Krypton in PDB 7q35: Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Protein crystallography data
The structure of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton, PDB code: 7q35
was solved by
I.Melnikov,
M.Rulev,
R.Astashkin,
K.Kovalev,
P.Carpentier,
V.Gordeliy,
A.Popov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.61 /
2.00
|
Space group
|
C 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.33,
119.986,
36.461,
90,
90,
90
|
R / Rfree (%)
|
16.9 /
23.2
|
Krypton Binding Sites:
Krypton binding site 1 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 1 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 1 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr320
b:23.1
occ:0.38
|
CD1
|
A:LEU97
|
3.5
|
28.5
|
1.0
|
CG2
|
A:THR178
|
3.6
|
25.2
|
1.0
|
CZ2
|
A:TRP182
|
3.6
|
20.1
|
1.0
|
C
|
A:LEU93
|
3.6
|
21.1
|
1.0
|
O
|
A:LEU93
|
3.6
|
19.8
|
1.0
|
OG1
|
A:THR178
|
3.6
|
24.9
|
1.0
|
CB
|
A:LEU93
|
3.7
|
22.1
|
1.0
|
CD2
|
A:LEU94
|
3.8
|
26.6
|
1.0
|
N
|
A:LEU94
|
3.9
|
21.3
|
1.0
|
CE2
|
A:PHE219
|
3.9
|
23.1
|
1.0
|
CG
|
A:LEU97
|
4.0
|
27.2
|
1.0
|
O
|
A:HOH449
|
4.1
|
26.9
|
1.0
|
CE2
|
A:TRP182
|
4.1
|
21.4
|
1.0
|
CA
|
A:LEU94
|
4.2
|
22.2
|
1.0
|
CZ
|
A:PHE219
|
4.2
|
23.5
|
1.0
|
CA
|
A:LEU93
|
4.2
|
19.9
|
1.0
|
CB
|
A:THR178
|
4.2
|
24.3
|
1.0
|
NE1
|
A:TRP182
|
4.3
|
21.9
|
1.0
|
CH2
|
A:TRP182
|
4.3
|
22.0
|
1.0
|
CG
|
A:LEU94
|
4.5
|
23.6
|
1.0
|
CD1
|
A:LEU152
|
4.7
|
23.8
|
1.0
|
CD2
|
A:PHE219
|
4.7
|
24.5
|
1.0
|
CG
|
A:LEU93
|
4.8
|
22.8
|
1.0
|
CB
|
A:LEU94
|
4.9
|
21.7
|
1.0
|
|
Krypton binding site 2 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 2 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 2 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr321
b:23.2
occ:0.38
|
CA
|
A:LEU15
|
3.7
|
21.8
|
1.0
|
N
|
A:LEU15
|
3.8
|
22.2
|
1.0
|
C
|
A:ALA14
|
3.8
|
22.7
|
1.0
|
O
|
A:ALA14
|
3.9
|
21.5
|
1.0
|
C17
|
A:LFA302
|
4.1
|
51.3
|
0.8
|
CB
|
A:ALA18
|
4.1
|
22.8
|
1.0
|
C18
|
A:LFA302
|
4.1
|
50.0
|
0.8
|
CD1
|
A:LEU15
|
4.2
|
26.9
|
1.0
|
CB
|
A:ALA14
|
4.3
|
23.6
|
1.0
|
C5
|
A:LFA310
|
4.3
|
49.5
|
0.8
|
CB
|
A:LEU15
|
4.4
|
24.1
|
1.0
|
KR
|
A:KR352
|
4.6
|
34.8
|
0.1
|
CA
|
A:ALA14
|
4.7
|
22.4
|
1.0
|
C3
|
A:LFA310
|
4.9
|
42.3
|
0.8
|
CG
|
A:LEU15
|
5.0
|
26.8
|
1.0
|
C
|
A:LEU15
|
5.0
|
20.2
|
1.0
|
C4
|
A:LFA310
|
5.0
|
45.7
|
0.8
|
|
Krypton binding site 3 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 3 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 3 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr322
b:25.9
occ:0.50
|
N
|
A:LEU95
|
3.4
|
21.8
|
1.0
|
C
|
A:LEU94
|
3.5
|
23.4
|
1.0
|
CB
|
A:LEU94
|
3.6
|
21.7
|
1.0
|
CA
|
A:LEU95
|
3.7
|
22.4
|
1.0
|
O
|
A:LEU94
|
3.8
|
24.2
|
1.0
|
O
|
A:ILE108
|
3.9
|
26.1
|
1.0
|
CG2
|
A:ILE108
|
3.9
|
29.1
|
1.0
|
CB
|
A:LEU111
|
4.1
|
25.1
|
1.0
|
CG2
|
A:VAL112
|
4.1
|
27.2
|
1.0
|
CA
|
A:ILE108
|
4.2
|
28.0
|
1.0
|
CB
|
A:ALA98
|
4.2
|
24.1
|
1.0
|
CA
|
A:LEU94
|
4.2
|
22.2
|
1.0
|
CD1
|
A:LEU111
|
4.3
|
35.1
|
1.0
|
O
|
A:PRO91
|
4.3
|
22.1
|
1.0
|
CB
|
A:ILE108
|
4.3
|
28.6
|
1.0
|
CG1
|
A:ILE108
|
4.3
|
29.7
|
1.0
|
CB
|
A:LEU95
|
4.4
|
25.0
|
1.0
|
C
|
A:ILE108
|
4.5
|
28.8
|
1.0
|
CD1
|
A:LEU95
|
4.8
|
27.7
|
1.0
|
N
|
A:VAL112
|
4.8
|
24.6
|
1.0
|
CG
|
A:LEU111
|
4.9
|
30.5
|
1.0
|
CG
|
A:LEU94
|
4.9
|
23.6
|
1.0
|
|
Krypton binding site 4 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 4 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 4 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr323
b:24.9
occ:0.38
|
C2
|
A:LFA311
|
0.6
|
20.5
|
0.4
|
C3
|
A:LFA311
|
1.5
|
20.6
|
0.4
|
C4
|
A:LFA311
|
2.7
|
19.9
|
0.4
|
CB
|
A:ALA114
|
3.6
|
24.0
|
1.0
|
CA
|
A:ALA114
|
3.9
|
22.1
|
1.0
|
C5
|
A:LFA311
|
3.9
|
19.0
|
0.4
|
CD1
|
A:ILE117
|
4.0
|
27.4
|
1.0
|
CD2
|
A:TYR147
|
4.1
|
34.0
|
1.0
|
C6
|
A:LFA311
|
4.3
|
18.3
|
0.4
|
CB
|
A:ALA144
|
4.4
|
18.3
|
1.0
|
KR
|
A:KR354
|
4.4
|
20.6
|
0.1
|
CG
|
A:TYR147
|
4.5
|
29.7
|
1.0
|
CA
|
A:ALA144
|
4.6
|
18.9
|
1.0
|
C14
|
A:OLA315
|
4.6
|
64.9
|
1.0
|
CE2
|
A:TYR147
|
4.6
|
38.7
|
1.0
|
CB
|
A:TYR147
|
4.7
|
24.9
|
1.0
|
C11
|
A:OLA315
|
4.8
|
64.2
|
1.0
|
N
|
A:ALA114
|
4.8
|
20.1
|
1.0
|
CB
|
A:ILE117
|
4.9
|
25.1
|
1.0
|
O
|
A:ALA114
|
4.9
|
20.8
|
1.0
|
C
|
A:ALA114
|
4.9
|
19.9
|
1.0
|
C15
|
A:OLA315
|
5.0
|
63.6
|
1.0
|
|
Krypton binding site 5 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 5 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 5 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr324
b:26.0
occ:0.35
|
CD2
|
A:LEU123
|
3.6
|
34.2
|
1.0
|
C7
|
A:LFA306
|
3.8
|
73.0
|
1.0
|
O
|
A:TYR83
|
3.9
|
25.3
|
1.0
|
CD2
|
A:LEU87
|
3.9
|
32.3
|
1.0
|
C6
|
A:LFA306
|
4.0
|
77.5
|
1.0
|
CG2
|
A:ILE119
|
4.0
|
24.9
|
1.0
|
CB
|
A:TYR83
|
4.1
|
21.9
|
1.0
|
CB
|
A:LEU87
|
4.1
|
27.7
|
1.0
|
C
|
A:TYR83
|
4.1
|
22.6
|
1.0
|
CB
|
A:LEU123
|
4.4
|
26.1
|
1.0
|
CG
|
A:LEU87
|
4.4
|
31.1
|
1.0
|
CD1
|
A:LEU87
|
4.4
|
31.3
|
1.0
|
O
|
A:ILE119
|
4.5
|
22.2
|
1.0
|
C8
|
A:LFA306
|
4.5
|
67.1
|
1.0
|
N
|
A:ALA84
|
4.5
|
26.1
|
1.0
|
CG
|
A:LEU123
|
4.6
|
28.7
|
1.0
|
CA
|
A:GLY120
|
4.6
|
19.8
|
1.0
|
C
|
A:ILE119
|
4.7
|
22.6
|
1.0
|
CA
|
A:TYR83
|
4.7
|
21.5
|
1.0
|
N
|
A:GLY120
|
4.8
|
23.9
|
1.0
|
CA
|
A:ALA84
|
4.8
|
25.2
|
1.0
|
C6
|
A:HEX317
|
4.9
|
53.7
|
1.0
|
|
Krypton binding site 6 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 6 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 6 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr325
b:23.4
occ:0.25
|
C7
|
A:OLA314
|
3.0
|
55.1
|
1.0
|
O
|
A:SER214
|
3.6
|
20.7
|
1.0
|
CG1
|
A:VAL177
|
3.7
|
27.2
|
1.0
|
CA
|
A:GLY218
|
3.9
|
22.3
|
1.0
|
C
|
A:GLY218
|
3.9
|
22.8
|
1.0
|
N
|
A:PHE219
|
4.1
|
24.7
|
1.0
|
CD1
|
A:ILE222
|
4.1
|
24.0
|
1.0
|
CG2
|
A:VAL177
|
4.3
|
25.9
|
1.0
|
O
|
A:GLY218
|
4.3
|
22.0
|
1.0
|
C9
|
A:LFA305
|
4.4
|
53.8
|
1.0
|
CD1
|
A:LEU181
|
4.4
|
23.9
|
1.0
|
C6
|
A:OLA314
|
4.4
|
53.8
|
1.0
|
C
|
A:SER214
|
4.5
|
22.0
|
1.0
|
KR
|
A:KR326
|
4.5
|
23.6
|
0.2
|
CB
|
A:VAL177
|
4.6
|
24.0
|
1.0
|
CB
|
A:SER214
|
4.7
|
23.8
|
1.0
|
CA
|
A:SER214
|
4.8
|
23.0
|
1.0
|
CA
|
A:PHE219
|
4.9
|
21.6
|
1.0
|
|
Krypton binding site 7 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 7 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 7 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr326
b:23.6
occ:0.20
|
KR
|
A:KR353
|
3.4
|
23.3
|
0.0
|
CG
|
A:LEU181
|
3.8
|
21.1
|
1.0
|
CD2
|
A:LEU181
|
3.8
|
23.2
|
1.0
|
CG1
|
A:VAL180
|
4.0
|
25.1
|
1.0
|
CA
|
A:VAL177
|
4.2
|
21.6
|
1.0
|
CB
|
A:VAL180
|
4.2
|
24.4
|
1.0
|
CD1
|
A:LEU181
|
4.3
|
23.9
|
1.0
|
CG1
|
A:VAL177
|
4.3
|
27.2
|
1.0
|
CG2
|
A:VAL177
|
4.3
|
25.9
|
1.0
|
O
|
A:VAL177
|
4.3
|
21.1
|
1.0
|
CB
|
A:VAL177
|
4.5
|
24.0
|
1.0
|
KR
|
A:KR325
|
4.5
|
23.4
|
0.2
|
C
|
A:VAL177
|
4.8
|
23.0
|
1.0
|
CG2
|
A:VAL180
|
5.0
|
28.0
|
1.0
|
N
|
A:LEU181
|
5.0
|
18.8
|
1.0
|
C9
|
A:LFA305
|
5.0
|
53.8
|
1.0
|
|
Krypton binding site 8 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 8 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 8 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr327
b:25.2
occ:0.08
|
C19
|
A:LFA308
|
1.5
|
38.7
|
1.0
|
C18
|
A:LFA308
|
2.0
|
47.3
|
1.0
|
C17
|
A:LFA308
|
3.4
|
48.6
|
1.0
|
CG1
|
A:VAL217
|
3.7
|
25.1
|
1.0
|
CD1
|
A:LEU221
|
3.9
|
33.2
|
1.0
|
N
|
A:GLY218
|
4.3
|
23.5
|
1.0
|
CB
|
A:VAL217
|
4.3
|
23.3
|
1.0
|
C16
|
A:LFA308
|
4.5
|
48.7
|
1.0
|
CA
|
A:GLY218
|
4.5
|
22.3
|
1.0
|
C
|
A:VAL217
|
4.6
|
21.2
|
1.0
|
CG1
|
A:VAL213
|
4.8
|
28.0
|
1.0
|
|
Krypton binding site 9 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 9 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 9 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr328
b:30.3
occ:0.14
|
CG
|
A:LEU109
|
2.8
|
40.5
|
1.0
|
CD2
|
A:LEU109
|
2.9
|
47.1
|
1.0
|
CB
|
A:LEU109
|
3.2
|
33.9
|
1.0
|
N
|
A:ALA110
|
3.3
|
23.0
|
1.0
|
C
|
A:LEU109
|
3.3
|
23.8
|
1.0
|
O
|
A:LEU109
|
3.6
|
25.8
|
1.0
|
CA
|
A:ALA110
|
3.7
|
24.7
|
1.0
|
CA
|
A:LEU109
|
3.9
|
27.4
|
1.0
|
CD1
|
A:LEU109
|
4.2
|
46.2
|
1.0
|
O
|
A:GLY106
|
4.3
|
24.0
|
1.0
|
CB
|
A:ALA110
|
4.3
|
26.2
|
1.0
|
N
|
A:LEU109
|
4.9
|
27.6
|
1.0
|
C
|
A:ALA110
|
5.0
|
23.2
|
1.0
|
|
Krypton binding site 10 out
of 35 in 7q35
Go back to
Krypton Binding Sites List in 7q35
Krypton binding site 10 out
of 35 in the Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 10 of Crystal Structure of the Mutant Bacteriorhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr329
b:27.3
occ:0.23
|
CB
|
A:LEU28
|
3.8
|
25.1
|
1.0
|
CG2
|
A:VAL29
|
4.1
|
27.5
|
1.0
|
CD2
|
A:LEU25
|
4.2
|
40.3
|
1.0
|
CD1
|
A:LEU28
|
4.2
|
29.4
|
1.0
|
O
|
A:LEU25
|
4.6
|
24.9
|
1.0
|
N
|
A:VAL29
|
4.6
|
23.1
|
1.0
|
CG
|
A:LEU28
|
4.7
|
28.1
|
1.0
|
C
|
A:LEU28
|
4.8
|
23.9
|
1.0
|
CA
|
A:LEU28
|
5.0
|
23.3
|
1.0
|
|
Reference:
I.Melnikov,
P.Orekhov,
M.Rulev,
K.Kovalev,
R.Astashkin,
D.Bratanov,
Y.Ryzhykau,
T.Balandin,
S.Bukhdruker,
I.Okhrimenko,
V.Borshchevskiy,
G.Bourenkov,
C.Mueller-Dieckmann,
P.Van Der Linden,
P.Carpentier,
G.Leonard,
V.Gordeliy,
A.Popov.
High-Pressure Crystallography Shows Noble Gas Intervention Into Protein-Lipid Interaction and Suggests A Model For Anaesthetic Action. Commun Biol V. 5 360 2022.
ISSN: ESSN 2399-3642
PubMed: 35422073
DOI: 10.1038/S42003-022-03233-Y
Page generated: Tue Aug 13 01:36:17 2024
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