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Strontium in PDB 2qjk: Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin

Enzymatic activity of Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin

All present enzymatic activity of Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin:
1.10.2.2;

Protein crystallography data

The structure of Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin, PDB code: 2qjk was solved by L.Esser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 352.291, 147.396, 160.762, 90.00, 104.13, 90.00
R / Rfree (%) 23.9 / 26.6

Other elements in 2qjk:

The structure of Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin also contains other interesting chemical elements:

Iron (Fe) 30 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin (pdb code 2qjk). 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 Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin, PDB code: 2qjk:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 2qjk

Go back to Strontium Binding Sites List in 2qjk
Strontium binding site 1 out of 6 in the Crystal Structure Analysis of Mutant 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 Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr257

b:0.1
occ:1.00
O B:VAL9 2.6 0.9 1.0
OE1 B:GLU14 2.7 0.2 1.0
OE2 B:GLU129 2.9 80.3 1.0
OD1 B:ASP8 2.9 0.7 1.0
C B:VAL9 3.5 0.0 1.0
CD B:GLU14 3.6 0.5 1.0
CG B:ASP8 3.7 0.4 1.0
OE2 B:GLU14 3.9 0.3 1.0
CD B:GLU129 4.0 79.7 1.0
CA B:PRO10 4.0 1.0 1.0
OD2 B:ASP8 4.1 0.1 1.0
N B:PRO10 4.1 0.0 1.0
N B:VAL9 4.2 1.0 1.0
C B:ASP8 4.3 0.0 1.0
CG B:GLU129 4.4 76.8 1.0
CA B:VAL9 4.5 0.1 1.0
O B:ASP8 4.6 0.2 1.0
N B:PHE11 4.6 0.3 1.0
CA B:ASP8 4.8 0.7 1.0
CB B:ASP8 4.9 0.9 1.0
C B:PRO10 4.9 0.5 1.0
CZ B:PHE110 5.0 0.8 1.0
CG B:GLU14 5.0 0.0 1.0

Strontium binding site 2 out of 6 in 2qjk

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Strontium binding site 2 out of 6 in the Crystal Structure Analysis of Mutant 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 Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr257

b:0.0
occ:1.00
OE1 E:GLU14 2.4 0.3 1.0
OE2 E:GLU129 2.9 74.0 1.0
O E:VAL9 3.0 0.7 1.0
CD E:GLU14 3.2 0.7 1.0
OE2 E:GLU14 3.2 0.2 1.0
OD2 E:ASP8 3.4 0.5 1.0
OD1 E:ASP8 3.6 0.8 1.0
CG E:ASP8 3.7 0.8 1.0
C E:VAL9 3.9 0.8 1.0
CD E:GLU129 4.1 73.9 1.0
CA E:PRO10 4.3 0.4 1.0
N E:PRO10 4.4 0.4 1.0
C E:ASP8 4.5 0.8 1.0
N E:VAL9 4.5 0.7 1.0
CG E:GLU14 4.6 0.0 1.0
O E:ASN123 4.7 0.5 1.0
O E:ASP8 4.8 0.7 1.0
CG E:GLU129 4.8 70.2 1.0
CZ E:PHE110 4.8 0.6 1.0
CA E:VAL9 4.9 0.6 1.0
CB E:ASP8 4.9 0.1 1.0
CA E:ASP8 4.9 0.7 1.0
N E:PHE11 4.9 0.5 1.0
CE2 E:PHE110 5.0 0.9 1.0

Strontium binding site 3 out of 6 in 2qjk

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Strontium binding site 3 out of 6 in the Crystal Structure Analysis of Mutant 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 Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sr257

b:0.8
occ:1.00
OE2 H:GLU14 2.1 0.5 1.0
O H:VAL9 2.5 0.7 1.0
OD1 H:ASP8 2.8 0.5 1.0
CD H:GLU14 3.3 0.8 1.0
OE2 H:GLU129 3.4 86.3 1.0
C H:VAL9 3.5 0.6 1.0
CG H:ASP8 3.8 0.3 1.0
CD H:GLU129 4.0 82.2 1.0
CA H:PRO10 4.1 0.9 1.0
OE1 H:GLU14 4.2 0.5 1.0
N H:PRO10 4.2 0.8 1.0
OD2 H:ASP8 4.2 0.7 1.0
CG H:GLU14 4.3 0.4 1.0
CG H:GLU129 4.3 75.2 1.0
N H:VAL9 4.3 0.4 1.0
C H:ASP8 4.5 0.6 1.0
N H:PHE11 4.5 0.7 1.0
CA H:VAL9 4.6 0.2 1.0
O H:ASP8 4.8 1.0 1.0
C H:PRO10 4.9 0.0 1.0
CA H:ASP8 4.9 0.5 1.0
OE1 H:GLU129 4.9 86.0 1.0
CZ H:PHE110 4.9 1.0 1.0
CB H:ASP8 5.0 0.9 1.0
O H:ASN123 5.0 0.8 1.0

Strontium binding site 4 out of 6 in 2qjk

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Strontium binding site 4 out of 6 in the Crystal Structure Analysis of Mutant 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 Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Sr257

b:0.9
occ:1.00
OE1 K:GLU14 2.4 0.8 1.0
OD1 K:ASP8 2.5 0.3 1.0
O K:VAL9 2.8 0.5 1.0
CD K:GLU14 3.4 0.5 1.0
CG K:ASP8 3.5 0.3 1.0
C K:VAL9 3.7 0.3 1.0
OD2 K:ASP8 3.8 0.2 1.0
OE2 K:GLU14 3.9 0.0 1.0
OE2 K:GLU129 4.0 81.9 1.0
CD K:GLU129 4.2 80.8 1.0
CA K:PRO10 4.3 0.1 1.0
N K:PRO10 4.4 0.7 1.0
N K:VAL9 4.4 0.1 1.0
C K:ASP8 4.4 0.8 1.0
CG K:GLU129 4.5 75.2 1.0
CG K:GLU14 4.6 0.7 1.0
CB K:ASP8 4.7 0.8 1.0
O K:ASP8 4.7 0.5 1.0
CA K:VAL9 4.7 0.8 1.0
CA K:ASP8 4.8 0.6 1.0
OE1 K:GLU129 4.8 84.2 1.0
O K:ASN123 4.8 1.0 1.0
N K:PHE11 4.8 0.2 1.0

Strontium binding site 5 out of 6 in 2qjk

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Strontium binding site 5 out of 6 in the Crystal Structure Analysis of Mutant 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 Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Sr257

b:0.8
occ:1.00
O N:VAL9 2.6 0.8 1.0
OE1 N:GLU14 2.7 0.3 1.0
OE2 N:GLU129 2.9 92.4 1.0
OD1 N:ASP8 3.1 0.6 1.0
OE2 N:GLU14 3.3 0.9 1.0
CD N:GLU14 3.4 0.9 1.0
C N:VAL9 3.6 0.6 1.0
CG N:ASP8 3.7 0.6 1.0
CD N:GLU129 3.7 90.3 1.0
CG N:GLU129 3.9 86.1 1.0
N N:VAL9 4.0 0.0 1.0
OD2 N:ASP8 4.0 0.2 1.0
C N:ASP8 4.1 0.8 1.0
N N:PRO10 4.3 0.7 1.0
CZ N:PHE110 4.4 0.4 1.0
CA N:ASP8 4.4 0.8 1.0
CA N:VAL9 4.4 0.9 1.0
CA N:PRO10 4.4 0.9 1.0
O N:ASP8 4.5 0.8 1.0
CB N:ASP8 4.6 0.2 1.0
CE2 N:PHE110 4.6 0.4 1.0
OE1 N:GLU129 4.7 91.6 1.0
CG N:GLU14 4.9 0.3 1.0
N N:PHE11 4.9 0.8 1.0

Strontium binding site 6 out of 6 in 2qjk

Go back to Strontium Binding Sites List in 2qjk
Strontium binding site 6 out of 6 in the Crystal Structure Analysis of Mutant 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 Crystal Structure Analysis of Mutant Rhodobacter Sphaeroides BC1 with Stigmatellin and Antimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Sr258

b:0.7
occ:1.00
OE1 Q:GLU14 2.4 0.3 1.0
O Q:VAL9 2.6 0.9 1.0
OE2 Q:GLU129 3.4 82.8 1.0
OD1 Q:ASP8 3.5 0.2 1.0
C Q:VAL9 3.5 0.4 1.0
CD Q:GLU14 3.6 0.8 1.0
CA Q:PRO10 3.9 0.1 1.0
CG Q:ASP8 3.9 0.8 1.0
N Q:PRO10 4.0 0.1 1.0
OD2 Q:ASP8 4.1 0.0 1.0
OE2 Q:GLU14 4.2 0.3 1.0
CD Q:GLU129 4.2 83.0 1.0
N Q:VAL9 4.3 0.2 1.0
C Q:ASP8 4.4 0.2 1.0
N Q:PHE11 4.5 0.4 1.0
CA Q:VAL9 4.6 0.4 1.0
O Q:ASP8 4.6 0.6 1.0
CG Q:GLU129 4.7 78.9 1.0
CG Q:GLU14 4.8 0.7 1.0
C Q:PRO10 4.8 1.0 1.0
CA Q:ASP8 4.9 0.3 1.0
CB Q:PRO10 4.9 0.8 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 02:16:15 2020

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