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Strontium in PDB 6nin: Rhodobacter Sphaeroides BC1 with Stigmatellin A

Enzymatic activity of Rhodobacter Sphaeroides BC1 with Stigmatellin A

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

Protein crystallography data

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

Resolution Low / High (Å) 28.91 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 356.661, 145.752, 162.223, 90.00, 104.97, 90.00
R / Rfree (%) 24.9 / 28

Other elements in 6nin:

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

Iron (Fe) 30 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Rhodobacter Sphaeroides BC1 with Stigmatellin A (pdb code 6nin). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 6 binding sites of Strontium where determined in the Rhodobacter Sphaeroides BC1 with Stigmatellin A, PDB code: 6nin:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 6nin

Go back to Strontium Binding Sites List in 6nin
Strontium binding site 1 out of 6 in the Rhodobacter Sphaeroides BC1 with Stigmatellin A


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 Stigmatellin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1002

b:0.5
occ:1.00
 OD1 B:ASP8 2.6 0.5 1.0
OE2 B:GLU129 2.6 0.0 1.0
OE1 B:GLU14 2.7 0.3 1.0
OE2 B:GLU14 2.7 0.5 1.0
O B:VAL9 2.7 0.5 1.0
CD B:GLU14 3.0 0.8 1.0
CD B:GLU129 3.7 0.8 1.0
CG B:ASP8 3.8 0.4 1.0
C B:VAL9 3.9 0.1 1.0
HG2 B:GLU129 3.9 0.3 1.0
HA B:PRO10 4.0 0.6 1.0
HZ B:PHE110 4.1 0.3 1.0
H B:PHE11 4.1 0.7 1.0
H B:VAL9 4.2 0.6 1.0
HA B:ASP8 4.2 0.4 1.0
CG B:GLU129 4.3 0.8 1.0
N B:VAL9 4.3 0.4 1.0
HD2 B:PHE11 4.3 0.8 1.0
HG3 B:GLU129 4.3 0.3 1.0
OD2 B:ASP8 4.4 0.9 1.0
CG B:GLU14 4.4 0.1 1.0
C B:ASP8 4.6 0.8 1.0
HG2 B:GLU14 4.7 0.4 1.0
HE2 B:PHE110 4.7 0.7 1.0
CA B:VAL9 4.7 0.8 1.0
OE1 B:GLU129 4.7 0.4 1.0
CA B:PRO10 4.7 0.2 1.0
CA B:ASP8 4.8 0.3 1.0
N B:PRO10 4.8 0.1 1.0
CZ B:PHE110 4.8 0.0 1.0
HB3 B:GLU14 4.9 0.4 1.0
CB B:ASP8 4.9 0.7 1.0
N B:PHE11 4.9 0.2 1.0
HB2 B:GLU14 5.0 0.4 1.0
HB B:VAL9 5.0 0.6 1.0

Strontium binding site 2 out of 6 in 6nin

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Strontium binding site 2 out of 6 in the Rhodobacter Sphaeroides BC1 with Stigmatellin A


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 Stigmatellin A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr1003

b:1.0
occ:1.00
 OD1 F:ASP8 2.6 0.2 1.0
OE2 F:GLU129 2.6 0.3 1.0
OE1 F:GLU14 2.7 0.9 1.0
OE2 F:GLU14 2.7 0.4 1.0
O F:VAL9 2.7 0.5 1.0
CD F:GLU14 3.0 0.1 1.0
CD F:GLU129 3.7 0.9 1.0
CG F:ASP8 3.8 0.9 1.0
HZ F:PHE110 3.8 0.4 1.0
C F:VAL9 3.9 0.3 1.0
HG2 F:GLU129 3.9 0.5 1.0
HA F:PRO10 4.0 0.0 1.0
H F:PHE11 4.1 0.1 1.0
H F:VAL9 4.2 0.2 1.0
HA F:ASP8 4.3 1.0 1.0
CG F:GLU129 4.3 0.3 1.0
N F:VAL9 4.3 0.8 1.0
HD2 F:PHE11 4.3 0.6 1.0
HE2 F:PHE110 4.4 0.8 1.0
HG3 F:GLU129 4.4 0.5 1.0
OD2 F:ASP8 4.4 0.8 1.0
CG F:GLU14 4.5 0.0 1.0
O F:ASN123 4.5 0.3 1.0
CZ F:PHE110 4.5 1.0 1.0
C F:ASP8 4.6 0.6 1.0
OE1 F:GLU129 4.7 0.8 1.0
CA F:PRO10 4.7 0.6 1.0
CA F:VAL9 4.8 0.1 1.0
HG2 F:GLU14 4.8 0.1 1.0
CA F:ASP8 4.8 0.6 1.0
N F:PRO10 4.8 0.5 1.0
CE2 F:PHE110 4.8 0.8 1.0
CB F:ASP8 4.9 0.9 1.0
N F:PHE11 4.9 0.6 1.0
HB3 F:GLU14 5.0 0.9 1.0

Strontium binding site 3 out of 6 in 6nin

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Strontium binding site 3 out of 6 in the Rhodobacter Sphaeroides BC1 with Stigmatellin A


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 Stigmatellin A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Sr1002

b:0.1
occ:1.00
 OD1 L:ASP8 2.5 0.8 1.0
O L:VAL9 2.6 0.5 1.0
OE2 L:GLU14 2.7 0.8 1.0
OE1 L:GLU14 2.7 0.1 1.0
OE2 L:GLU129 2.7 0.9 1.0
CD L:GLU14 3.0 0.9 1.0
HA L:PRO10 3.7 1.0 1.0
CG L:ASP8 3.8 0.7 1.0
C L:VAL9 3.8 0.6 1.0
CD L:GLU129 3.8 0.3 1.0
HG2 L:GLU129 3.9 0.7 1.0
H L:PHE11 4.1 0.5 1.0
HZ L:PHE110 4.1 0.2 1.0
H L:VAL9 4.3 0.7 1.0
CG L:GLU129 4.3 0.3 1.0
N L:VAL9 4.3 0.5 1.0
HA L:ASP8 4.4 0.3 1.0
OD2 L:ASP8 4.4 0.2 1.0
HG3 L:GLU129 4.4 0.7 1.0
CG L:GLU14 4.4 0.9 1.0
CA L:PRO10 4.5 0.4 1.0
C L:ASP8 4.5 0.3 1.0
HD2 L:PHE11 4.5 0.8 1.0
N L:PRO10 4.6 0.0 1.0
CA L:VAL9 4.7 0.3 1.0
HG2 L:GLU14 4.7 0.2 1.0
CA L:ASP8 4.8 0.7 1.0
HE2 L:PHE110 4.8 0.2 1.0
N L:PHE11 4.8 0.4 1.0
OE1 L:GLU129 4.9 0.6 1.0
CB L:ASP8 4.9 0.9 1.0
CZ L:PHE110 4.9 0.6 1.0
HB3 L:GLU14 4.9 0.8 1.0
O L:ASN123 5.0 0.9 1.0

Strontium binding site 4 out of 6 in 6nin

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Strontium binding site 4 out of 6 in the Rhodobacter Sphaeroides BC1 with Stigmatellin A


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Rhodobacter Sphaeroides BC1 with Stigmatellin A within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Sr1003

b:0.4
occ:1.00
 OD1 P:ASP8 2.6 0.9 1.0
OE1 P:GLU14 2.6 0.8 1.0
OE2 P:GLU129 2.7 0.9 1.0
OE2 P:GLU14 2.7 0.5 1.0
O P:VAL9 2.7 1.0 1.0
CD P:GLU14 3.0 0.2 1.0
HA P:PRO10 3.8 0.4 1.0
CG P:ASP8 3.8 0.5 1.0
CD P:GLU129 3.8 0.2 1.0
C P:VAL9 3.9 0.6 1.0
HG2 P:GLU129 4.0 0.7 1.0
H P:PHE11 4.1 0.4 1.0
H P:VAL9 4.4 0.1 1.0
HZ P:PHE110 4.4 0.1 1.0
OD2 P:ASP8 4.4 0.1 1.0
N P:VAL9 4.4 0.2 1.0
CG P:GLU129 4.4 0.9 1.0
CG P:GLU14 4.4 0.3 1.0
HA P:ASP8 4.4 0.1 1.0
HE2 P:PHE110 4.5 1.0 1.0
HG3 P:GLU129 4.6 0.7 1.0
CA P:PRO10 4.6 1.0 1.0
C P:ASP8 4.6 0.0 1.0
HD2 P:PHE11 4.6 0.8 1.0
N P:PRO10 4.7 0.2 1.0
O P:ASN123 4.7 0.2 1.0
HG2 P:GLU14 4.7 0.6 1.0
CA P:VAL9 4.8 0.7 1.0
HB3 P:GLU14 4.8 0.2 1.0
OE1 P:GLU129 4.9 0.8 1.0
CA P:ASP8 4.9 0.5 1.0
N P:PHE11 4.9 0.4 1.0
CB P:ASP8 4.9 0.4 1.0
HB2 P:GLU14 4.9 0.2 1.0
CZ P:PHE110 5.0 0.3 1.0
HG3 P:GLU14 5.0 0.6 1.0

Strontium binding site 5 out of 6 in 6nin

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Strontium binding site 5 out of 6 in the Rhodobacter Sphaeroides BC1 with Stigmatellin A


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Rhodobacter Sphaeroides BC1 with Stigmatellin A within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Sr1002

b:0.1
occ:1.00
 OD1 T:ASP8 2.6 0.8 1.0
O T:VAL9 2.6 0.8 1.0
OE2 T:GLU129 2.6 0.3 1.0
OE1 T:GLU14 2.7 0.9 1.0
OE2 T:GLU14 2.7 0.2 1.0
CD T:GLU14 3.0 0.8 1.0
CD T:GLU129 3.7 0.3 1.0
C T:VAL9 3.7 0.0 1.0
CG T:ASP8 3.8 0.0 1.0
HA T:PRO10 3.8 0.9 1.0
HG2 T:GLU129 3.9 0.9 1.0
H T:PHE11 4.1 0.7 1.0
H T:VAL9 4.1 0.2 1.0
N T:VAL9 4.2 1.0 1.0
HZ T:PHE110 4.2 0.4 1.0
CG T:GLU129 4.2 1.0 1.0
HA T:ASP8 4.2 0.5 1.0
HG3 T:GLU129 4.3 0.9 1.0
CG T:GLU14 4.4 0.2 1.0
HD2 T:PHE11 4.4 0.9 1.0
C T:ASP8 4.5 0.9 1.0
OD2 T:ASP8 4.5 0.2 1.0
HE2 T:PHE110 4.6 0.1 1.0
CA T:VAL9 4.6 0.9 1.0
CA T:PRO10 4.6 0.0 1.0
N T:PRO10 4.6 0.0 1.0
HG2 T:GLU14 4.7 0.1 1.0
CA T:ASP8 4.7 0.0 1.0
OE1 T:GLU129 4.7 0.1 1.0
O T:ASN123 4.8 0.3 1.0
CB T:ASP8 4.9 0.9 1.0
CZ T:PHE110 4.9 0.8 1.0
HB3 T:GLU14 4.9 0.9 1.0
N T:PHE11 4.9 0.8 1.0
HB T:VAL9 4.9 0.1 1.0
HB2 T:GLU14 5.0 0.9 1.0

Strontium binding site 6 out of 6 in 6nin

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Strontium binding site 6 out of 6 in the Rhodobacter Sphaeroides BC1 with Stigmatellin A


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Rhodobacter Sphaeroides BC1 with Stigmatellin A within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Sr1002

b:0.3
occ:1.00
 OD1 X:ASP8 2.6 0.7 1.0
OE1 X:GLU14 2.6 0.7 1.0
OE2 X:GLU14 2.6 1.0 1.0
O X:VAL9 2.6 0.0 1.0
OE2 X:GLU129 2.7 0.6 1.0
CD X:GLU14 2.9 0.5 1.0
CD X:GLU129 3.8 0.2 1.0
C X:VAL9 3.8 0.4 1.0
CG X:ASP8 3.8 0.1 1.0
HA X:PRO10 3.8 0.9 1.0
HZ X:PHE110 3.9 0.1 1.0
H X:PHE11 4.0 0.5 1.0
HG2 X:GLU129 4.1 0.3 1.0
H X:VAL9 4.2 0.7 1.0
HA X:ASP8 4.2 0.4 1.0
N X:VAL9 4.3 0.2 1.0
HD2 X:PHE11 4.4 0.5 1.0
CG X:GLU129 4.4 0.3 1.0
CG X:GLU14 4.4 0.5 1.0
OD2 X:ASP8 4.5 0.0 1.0
HG3 X:GLU129 4.5 0.3 1.0
HE2 X:PHE110 4.5 0.6 1.0
C X:ASP8 4.5 0.4 1.0
CA X:PRO10 4.6 0.1 1.0
CZ X:PHE110 4.6 0.4 1.0
N X:PRO10 4.7 0.6 1.0
CA X:VAL9 4.7 0.8 1.0
HG2 X:GLU14 4.7 0.8 1.0
O X:ASN123 4.7 0.5 1.0
CA X:ASP8 4.7 0.6 1.0
OE1 X:GLU129 4.8 0.6 1.0
N X:PHE11 4.8 0.2 1.0
CB X:ASP8 4.9 0.9 1.0
HG3 X:GLU14 4.9 0.8 1.0
CE2 X:PHE110 5.0 0.1 1.0
HB X:VAL9 5.0 0.5 1.0
HB3 X:GLU14 5.0 0.2 1.0
HB2 X:GLU14 5.0 0.2 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: Fri Oct 11 06:48:16 2024

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