Krypton in PDB 7q36: Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton
Protein crystallography data
The structure of Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton, PDB code: 7q36
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)
|
116.72 /
2.60
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.489,
82.18,
233.442,
90,
90,
90
|
R / Rfree (%)
|
21.6 /
26.9
|
Other elements in 7q36:
The structure of Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton also contains other interesting chemical elements:
Krypton Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Krypton atom in the Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton
(pdb code 7q36). This binding sites where shown within
5.0 Angstroms radius around Krypton atom.
In total 11 binding sites of Krypton where determined in the
Crystal Structure of KR2 Sodium Pump Rhodopsin Pressurized with Krypton, PDB code: 7q36:
Jump to Krypton binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Krypton binding site 1 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 1 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr330
b:54.6
occ:0.58
|
CD1
|
A:PHE20
|
3.1
|
52.4
|
1.0
|
CE1
|
A:PHE20
|
3.5
|
53.2
|
1.0
|
O
|
A:GLU237
|
3.6
|
62.3
|
1.0
|
CG1
|
A:VAL240
|
3.6
|
49.5
|
1.0
|
CB
|
A:ALA24
|
3.6
|
56.1
|
1.0
|
CH2
|
A:TRP82
|
3.7
|
48.6
|
1.0
|
CG
|
A:PHE20
|
3.7
|
50.3
|
1.0
|
CZ2
|
A:TRP82
|
3.8
|
48.4
|
1.0
|
OG1
|
A:THR28
|
3.8
|
49.0
|
1.0
|
CB
|
A:VAL240
|
3.9
|
51.5
|
1.0
|
O
|
A:ALA24
|
3.9
|
59.2
|
1.0
|
C
|
A:ALA24
|
4.0
|
55.0
|
1.0
|
CB
|
A:GLU237
|
4.1
|
66.8
|
1.0
|
CG
|
A:MET241
|
4.2
|
68.7
|
1.0
|
CB
|
A:PHE20
|
4.2
|
49.6
|
1.0
|
CZ
|
A:PHE20
|
4.3
|
51.5
|
1.0
|
CA
|
A:GLU237
|
4.3
|
64.7
|
1.0
|
N
|
A:MET241
|
4.3
|
55.1
|
1.0
|
CA
|
A:ALA24
|
4.3
|
57.5
|
1.0
|
N
|
A:TYR25
|
4.3
|
52.7
|
1.0
|
C
|
A:GLU237
|
4.4
|
64.7
|
1.0
|
CD2
|
A:PHE20
|
4.5
|
51.6
|
1.0
|
CB
|
A:THR28
|
4.6
|
51.0
|
1.0
|
CE2
|
A:PHE20
|
4.7
|
51.2
|
1.0
|
C
|
A:VAL240
|
4.8
|
54.4
|
1.0
|
CA
|
A:TYR25
|
4.8
|
51.9
|
1.0
|
CA
|
A:MET241
|
4.8
|
57.0
|
1.0
|
CG2
|
A:VAL240
|
4.9
|
52.3
|
1.0
|
CZ3
|
A:TRP82
|
4.9
|
48.5
|
1.0
|
CA
|
A:VAL240
|
4.9
|
53.6
|
1.0
|
|
Krypton binding site 2 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 2 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr331
b:51.6
occ:0.43
|
C2
|
A:LFA321
|
1.2
|
34.8
|
0.5
|
C3
|
A:LFA321
|
1.9
|
35.6
|
0.5
|
C4
|
A:LFA321
|
3.1
|
35.5
|
0.5
|
C4
|
A:RET341
|
3.6
|
52.2
|
1.0
|
C3
|
A:RET341
|
3.7
|
52.3
|
1.0
|
CD1
|
A:LEU223
|
3.7
|
52.4
|
1.0
|
CG
|
A:LEU223
|
3.7
|
52.0
|
1.0
|
CB
|
A:PRO219
|
3.7
|
52.0
|
1.0
|
CD1
|
A:TYR222
|
3.7
|
50.6
|
1.0
|
OG
|
A:SER175
|
3.8
|
49.7
|
1.0
|
O
|
A:PRO219
|
3.9
|
52.5
|
1.0
|
O
|
A:GLY171
|
4.0
|
54.3
|
1.0
|
CA
|
A:PRO219
|
4.1
|
50.9
|
1.0
|
CD2
|
A:LEU223
|
4.1
|
50.8
|
1.0
|
CE1
|
A:TYR222
|
4.2
|
51.5
|
1.0
|
C5
|
A:LFA321
|
4.3
|
35.1
|
0.5
|
C
|
A:GLY171
|
4.4
|
52.3
|
1.0
|
C
|
A:PRO219
|
4.4
|
51.9
|
1.0
|
CA
|
A:GLY171
|
4.4
|
52.3
|
1.0
|
CG
|
A:TYR222
|
4.5
|
49.9
|
1.0
|
CB
|
A:TYR222
|
4.7
|
50.8
|
1.0
|
C5
|
A:RET341
|
4.8
|
51.0
|
1.0
|
KR
|
A:KR340
|
4.9
|
55.8
|
0.3
|
|
Krypton binding site 3 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 3 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr332
b:45.5
occ:0.78
|
CD1
|
A:ILE50
|
3.4
|
53.1
|
1.0
|
CB
|
A:ALA65
|
3.8
|
40.1
|
1.0
|
O
|
A:PHE46
|
4.0
|
44.3
|
1.0
|
CA
|
A:ILE62
|
4.0
|
41.4
|
1.0
|
O
|
A:ASN61
|
4.0
|
46.1
|
1.0
|
CA
|
A:ILE47
|
4.2
|
45.7
|
1.0
|
N
|
A:ILE62
|
4.3
|
42.1
|
1.0
|
C
|
A:ASN61
|
4.3
|
45.2
|
1.0
|
CG1
|
A:ILE62
|
4.4
|
41.7
|
1.0
|
C
|
A:PHE46
|
4.4
|
42.3
|
1.0
|
CB
|
A:ILE50
|
4.4
|
50.1
|
1.0
|
N
|
A:ILE47
|
4.5
|
45.2
|
1.0
|
CG1
|
A:ILE50
|
4.5
|
52.4
|
1.0
|
CG1
|
A:ILE47
|
4.5
|
48.8
|
1.0
|
CB
|
A:ILE62
|
4.8
|
42.0
|
1.0
|
CG2
|
A:ILE50
|
4.8
|
50.0
|
1.0
|
O
|
A:ILE62
|
4.9
|
41.0
|
1.0
|
O
|
A:ILE47
|
4.9
|
46.3
|
1.0
|
CB
|
A:ILE47
|
4.9
|
46.9
|
1.0
|
|
Krypton binding site 4 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 4 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr333
b:46.6
occ:0.19
|
CZ
|
A:PHE72
|
4.0
|
45.4
|
1.0
|
CE2
|
A:PHE72
|
4.0
|
44.8
|
1.0
|
CE1
|
A:TYR76
|
4.1
|
48.0
|
1.0
|
CD1
|
A:TYR76
|
4.1
|
47.2
|
1.0
|
CZ
|
A:TYR76
|
4.3
|
48.6
|
1.0
|
CG
|
A:TYR76
|
4.4
|
45.6
|
1.0
|
CD2
|
A:LEU73
|
4.6
|
44.6
|
1.0
|
CE2
|
A:TYR76
|
4.6
|
46.6
|
1.0
|
CD2
|
A:TYR76
|
4.7
|
45.4
|
1.0
|
OH
|
A:TYR76
|
4.9
|
50.1
|
1.0
|
|
Krypton binding site 5 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 5 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr334
b:41.5
occ:0.29
|
OG
|
A:SER133
|
3.3
|
44.2
|
1.0
|
OE2
|
A:GLU191
|
3.6
|
45.5
|
1.0
|
CG2
|
A:VAL188
|
3.6
|
39.3
|
1.0
|
CG2
|
A:VAL138
|
3.6
|
42.4
|
1.0
|
CB
|
A:SER133
|
3.6
|
43.3
|
1.0
|
CG
|
A:LYS187
|
3.6
|
38.2
|
1.0
|
N
|
A:VAL188
|
3.7
|
38.3
|
1.0
|
CB
|
A:LYS187
|
3.8
|
39.4
|
1.0
|
CA
|
A:VAL188
|
3.9
|
39.0
|
1.0
|
C
|
A:LYS187
|
3.9
|
38.1
|
1.0
|
CD
|
A:GLU191
|
4.0
|
44.5
|
1.0
|
CD2
|
A:LEU130
|
4.1
|
42.8
|
1.0
|
O
|
A:VAL184
|
4.2
|
43.3
|
1.0
|
OE1
|
A:GLU191
|
4.3
|
44.6
|
1.0
|
O
|
A:LYS187
|
4.3
|
38.7
|
1.0
|
CB
|
A:VAL188
|
4.4
|
38.8
|
1.0
|
CA
|
A:LYS187
|
4.5
|
39.0
|
1.0
|
CG1
|
A:VAL138
|
4.8
|
42.2
|
1.0
|
CG1
|
A:VAL184
|
4.8
|
43.5
|
1.0
|
CB
|
A:VAL138
|
4.8
|
42.5
|
1.0
|
CG
|
A:GLU191
|
4.9
|
43.5
|
1.0
|
|
Krypton binding site 6 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 6 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr335
b:44.6
occ:0.34
|
CD2
|
A:LEU43
|
3.8
|
43.7
|
1.0
|
CD2
|
A:PHE72
|
3.8
|
44.2
|
1.0
|
CE2
|
A:PHE72
|
4.0
|
44.8
|
1.0
|
CG
|
A:PHE72
|
4.8
|
44.1
|
1.0
|
CD2
|
A:LEU73
|
4.8
|
44.6
|
1.0
|
CD1
|
A:LEU40
|
4.9
|
51.5
|
1.0
|
CG1
|
A:VAL69
|
4.9
|
39.4
|
1.0
|
|
Krypton binding site 7 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 7 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr336
b:45.6
occ:0.19
|
C2
|
A:HEX325
|
2.5
|
105.5
|
1.0
|
C1
|
A:HEX325
|
2.7
|
104.6
|
1.0
|
C4
|
A:HEX325
|
2.7
|
102.2
|
1.0
|
C3
|
A:HEX325
|
2.7
|
105.0
|
1.0
|
OG
|
A:SER253
|
3.2
|
42.2
|
1.0
|
O
|
A:ILE249
|
3.4
|
45.4
|
1.0
|
CG2
|
A:ILE249
|
3.8
|
46.3
|
1.0
|
CA
|
A:ILE249
|
3.9
|
44.7
|
1.0
|
CG1
|
A:VAL252
|
3.9
|
46.5
|
1.0
|
CB
|
A:VAL252
|
4.0
|
46.8
|
1.0
|
C
|
A:ILE249
|
4.1
|
44.4
|
1.0
|
C5
|
A:HEX325
|
4.2
|
100.1
|
1.0
|
CB
|
A:ILE249
|
4.3
|
46.6
|
1.0
|
N
|
A:SER253
|
4.4
|
43.6
|
1.0
|
CD1
|
A:ILE257
|
4.5
|
47.2
|
1.0
|
CB
|
A:SER253
|
4.5
|
43.2
|
1.0
|
CG1
|
A:ILE249
|
4.6
|
48.5
|
1.0
|
C6
|
A:HEX325
|
4.7
|
97.0
|
1.0
|
CA
|
A:SER253
|
4.8
|
43.8
|
1.0
|
C
|
A:VAL252
|
4.9
|
45.9
|
1.0
|
CG2
|
A:VAL252
|
5.0
|
48.5
|
1.0
|
|
Krypton binding site 8 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 8 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr337
b:46.9
occ:0.23
|
O
|
A:GLN141
|
3.3
|
45.3
|
1.0
|
CD2
|
A:HIS180
|
3.3
|
49.0
|
1.0
|
C
|
A:GLN141
|
3.5
|
46.0
|
1.0
|
OG
|
A:SER145
|
3.6
|
52.5
|
1.0
|
CG2
|
A:VAL184
|
3.6
|
45.5
|
1.0
|
CA
|
A:ILE181
|
3.7
|
43.5
|
1.0
|
CB
|
A:SER145
|
3.7
|
50.7
|
1.0
|
O
|
A:HIS180
|
3.7
|
46.9
|
1.0
|
NE2
|
A:HIS180
|
3.8
|
48.5
|
1.0
|
N
|
A:ILE181
|
3.8
|
44.1
|
1.0
|
C
|
A:HIS180
|
3.9
|
44.6
|
1.0
|
CG1
|
A:ILE181
|
3.9
|
42.4
|
1.0
|
N
|
A:PHE142
|
3.9
|
44.2
|
1.0
|
CB
|
A:GLN141
|
3.9
|
51.6
|
1.0
|
CD1
|
A:PHE142
|
4.0
|
39.3
|
1.0
|
CB
|
A:VAL184
|
4.0
|
44.5
|
1.0
|
CG
|
A:HIS180
|
4.0
|
47.2
|
1.0
|
CA
|
A:PHE142
|
4.1
|
44.0
|
1.0
|
CA
|
A:GLN141
|
4.3
|
46.2
|
1.0
|
CB
|
A:ILE181
|
4.4
|
43.0
|
1.0
|
CG1
|
A:VAL184
|
4.5
|
43.5
|
1.0
|
CE1
|
A:PHE142
|
4.5
|
38.8
|
1.0
|
CB
|
A:HIS180
|
4.6
|
45.4
|
1.0
|
CE1
|
A:HIS180
|
4.7
|
49.3
|
1.0
|
C
|
A:ILE181
|
4.8
|
43.8
|
1.0
|
ND1
|
A:HIS180
|
4.8
|
47.3
|
1.0
|
O
|
A:ILE181
|
4.8
|
43.6
|
1.0
|
CA
|
A:HIS180
|
4.9
|
44.9
|
1.0
|
CG
|
A:PHE142
|
4.9
|
40.5
|
1.0
|
OE1
|
A:GLN141
|
4.9
|
74.4
|
1.0
|
CD
|
A:GLN141
|
5.0
|
63.2
|
1.0
|
O
|
A:PHE142
|
5.0
|
45.8
|
1.0
|
|
Krypton binding site 9 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 9 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr338
b:43.4
occ:0.20
|
C12
|
A:LFA302
|
0.6
|
39.8
|
0.5
|
C11
|
A:LFA302
|
1.3
|
40.3
|
0.5
|
C10
|
A:LFA302
|
2.5
|
40.9
|
0.5
|
CG2
|
A:ILE213
|
3.6
|
46.2
|
1.0
|
OG
|
A:SER253
|
3.7
|
42.2
|
1.0
|
C9
|
A:LFA302
|
3.7
|
40.9
|
0.5
|
CB
|
A:SER253
|
3.9
|
43.2
|
1.0
|
CD1
|
A:LEU217
|
4.2
|
37.7
|
1.0
|
N
|
A:SER214
|
4.2
|
42.7
|
1.0
|
CA
|
A:SER214
|
4.2
|
42.9
|
1.0
|
CB
|
A:SER214
|
4.4
|
43.1
|
1.0
|
CB
|
A:ILE213
|
4.4
|
45.8
|
1.0
|
CD1
|
A:LEU210
|
4.6
|
42.0
|
1.0
|
CG2
|
A:ILE249
|
4.6
|
46.3
|
1.0
|
C
|
A:ILE213
|
4.7
|
45.3
|
1.0
|
C8
|
A:LFA302
|
5.0
|
40.7
|
0.5
|
|
Krypton binding site 10 out
of 11 in 7q36
Go back to
Krypton Binding Sites List in 7q36
Krypton binding site 10 out
of 11 in the Crystal Structure of KR2 Sodium Pump Rhodopsin 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 KR2 Sodium Pump Rhodopsin Pressurized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr339
b:40.7
occ:0.21
|
CB
|
A:SER70
|
3.9
|
44.5
|
1.0
|
C3
|
A:HEX327
|
4.1
|
33.0
|
1.0
|
O
|
A:VAL66
|
4.2
|
37.8
|
1.0
|
CG1
|
A:VAL69
|
4.2
|
39.4
|
1.0
|
N
|
A:SER70
|
4.2
|
40.5
|
1.0
|
CA
|
A:SER70
|
4.3
|
42.6
|
1.0
|
CG1
|
A:VAL66
|
4.3
|
42.1
|
1.0
|
CB
|
A:VAL69
|
4.6
|
38.8
|
1.0
|
C
|
A:VAL69
|
5.0
|
39.8
|
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 01:38:33 2024
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