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Strontium in PDB 2qjy: Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2

Enzymatic activity of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2

All present enzymatic activity of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2:
1.10.2.2;

Protein crystallography data

The structure of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2, PDB code: 2qjy was solved by L.Esser, D.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 351.891, 147.042, 161.312, 90.00, 104.25, 90.00
R / Rfree (%) 22.6 / 25.1

Other elements in 2qjy:

The structure of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 also contains other interesting chemical elements:

Iron (Fe) 30 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 (pdb code 2qjy). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 9 binding sites of Strontium where determined in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2, PDB code: 2qjy:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Strontium binding site 1 out of 9 in 2qjy

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Strontium binding site 1 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1017

b:0.6
occ:1.00
OD1 A:ASP311 4.5 72.2 1.0

Strontium binding site 2 out of 9 in 2qjy

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Strontium binding site 2 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1011

b:0.2
occ:1.00
O B:VAL9 2.6 94.6 1.0
OD1 B:ASP8 2.6 0.8 1.0
OE1 B:GLU14 2.7 83.8 1.0
CD B:GLU14 3.5 81.5 1.0
OE2 B:GLU14 3.5 80.5 1.0
CG B:ASP8 3.5 0.5 1.0
C B:VAL9 3.6 93.3 1.0
OE2 B:GLU129 3.6 82.3 1.0
OD2 B:ASP8 3.9 0.8 1.0
CG B:GLU129 4.2 75.5 1.0
CA B:PRO10 4.2 87.3 1.0
N B:VAL9 4.2 97.7 1.0
CD B:GLU129 4.3 79.2 1.0
N B:PRO10 4.3 90.6 1.0
C B:ASP8 4.3 0.1 1.0
CA B:VAL9 4.5 95.0 1.0
O B:ASP8 4.7 0.6 1.0
N B:PHE11 4.7 78.7 1.0
CA B:ASP8 4.7 0.7 1.0
CB B:ASP8 4.7 0.2 1.0
CZ B:PHE110 4.8 0.3 1.0
CG B:GLU14 4.9 80.0 1.0

Strontium binding site 3 out of 9 in 2qjy

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Strontium binding site 3 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr1012

b:0.5
occ:1.00
OE1 E:GLU14 2.4 93.0 1.0
OD1 E:ASP8 2.7 0.1 1.0
OE2 E:GLU129 2.7 73.8 1.0
O E:VAL9 2.8 94.0 1.0
CD E:GLU14 3.4 90.8 1.0
OE2 E:GLU14 3.6 92.3 1.0
C E:VAL9 3.8 94.0 1.0
CD E:GLU129 3.9 71.0 1.0
CG E:ASP8 3.9 0.3 1.0
CA E:PRO10 4.3 89.1 1.0
CG E:GLU129 4.4 66.6 1.0
N E:PRO10 4.5 91.3 1.0
N E:VAL9 4.5 99.1 1.0
OD2 E:ASP8 4.5 0.0 1.0
C E:ASP8 4.6 0.6 1.0
CG E:GLU14 4.7 87.9 1.0
CZ E:PHE110 4.7 0.0 1.0
N E:PHE11 4.8 82.4 1.0
CA E:VAL9 4.8 96.0 1.0
O E:ASN123 4.8 95.1 1.0
O E:ASP8 4.9 0.0 1.0
OE1 E:GLU129 4.9 73.3 1.0
CA E:ASP8 4.9 0.3 1.0
CB E:ASP8 5.0 0.4 1.0

Strontium binding site 4 out of 9 in 2qjy

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Strontium binding site 4 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Sr1018

b:98.9
occ:1.00
OD1 G:ASP311 4.6 72.7 1.0
OE1 G:GLN316 5.0 49.6 1.0
NE2 G:GLN316 5.0 45.2 1.0

Strontium binding site 5 out of 9 in 2qjy

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Strontium binding site 5 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sr1013

b:1.0
occ:1.00
OE1 H:GLU14 2.4 89.8 1.0
O H:VAL9 2.6 88.4 1.0
OD1 H:ASP8 3.1 0.3 1.0
OE2 H:GLU129 3.3 68.0 1.0
CD H:GLU14 3.4 89.0 1.0
OE2 H:GLU14 3.6 91.7 1.0
C H:VAL9 3.6 88.4 1.0
CG H:ASP8 3.7 0.5 1.0
OD2 H:ASP8 3.8 0.5 1.0
CD H:GLU129 4.1 64.1 1.0
CG H:GLU129 4.1 59.5 1.0
CA H:PRO10 4.2 83.5 1.0
N H:VAL9 4.3 94.2 1.0
N H:PRO10 4.3 85.8 1.0
C H:ASP8 4.4 97.2 1.0
CA H:VAL9 4.6 90.5 1.0
N H:PHE11 4.6 76.9 1.0
CG H:GLU14 4.7 85.6 1.0
O H:ASP8 4.8 98.4 1.0
CZ H:PHE110 4.8 0.4 1.0
CA H:ASP8 4.8 98.8 1.0
CB H:ASP8 4.9 100.0 1.0
O H:ASN123 4.9 98.1 1.0

Strontium binding site 6 out of 9 in 2qjy

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Strontium binding site 6 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Sr1014

b:0.2
occ:1.00
OE1 K:GLU14 2.5 0.9 1.0
OD1 K:ASP8 2.7 0.2 1.0
O K:VAL9 2.8 0.5 1.0
OE2 K:GLU129 3.3 83.0 1.0
CG K:ASP8 3.5 0.2 1.0
CD K:GLU14 3.5 97.4 1.0
OD2 K:ASP8 3.6 0.5 1.0
C K:VAL9 3.7 0.4 1.0
OE2 K:GLU14 3.9 98.9 1.0
CA K:PRO10 4.2 96.8 1.0
CD K:GLU129 4.2 81.3 1.0
N K:PRO10 4.3 98.9 1.0
N K:VAL9 4.4 0.5 1.0
C K:ASP8 4.5 0.1 1.0
CG K:GLU129 4.5 77.1 1.0
O K:ASP8 4.7 0.7 1.0
CA K:VAL9 4.7 0.4 1.0
CB K:ASP8 4.7 0.7 1.0
N K:PHE11 4.8 90.8 1.0
CG K:GLU14 4.8 93.9 1.0
CA K:ASP8 4.9 0.1 1.0

Strontium binding site 7 out of 9 in 2qjy

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Strontium binding site 7 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Sr1019

b:0.7
occ:1.00
NE1 J:TRP313 4.2 68.2 1.0
NE2 M:GLN316 4.3 69.5 1.0
NE1 M:TRP313 4.3 62.2 1.0
OE1 M:GLN316 4.5 70.1 1.0
CD1 M:TRP313 4.7 63.0 1.0
CD1 J:TRP313 4.7 68.9 1.0
CD M:GLN316 4.9 69.8 1.0
O M:ASP311 5.0 74.1 1.0

Strontium binding site 8 out of 9 in 2qjy

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Strontium binding site 8 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Sr1015

b:0.4
occ:1.00
O N:VAL9 2.5 0.1 1.0
OE2 N:GLU129 2.9 0.7 1.0
OD1 N:ASP8 3.5 0.0 1.0
C N:VAL9 3.6 0.9 1.0
CD N:GLU129 3.7 97.6 1.0
OE1 N:GLU14 3.9 0.3 1.0
CD N:GLU14 3.9 0.6 1.0
CG N:GLU14 4.1 0.9 1.0
CA N:PRO10 4.1 0.0 1.0
CG N:GLU129 4.1 93.1 1.0
N N:PRO10 4.3 1.0 1.0
N N:PHE11 4.4 98.9 1.0
CG N:ASP8 4.4 0.1 1.0
N N:VAL9 4.4 0.4 1.0
OE2 N:GLU14 4.4 0.5 1.0
CA N:VAL9 4.6 0.4 1.0
C N:ASP8 4.6 0.1 1.0
OE1 N:GLU129 4.6 0.0 1.0
C N:PRO10 4.8 0.6 1.0
OD2 N:ASP8 4.8 0.7 1.0
CB N:GLU14 4.9 98.6 1.0
CD2 N:PHE11 4.9 85.8 1.0
O N:ASP8 4.9 0.1 1.0

Strontium binding site 9 out of 9 in 2qjy

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Strontium binding site 9 out of 9 in the Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structure of Rhodobacter Sphaeroides Double Mutant with Stigmatellin and UQ2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Sr1016

b:0.6
occ:1.00
O Q:VAL9 2.8 0.8 1.0
OE1 Q:GLU14 2.8 90.6 1.0
OD1 Q:ASP8 3.0 0.0 1.0
OE2 Q:GLU129 3.2 85.0 1.0
CD Q:GLU14 3.6 90.6 1.0
C Q:VAL9 3.8 0.8 1.0
OE2 Q:GLU14 3.9 90.7 1.0
CD Q:GLU129 3.9 81.8 1.0
CG Q:GLU129 4.1 76.8 1.0
CG Q:ASP8 4.2 0.5 1.0
N Q:VAL9 4.4 0.6 1.0
C Q:ASP8 4.5 0.5 1.0
CA Q:PRO10 4.5 96.6 1.0
CZ Q:PHE110 4.5 0.4 1.0
N Q:PRO10 4.6 99.0 1.0
CG Q:GLU14 4.7 89.8 1.0
O Q:ASN123 4.7 0.1 1.0
CA Q:VAL9 4.7 0.1 1.0
CA Q:ASP8 4.8 0.3 1.0
CE2 Q:PHE110 4.8 0.4 1.0
O Q:ASP8 4.8 0.0 1.0
N Q:PHE11 4.9 91.7 1.0
OE1 Q:GLU129 5.0 84.5 1.0

Reference:

L.Esser, M.Elberry, F.Zhou, C.A.Yu, L.Yu, D.Xia. Inhibitor-Complexed Structures of the Cytochrome BC1 From the Photosynthetic Bacterium Rhodobacter Sphaeroides. J.Biol.Chem. V. 283 2846 2008.
ISSN: ISSN 0021-9258
PubMed: 18039651
DOI: 10.1074/JBC.M708608200
Page generated: Wed Dec 16 02:18:29 2020

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