzymatic activity of Rhodobacter Sphaeroides BC1 with Azoxystrobin

All present enzymatic activity of Rhodobacter Sphaeroides BC1 with Azoxystrobin:
1.10.2.2;

Protein crystallography data

The structure of Rhodobacter Sphaeroides BC1 with Azoxystrobin, PDB code: 6nhh was solved by D.Xia, F.Zhou, C.A.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.29 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.309, 154.655, 100.939, 90.00, 95.36, 90.00
R / Rfree (%) 26.4 / 28.2

Other elements in 6nhh:

The structure of Rhodobacter Sphaeroides BC1 with Azoxystrobin also contains other interesting chemical elements:

Iron (Fe) 10 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Rhodobacter Sphaeroides BC1 with Azoxystrobin (pdb code 6nhh). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 3 binding sites of Strontium where determined in the Rhodobacter Sphaeroides BC1 with Azoxystrobin, PDB code: 6nhh:
Jump to Strontium binding site number: 1; 2; 3;

Strontium binding site 1 out of 3 in 6nhh

Go back to Strontium Binding Sites List in 6nhh
Strontium binding site 1 out of 3 in the Rhodobacter Sphaeroides BC1 with Azoxystrobin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Rhodobacter Sphaeroides BC1 with Azoxystrobin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1006

b:0.9
occ:1.00
HE22 A:GLN316 3.9 0.1 1.0
HE1 A:TRP313 4.1 0.3 1.0
HB2 A:ASP311 4.4 95.8 1.0
NE2 A:GLN316 4.7 92.5 1.0
NE1 A:TRP313 4.8 96.1 1.0
HD1 A:TRP313 5.0 0.5 1.0
O A:ASP311 5.0 80.4 1.0

Strontium binding site 2 out of 3 in 6nhh

Go back to Strontium Binding Sites List in 6nhh
Strontium binding site 2 out of 3 in the Rhodobacter Sphaeroides BC1 with Azoxystrobin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Rhodobacter Sphaeroides BC1 with Azoxystrobin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr303

b:0.1
occ:1.00
OE1 B:GLU14 2.5 69.0 1.0
OE1 B:GLU129 2.6 63.7 1.0
OD1 B:ASP8 2.6 83.1 1.0
OE2 B:GLU14 2.6 67.5 1.0
OE2 B:GLU129 2.7 62.8 1.0
O B:VAL9 2.7 71.8 1.0
CD B:GLU129 2.9 63.0 1.0
CD B:GLU14 2.9 67.6 1.0
CG B:ASP8 3.4 83.5 1.0
C B:VAL9 3.7 72.7 1.0
H B:VAL9 3.8 89.0 1.0
OD2 B:ASP8 3.8 84.6 1.0
HA B:PRO10 3.9 90.9 1.0
H B:PHE11 3.9 82.9 1.0
N B:VAL9 4.0 74.1 1.0
HA B:ASP8 4.2 96.1 1.0
CG B:GLU129 4.2 62.6 1.0
HZ B:PHE110 4.3 76.3 1.0
HG2 B:GLU129 4.3 74.8 1.0
HD2 B:PHE11 4.3 75.0 1.0
C B:ASP8 4.3 78.4 1.0
CG B:GLU14 4.4 66.6 1.0
CA B:VAL9 4.5 71.6 1.0
N B:PRO10 4.5 75.7 1.0
CA B:ASP8 4.6 80.0 1.0
CB B:ASP8 4.6 82.3 1.0
CA B:PRO10 4.6 75.7 1.0
N B:PHE11 4.7 69.0 1.0
HG2 B:GLU14 4.7 80.0 1.0
HG3 B:GLU129 4.7 74.8 1.0
HB2 B:PHE11 4.8 77.1 1.0
HE2 B:PHE110 4.8 75.4 1.0
HB B:VAL9 4.9 83.3 1.0
HG3 B:GLU14 4.9 80.0 1.0
HB3 B:GLU14 4.9 80.2 1.0
HB3 B:GLU129 4.9 75.2 1.0
HB2 B:GLU14 5.0 80.2 1.0
O B:ASP8 5.0 81.3 1.0
HB2 B:ASP8 5.0 98.8 1.0

Strontium binding site 3 out of 3 in 6nhh

Go back to Strontium Binding Sites List in 6nhh
Strontium binding site 3 out of 3 in the Rhodobacter Sphaeroides BC1 with Azoxystrobin


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Rhodobacter Sphaeroides BC1 with Azoxystrobin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr304

b:0.8
occ:1.00
OE1 F:GLU129 2.6 78.3 1.0
OE1 F:GLU14 2.6 87.5 1.0
OE2 F:GLU14 2.6 86.9 1.0
O F:VAL9 2.6 91.5 1.0
OD1 F:ASP8 2.7 0.4 1.0
OE2 F:GLU129 2.7 77.8 1.0
CD F:GLU129 2.9 75.9 1.0
CD F:GLU14 2.9 85.8 1.0
CG F:ASP8 3.5 0.7 1.0
C F:VAL9 3.6 93.6 1.0
H F:VAL9 3.8 0.1 1.0
HA F:PRO10 3.8 0.7 1.0
H F:PHE11 3.8 0.6 1.0
OD2 F:ASP8 3.9 0.8 1.0
N F:VAL9 4.0 99.2 1.0
HA F:ASP8 4.2 0.0 1.0
CG F:GLU129 4.2 70.8 1.0
HG2 F:GLU129 4.3 85.0 1.0
HD2 F:PHE11 4.4 93.0 1.0
C F:ASP8 4.4 0.7 1.0
HZ F:PHE110 4.4 77.2 1.0
CG F:GLU14 4.4 82.4 1.0
N F:PRO10 4.4 95.2 1.0
CA F:VAL9 4.4 95.1 1.0
CA F:PRO10 4.5 93.8 1.0
CA F:ASP8 4.6 0.5 1.0
N F:PHE11 4.6 86.2 1.0
CB F:ASP8 4.6 0.6 1.0
HG2 F:GLU14 4.7 98.9 1.0
HG3 F:GLU129 4.7 85.0 1.0
HB2 F:PHE11 4.8 95.9 1.0
HE2 F:PHE110 4.8 75.7 1.0
HB F:VAL9 4.9 0.8 1.0
HG3 F:GLU14 4.9 98.9 1.0
HB3 F:GLU129 5.0 79.2 1.0
HB2 F:GLU14 5.0 95.6 1.0

Reference:

L.Esser, F.Zhou, C.A.Yu, D.Xia. Crystal Structure of Bacterial CYTOCHROMEBC1IN Complex with Azoxystrobin Reveals A Conformational Switch of the Rieske Iron-Sulfur Protein Subunit. J.Biol.Chem. V. 294 12007 2019.
ISSN: ESSN 1083-351X
PubMed: 31182483
DOI: 10.1074/JBC.RA119.008381
Page generated: Wed Dec 16 02:25:00 2020

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