Atomistry » Strontium » PDB 4rum-6ny9 » 5kkz
Atomistry »
  Strontium »
    PDB 4rum-6ny9 »
      5kkz »

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

Go back to Strontium Binding Sites List in 5kkz
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

Go back to Strontium Binding Sites List in 5kkz
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

Go back to Strontium Binding Sites List in 5kkz
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

Go back to Strontium Binding Sites List in 5kkz
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

Go back to Strontium Binding Sites List in 5kkz
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

Go back to Strontium Binding Sites List in 5kkz
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy