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Strontium in PDB 5kli: Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin

Enzymatic activity of Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin

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

Protein crystallography data

The structure of Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin, PDB code: 5kli 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) 37.74 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 118.861, 126.929, 127.891, 64.64, 87.69, 61.80
R / Rfree (%) 21.1 / 24.3

Other elements in 5kli:

The structure of Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin 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 Stigmatellin and Antimycin (pdb code 5kli). 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 and Antimycin, PDB code: 5kli:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 5kli

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Strontium binding site 1 out of 6 in the Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin


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

b:0.5
occ:1.00
 HE1 A:TRP313 4.1 0.6 1.0
HE22 A:GLN316 4.2 0.2 1.0
NE1 A:TRP313 4.8 93.7 1.0
HB3 A:ASP311 4.9 0.9 1.0
O A:ASP311 5.0 98.4 1.0
NE2 A:GLN316 5.0 91.8 1.0

Strontium binding site 2 out of 6 in 5kli

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


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

b:0.5
occ:1.00
 OD1 B:ASP8 2.6 0.8 1.0
OE1 B:GLU14 2.6 99.6 1.0
OE2 B:GLU129 2.6 95.4 1.0
O B:VAL9 2.7 0.8 1.0
OE2 B:GLU14 2.8 96.7 1.0
CD B:GLU14 3.0 96.8 1.0
CD B:GLU129 3.7 94.3 1.0
HG2 B:GLU129 3.7 0.6 1.0
CG B:ASP8 3.8 0.7 1.0
HA B:PRO10 3.8 0.0 1.0
C B:VAL9 3.9 0.1 1.0
H B:PHE11 4.1 0.1 1.0
CG B:GLU129 4.1 92.1 1.0
HZ B:PHE110 4.1 0.5 1.0
HG3 B:GLU129 4.2 0.6 1.0
H B:VAL9 4.3 0.0 1.0
HA B:ASP8 4.3 0.7 1.0
N B:VAL9 4.3 0.6 1.0
OD2 B:ASP8 4.4 0.4 1.0
CG B:GLU14 4.5 93.5 1.0
HD2 B:PHE11 4.6 92.8 1.0
C B:ASP8 4.6 0.3 1.0
CA B:PRO10 4.6 0.8 1.0
HE2 B:PHE110 4.6 0.9 1.0
N B:PRO10 4.7 0.3 1.0
OE1 B:GLU129 4.7 94.5 1.0
CA B:VAL9 4.8 0.1 1.0
CA B:ASP8 4.8 0.5 1.0
O B:ASN123 4.8 86.7 1.0
HG2 B:GLU14 4.8 0.2 1.0
N B:PHE11 4.8 90.0 1.0
CZ B:PHE110 4.9 98.7 1.0
CB B:ASP8 4.9 0.6 1.0
HB2 B:GLU14 4.9 0.3 1.0
HB3 B:GLU14 5.0 0.3 1.0

Strontium binding site 3 out of 6 in 5kli

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


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

b:0.7
occ:1.00
 OD1 F:ASP8 2.5 0.9 1.0
OE2 F:GLU129 2.6 92.1 1.0
OE1 F:GLU14 2.7 0.3 1.0
O F:VAL9 2.7 96.5 1.0
OE2 F:GLU14 2.8 0.1 1.0
CD F:GLU14 3.0 0.3 1.0
HA F:PRO10 3.7 0.5 1.0
CG F:ASP8 3.7 0.5 1.0
C F:VAL9 3.8 97.8 1.0
CD F:GLU129 3.8 88.0 1.0
HG2 F:GLU129 3.9 0.6 1.0
H F:PHE11 4.1 0.9 1.0
H F:VAL9 4.3 0.6 1.0
N F:VAL9 4.3 0.9 1.0
HA F:ASP8 4.3 0.4 1.0
CG F:GLU129 4.3 83.8 1.0
OD2 F:ASP8 4.4 0.6 1.0
CG F:GLU14 4.4 0.8 1.0
HZ F:PHE110 4.4 0.8 1.0
HG3 F:GLU129 4.5 0.6 1.0
C F:ASP8 4.5 0.4 1.0
CA F:PRO10 4.5 94.5 1.0
N F:PRO10 4.6 95.9 1.0
HD2 F:PHE11 4.7 96.7 1.0
HG2 F:GLU14 4.7 0.9 1.0
CA F:VAL9 4.7 0.1 1.0
HE2 F:PHE110 4.7 0.3 1.0
CA F:ASP8 4.7 0.6 1.0
O F:ASN123 4.8 0.4 1.0
HB3 F:GLU14 4.8 0.8 1.0
OE1 F:GLU129 4.8 87.4 1.0
CB F:ASP8 4.8 0.1 1.0
N F:PHE11 4.9 89.8 1.0
HB2 F:GLU14 4.9 0.8 1.0
O F:ASP8 5.0 0.2 1.0
CB F:GLU14 5.0 0.1 1.0

Strontium binding site 4 out of 6 in 5kli

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


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

b:0.4
occ:1.00
 O K:ASP311 3.4 77.7 1.0
O E:ASP311 3.6 90.0 1.0
HB3 E:TRP313 3.9 0.5 1.0
HB3 K:ASP311 4.1 0.3 1.0
HE22 E:GLN316 4.5 89.0 1.0
HB3 E:ASP311 4.5 0.1 1.0
C K:ASP311 4.5 76.3 1.0
HB3 K:TRP313 4.5 0.9 1.0
C E:ASP311 4.7 89.2 1.0
HD1 E:TRP313 4.7 0.7 1.0
HD1 K:TRP313 4.7 0.0 1.0
OE1 E:GLN316 4.8 74.4 1.0
H E:TRP313 4.9 95.5 1.0
CB E:TRP313 4.9 87.0 1.0
HA K:VAL312 4.9 86.3 1.0
CB K:ASP311 5.0 88.5 1.0
NE2 E:GLN316 5.0 74.1 1.0
H K:TRP313 5.0 89.7 1.0

Strontium binding site 5 out of 6 in 5kli

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


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

b:0.5
occ:1.00
 OE1 L:GLU14 2.6 86.1 1.0
O L:VAL9 2.6 89.2 1.0
OE2 L:GLU129 2.6 82.1 1.0
OD1 L:ASP8 2.7 0.5 1.0
OE2 L:GLU14 2.8 86.0 1.0
CD L:GLU14 3.0 84.5 1.0
HA L:PRO10 3.7 97.4 1.0
CD L:GLU129 3.7 79.6 1.0
C L:VAL9 3.7 90.5 1.0
HG2 L:GLU129 3.8 91.3 1.0
CG L:ASP8 3.9 0.7 1.0
H L:PHE11 3.9 93.6 1.0
CG L:GLU129 4.2 76.0 1.0
H L:VAL9 4.2 0.1 1.0
HG3 L:GLU129 4.3 91.3 1.0
N L:VAL9 4.3 0.0 1.0
HD2 L:PHE11 4.3 85.6 1.0
HA L:ASP8 4.4 0.9 1.0
CG L:GLU14 4.4 80.5 1.0
CA L:PRO10 4.5 81.1 1.0
HZ L:PHE110 4.5 0.6 1.0
OD2 L:ASP8 4.6 0.5 1.0
N L:PRO10 4.6 86.0 1.0
C L:ASP8 4.6 0.8 1.0
CA L:VAL9 4.7 96.2 1.0
N L:PHE11 4.7 78.0 1.0
HG2 L:GLU14 4.7 96.6 1.0
OE1 L:GLU129 4.8 80.2 1.0
HB3 L:GLU14 4.8 94.5 1.0
CA L:ASP8 4.8 1.0 1.0
HB2 L:GLU14 4.8 94.5 1.0
HE2 L:PHE110 4.9 0.9 1.0
O L:ASN123 4.9 99.1 1.0
CB L:ASP8 5.0 0.8 1.0
CB L:GLU14 5.0 78.7 1.0
HB L:VAL9 5.0 0.5 1.0

Strontium binding site 6 out of 6 in 5kli

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


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

b:0.2
occ:1.00
 OD1 P:ASP8 2.5 1.0 1.0
OE1 P:GLU14 2.7 0.5 1.0
OE2 P:GLU14 2.7 0.0 1.0
O P:VAL9 2.7 0.4 1.0
OE2 P:GLU129 2.7 0.5 1.0
CD P:GLU14 3.0 0.7 1.0
CG P:ASP8 3.7 0.6 1.0
C P:VAL9 3.8 0.7 1.0
HA P:PRO10 3.8 0.9 1.0
CD P:GLU129 3.9 0.4 1.0
HG2 P:GLU129 4.0 0.2 1.0
H P:PHE11 4.2 0.0 1.0
H P:VAL9 4.2 0.3 1.0
HZ P:PHE110 4.3 0.1 1.0
N P:VAL9 4.3 0.7 1.0
HA P:ASP8 4.3 0.0 1.0
OD2 P:ASP8 4.3 0.7 1.0
CG P:GLU129 4.4 0.6 1.0
CG P:GLU14 4.5 0.2 1.0
HG3 P:GLU129 4.5 0.2 1.0
C P:ASP8 4.5 0.2 1.0
O P:ASN123 4.6 0.4 1.0
HE2 P:PHE110 4.6 0.3 1.0
CA P:PRO10 4.6 0.2 1.0
HD2 P:PHE11 4.7 0.8 1.0
N P:PRO10 4.7 0.9 1.0
CA P:VAL9 4.7 0.5 1.0
CA P:ASP8 4.7 0.3 1.0
HG2 P:GLU14 4.7 0.1 1.0
CB P:ASP8 4.8 0.8 1.0
OE1 P:GLU129 4.9 0.5 1.0
HB3 P:ASN123 4.9 0.6 1.0
HB3 P:GLU14 4.9 0.8 1.0
CZ P:PHE110 5.0 0.8 1.0
N P:PHE11 5.0 100.0 1.0
HB2 P:GLU14 5.0 0.8 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 06:21:06 2024

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