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Strontium in PDB 5kkz: Rhodobacter Sphaeroides BC1 with Famoxadone

Enzymatic activity of Rhodobacter Sphaeroides BC1 with Famoxadone

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

Protein crystallography data

The structure of Rhodobacter Sphaeroides BC1 with Famoxadone, PDB code: 5kkz was solved by D.Xia, L.Esser, F.Zhou, W.K.Tang, C.A.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 2.97
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 120.773, 128.277, 128.283, 63.92, 88.63, 63.38
R / Rfree (%) 21.5 / 25.8

Other elements in 5kkz:

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

Iron (Fe) 20 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Rhodobacter Sphaeroides BC1 with Famoxadone (pdb code 5kkz). 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 Famoxadone, PDB code: 5kkz:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 5kkz

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Strontium binding site 1 out of 6 in the Rhodobacter Sphaeroides BC1 with Famoxadone


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 Famoxadone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1005

b:0.9
occ:1.00
 HE1 A:TRP313 4.2 99.2 1.0
OE1 A:GLN316 4.4 69.0 1.0
HB2 A:ASP311 4.6 87.9 1.0
HD1 A:TRP313 4.8 97.8 1.0
NE1 A:TRP313 4.9 82.5 1.0
O A:ASP311 4.9 68.5 1.0
HE22 A:GLN316 4.9 83.0 1.0

Strontium binding site 2 out of 6 in 5kkz

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


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

b:96.5
occ:1.00
 OD1 B:ASP8 2.5 0.7 1.0
O B:VAL9 2.7 69.5 1.0
OE2 B:GLU129 2.7 78.1 1.0
OE2 B:GLU14 2.8 81.7 1.0
OE1 B:GLU14 2.8 84.6 1.0
CD B:GLU14 3.1 79.3 1.0
HA B:PRO10 3.6 86.5 1.0
C B:VAL9 3.7 70.8 1.0
CG B:ASP8 3.8 1.0 1.0
CD B:GLU129 3.8 77.8 1.0
HG2 B:GLU129 4.0 88.8 1.0
H B:PHE11 4.0 81.3 1.0
H B:VAL9 4.2 84.6 1.0
N B:VAL9 4.2 71.0 1.0
HA B:ASP8 4.2 0.8 1.0
HZ B:PHE110 4.3 0.2 1.0
CG B:GLU129 4.4 73.9 1.0
OD2 B:ASP8 4.4 0.5 1.0
HD2 B:PHE11 4.4 83.1 1.0
HG3 B:GLU129 4.4 88.8 1.0
C B:ASP8 4.5 0.4 1.0
CA B:PRO10 4.5 72.6 1.0
N B:PRO10 4.5 72.4 1.0
CG B:GLU14 4.6 70.7 1.0
CA B:VAL9 4.6 70.6 1.0
HE2 B:PHE110 4.7 0.6 1.0
CA B:ASP8 4.7 0.2 1.0
OE1 B:GLU129 4.8 78.6 1.0
N B:PHE11 4.8 68.2 1.0
CB B:ASP8 4.8 0.9 1.0
HG2 B:GLU14 4.9 85.0 1.0
O B:ASN123 4.9 76.9 1.0
CZ B:PHE110 5.0 85.9 1.0
O B:ASP8 5.0 0.8 1.0

Strontium binding site 3 out of 6 in 5kkz

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


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 Famoxadone within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr1002

b:0.2
occ:1.00
 OD1 F:ASP8 2.5 0.1 1.0
OE2 F:GLU129 2.6 85.1 1.0
OE1 F:GLU14 2.8 0.4 1.0
O F:VAL9 2.8 81.5 1.0
OE2 F:GLU14 2.9 0.3 1.0
CD F:GLU14 3.2 0.5 1.0
CG F:ASP8 3.7 0.1 1.0
CD F:GLU129 3.8 82.7 1.0
C F:VAL9 3.9 83.8 1.0
HA F:PRO10 3.9 84.5 1.0
HG2 F:GLU129 4.0 96.7 1.0
HZ F:PHE110 4.1 91.0 1.0
H F:PHE11 4.2 90.5 1.0
HA F:ASP8 4.2 0.2 1.0
H F:VAL9 4.2 0.9 1.0
OD2 F:ASP8 4.3 0.5 1.0
N F:VAL9 4.3 94.0 1.0
CG F:GLU129 4.4 80.5 1.0
HE2 F:PHE110 4.4 91.0 1.0
C F:ASP8 4.5 0.6 1.0
HG3 F:GLU129 4.5 96.7 1.0
CG F:GLU14 4.6 95.7 1.0
CA F:PRO10 4.7 70.3 1.0
CA F:ASP8 4.7 0.4 1.0
O F:ASN123 4.7 75.7 1.0
HD2 F:PHE11 4.7 77.4 1.0
OE1 F:GLU129 4.7 81.5 1.0
N F:PRO10 4.8 72.7 1.0
CA F:VAL9 4.8 87.9 1.0
CZ F:PHE110 4.8 75.7 1.0
CB F:ASP8 4.8 0.2 1.0
HG2 F:GLU14 4.9 0.9 1.0
CE2 F:PHE110 5.0 75.7 1.0
HB3 F:GLU14 5.0 0.3 1.0
N F:PHE11 5.0 75.3 1.0

Strontium binding site 4 out of 6 in 5kkz

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


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 Famoxadone within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Sr1005

b:0.0
occ:1.00
 HE1 E:TRP313 3.5 91.4 1.0
HE1 K:TRP313 3.7 63.4 1.0
OE1 K:GLN316 4.1 68.8 1.0
NE1 E:TRP313 4.2 76.0 1.0
OE1 E:GLN316 4.2 74.0 1.0
HE22 K:GLN316 4.2 85.7 1.0
NE1 K:TRP313 4.4 52.7 1.0
HD1 E:TRP313 4.5 92.2 1.0
HE22 E:GLN316 4.5 96.0 1.0
HD1 K:TRP313 4.6 67.2 1.0
CD1 E:TRP313 4.7 76.7 1.0
HB2 K:ASP311 4.8 82.0 1.0
O K:ASP311 4.8 69.5 1.0
HB2 E:ASP311 4.8 0.8 1.0
O E:ASP311 4.8 91.7 1.0
NE2 K:GLN316 4.9 71.3 1.0
CD1 K:TRP313 4.9 55.9 1.0
CD K:GLN316 4.9 68.1 1.0

Strontium binding site 5 out of 6 in 5kkz

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


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

b:88.1
occ:1.00
 OD1 L:ASP8 2.5 89.8 1.0
OE2 L:GLU129 2.6 67.1 1.0
OE1 L:GLU14 2.6 80.2 1.0
O L:VAL9 2.7 61.3 1.0
OE2 L:GLU14 3.1 77.5 1.0
CD L:GLU14 3.2 75.7 1.0
HA L:PRO10 3.5 47.7 1.0
CD L:GLU129 3.7 64.2 1.0
C L:VAL9 3.7 66.0 1.0
CG L:ASP8 3.7 88.9 1.0
H L:PHE11 3.9 63.9 1.0
HG2 L:GLU129 3.9 76.8 1.0
HZ L:PHE110 4.2 72.9 1.0
CG L:GLU129 4.3 63.9 1.0
N L:VAL9 4.3 75.4 1.0
H L:VAL9 4.3 90.6 1.0
HG3 L:GLU129 4.3 76.8 1.0
CA L:PRO10 4.4 39.7 1.0
OD2 L:ASP8 4.4 91.6 1.0
HA L:ASP8 4.4 99.4 1.0
HE2 L:PHE110 4.5 75.5 1.0
N L:PRO10 4.5 41.2 1.0
C L:ASP8 4.5 81.3 1.0
HD2 L:PHE11 4.5 60.1 1.0
CA L:VAL9 4.7 71.1 1.0
OE1 L:GLU129 4.7 62.8 1.0
CG L:GLU14 4.7 67.1 1.0
N L:PHE11 4.7 53.2 1.0
O L:ASN123 4.8 56.9 1.0
CA L:ASP8 4.8 82.8 1.0
CB L:ASP8 4.8 85.6 1.0
CZ L:PHE110 4.9 60.7 1.0
O L:ASP8 5.0 83.7 1.0
HB2 L:GLU14 5.0 73.0 1.0

Strontium binding site 6 out of 6 in 5kkz

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


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 Famoxadone within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Sr1002

b:0.6
occ:1.00
 O P:VAL9 2.6 94.1 1.0
OD1 P:ASP8 2.7 0.6 1.0
OE1 P:GLU14 2.7 0.4 1.0
OE2 P:GLU14 2.8 0.4 1.0
OE2 P:GLU129 2.8 96.5 1.0
CD P:GLU14 3.1 0.2 1.0
HA P:PRO10 3.6 0.4 1.0
C P:VAL9 3.7 95.8 1.0
CG P:ASP8 3.9 0.0 1.0
CD P:GLU129 3.9 93.0 1.0
H P:PHE11 3.9 0.2 1.0
HG2 P:GLU129 4.1 0.2 1.0
H P:VAL9 4.3 0.6 1.0
N P:VAL9 4.3 0.4 1.0
HD2 P:PHE11 4.4 0.5 1.0
HA P:ASP8 4.4 0.2 1.0
CG P:GLU129 4.4 90.9 1.0
CA P:PRO10 4.4 83.6 1.0
HZ P:PHE110 4.4 0.0 1.0
HG3 P:GLU129 4.5 0.2 1.0
OD2 P:ASP8 4.5 0.2 1.0
N P:PRO10 4.5 87.9 1.0
CG P:GLU14 4.6 99.4 1.0
C P:ASP8 4.6 0.5 1.0
CA P:VAL9 4.7 0.9 1.0
N P:PHE11 4.7 88.4 1.0
HE2 P:PHE110 4.8 0.4 1.0
HG2 P:GLU14 4.8 0.5 1.0
CA P:ASP8 4.9 0.3 1.0
OE1 P:GLU129 4.9 90.5 1.0
O P:ASN123 5.0 94.4 1.0
CB P:ASP8 5.0 0.6 1.0

Reference:

L.Esser, F.Zhou, Y.Zhou, Y.Xiao, W.K.Tang, C.A.Yu, Z.Qin, D.Xia. Hydrogen Bonding to the Substrate Is Not Required For Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. J.Biol.Chem. V. 291 25019 2016.
ISSN: ESSN 1083-351X
PubMed: 27758861
DOI: 10.1074/JBC.M116.744391
Page generated: Fri Oct 11 06:16:47 2024

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