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Strontium in PDB 2qjp: Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited

Enzymatic activity of Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited

All present enzymatic activity of Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited:
1.10.2.2;

Protein crystallography data

The structure of Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited, PDB code: 2qjp 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) 17.98 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.061, 146.520, 141.003, 90.00, 110.21, 90.00
R / Rfree (%) 24.4 / 27.7

Other elements in 2qjp:

The structure of Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited (pdb code 2qjp). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 6 binding sites of Strontium where determined in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited, PDB code: 2qjp:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 2qjp

Go back to Strontium Binding Sites List in 2qjp
Strontium binding site 1 out of 6 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr257

b:0.4
occ:1.00
 OE2 B:GLU14 2.4 89.6 1.0
O B:VAL9 2.5 0.8 1.0
OE1 B:GLU14 2.9 89.7 1.0
OE2 B:GLU129 2.9 65.8 1.0
CD B:GLU14 2.9 89.3 1.0
OD1 B:ASP8 3.1 0.4 1.0
C B:VAL9 3.6 0.6 1.0
CD B:GLU129 3.9 66.0 1.0
CG B:ASP8 3.9 0.0 1.0
CA B:PRO10 4.1 98.8 1.0
N B:PRO10 4.2 0.4 1.0
OD2 B:ASP8 4.2 0.0 1.0
N B:VAL9 4.3 0.5 1.0
CG B:GLU14 4.4 88.8 1.0
CG B:GLU129 4.4 66.8 1.0
N B:PHE11 4.6 93.5 1.0
CA B:VAL9 4.6 0.7 1.0
C B:ASP8 4.7 0.6 1.0
C B:PRO10 4.9 96.3 1.0
OE1 B:GLU129 4.9 65.8 1.0

Strontium binding site 2 out of 6 in 2qjp

Go back to Strontium Binding Sites List in 2qjp
Strontium binding site 2 out of 6 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr258

b:0.7
occ:1.00
 OE1 E:GLU14 2.6 88.3 1.0
O E:VAL9 2.7 0.2 1.0
OE2 E:GLU14 3.1 88.5 1.0
CD E:GLU14 3.1 88.5 1.0
OD1 E:ASP8 3.2 0.7 1.0
OE2 E:GLU129 3.4 79.8 1.0
C E:VAL9 3.7 0.2 1.0
CG E:ASP8 3.7 0.3 1.0
OD2 E:ASP8 3.8 0.7 1.0
CG E:GLU129 4.1 79.7 1.0
CD E:GLU129 4.1 79.8 1.0
N E:VAL9 4.3 0.8 1.0
CA E:PRO10 4.4 0.6 1.0
N E:PRO10 4.5 0.8 1.0
CG E:GLU14 4.5 88.7 1.0
C E:ASP8 4.6 0.8 1.0
CA E:VAL9 4.7 0.2 1.0
CZ E:PHE110 4.7 0.2 1.0
CA E:ASP8 4.9 0.2 1.0
N E:PHE11 4.9 95.8 1.0
CB E:ASP8 4.9 0.4 1.0
CE2 E:PHE110 4.9 0.1 1.0

Strontium binding site 3 out of 6 in 2qjp

Go back to Strontium Binding Sites List in 2qjp
Strontium binding site 3 out of 6 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Sr432

b:0.8
occ:1.00
 NE2 D:GLN316 4.8 56.5 1.0
NE1 G:TRP313 4.8 52.1 1.0
O G:ASP311 4.8 64.4 1.0
CB G:ASP311 5.0 65.6 1.0

Strontium binding site 4 out of 6 in 2qjp

Go back to Strontium Binding Sites List in 2qjp
Strontium binding site 4 out of 6 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sr257

b:0.8
occ:1.00
 OE1 H:GLU14 2.3 87.2 1.0
O H:VAL9 2.7 0.7 1.0
OE2 H:GLU129 2.7 65.8 1.0
OD1 H:ASP8 3.1 0.9 1.0
CD H:GLU14 3.1 87.0 1.0
OE2 H:GLU14 3.3 86.8 1.0
C H:VAL9 3.7 0.4 1.0
CD H:GLU129 3.7 66.0 1.0
CG H:ASP8 3.9 0.1 1.0
CG H:GLU129 4.2 66.8 1.0
OD2 H:ASP8 4.2 0.8 1.0
CA H:PRO10 4.3 97.9 1.0
N H:VAL9 4.4 0.7 1.0
N H:PRO10 4.4 0.3 1.0
CG H:GLU14 4.6 86.9 1.0
CZ H:PHE110 4.6 0.9 1.0
CA H:VAL9 4.7 0.8 1.0
C H:ASP8 4.7 0.8 1.0
N H:PHE11 4.7 92.7 1.0
CE2 H:PHE110 4.8 1.0 1.0
OE1 H:GLU129 4.8 65.5 1.0

Strontium binding site 5 out of 6 in 2qjp

Go back to Strontium Binding Sites List in 2qjp
Strontium binding site 5 out of 6 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Sr432

b:0.6
occ:1.00
 O J:ASP311 3.5 66.7 1.0
C J:ASP311 4.6 67.3 1.0
OE1 J:GLN316 4.8 51.7 1.0

Strontium binding site 6 out of 6 in 2qjp

Go back to Strontium Binding Sites List in 2qjp
Strontium binding site 6 out of 6 in the Crystal Structure of Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited


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 Wild Type Rhodobacter Sphaeroides with Stigmatellin and Antimycin Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Sr257

b:0.3
occ:1.00
 OE1 K:GLU14 2.5 88.9 1.0
O K:VAL9 2.9 0.6 1.0
OE2 K:GLU129 3.0 77.8 1.0
OD1 K:ASP8 3.1 0.6 1.0
CD K:GLU14 3.3 89.0 1.0
OD2 K:ASP8 3.6 0.4 1.0
CG K:ASP8 3.6 0.4 1.0
OE2 K:GLU14 3.7 89.0 1.0
C K:VAL9 3.9 0.5 1.0
CD K:GLU129 4.1 77.5 1.0
CA K:PRO10 4.4 1.0 1.0
CG K:GLU14 4.4 89.1 1.0
N K:PRO10 4.5 0.4 1.0
CG K:GLU129 4.5 77.0 1.0
N K:VAL9 4.5 0.6 1.0
CZ K:PHE110 4.7 0.9 1.0
C K:ASP8 4.8 0.6 1.0
CA K:VAL9 4.9 0.7 1.0
CB K:ASP8 4.9 0.2 1.0
CE2 K:PHE110 4.9 0.9 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 02:20:40 2020

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