Krypton in PDB 5fsp: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure:
3.4.24.27;
Protein crystallography data
The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fsp
was solved by
B.Lafumat,
C.Mueller-Dieckmann,
N.Colloc'h,
T.Prange,
A.Royant,
P.Van Derlinden,
P.Carpentier,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.50 /
1.70
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.007,
93.007,
129.120,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.5 /
17.8
|
Other elements in 5fsp:
The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure also contains other interesting chemical elements:
Krypton Binding Sites:
The binding sites of Krypton atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
(pdb code 5fsp). This binding sites where shown within
5.0 Angstroms radius around Krypton atom.
In total 8 binding sites of Krypton where determined in the
Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fsp:
Jump to Krypton binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Krypton binding site 1 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 1 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 1 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1318
b:24.9
occ:1.00
|
CD2
|
A:TYR84
|
3.6
|
11.4
|
1.0
|
C
|
A:SER92
|
3.6
|
11.3
|
1.0
|
N
|
A:TYR93
|
3.7
|
8.2
|
1.0
|
CD2
|
A:LEU144
|
3.7
|
23.4
|
1.0
|
CA
|
A:SER92
|
3.8
|
9.1
|
1.0
|
CG
|
A:LEU144
|
3.9
|
19.0
|
1.0
|
CA
|
A:TYR93
|
4.0
|
13.1
|
1.0
|
O
|
A:SER92
|
4.1
|
10.9
|
1.0
|
O
|
A:HOH2108
|
4.1
|
10.1
|
1.0
|
CG
|
A:TYR84
|
4.1
|
9.0
|
1.0
|
CB
|
A:TYR84
|
4.2
|
8.1
|
1.0
|
CE2
|
A:TYR84
|
4.3
|
7.2
|
1.0
|
CG2
|
A:VAL148
|
4.3
|
10.7
|
1.0
|
CB
|
A:TYR93
|
4.3
|
11.2
|
1.0
|
CA
|
A:TYR81
|
4.5
|
8.7
|
1.0
|
O
|
A:THR80
|
4.5
|
8.9
|
1.0
|
CD1
|
A:ILE100
|
4.5
|
12.1
|
1.0
|
CG2
|
A:THR80
|
4.6
|
7.8
|
1.0
|
CD1
|
A:LEU144
|
4.6
|
18.6
|
1.0
|
N
|
A:SER92
|
4.7
|
10.4
|
1.0
|
OG
|
A:SER92
|
4.7
|
10.3
|
1.0
|
N
|
A:TYR81
|
4.8
|
7.7
|
1.0
|
C
|
A:THR80
|
4.8
|
8.2
|
1.0
|
CB
|
A:SER92
|
4.9
|
9.5
|
1.0
|
|
Krypton binding site 2 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 2 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 2 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1319
b:27.3
occ:0.55
|
O
|
A:ALA98
|
3.2
|
11.3
|
1.0
|
O
|
A:ARG35
|
3.3
|
14.0
|
1.0
|
O
|
A:GLY38
|
3.4
|
10.4
|
1.0
|
CE2
|
A:TYR81
|
3.7
|
11.6
|
1.0
|
CD2
|
A:TYR81
|
3.8
|
9.1
|
1.0
|
OG
|
A:SER92
|
3.8
|
10.3
|
1.0
|
CD1
|
A:ILE100
|
3.9
|
12.1
|
1.0
|
CG1
|
A:ILE100
|
4.0
|
9.0
|
1.0
|
C
|
A:ARG35
|
4.0
|
10.8
|
1.0
|
N
|
A:GLY38
|
4.0
|
9.5
|
1.0
|
N
|
A:ASN37
|
4.0
|
11.9
|
1.0
|
C
|
A:GLY38
|
4.0
|
9.0
|
1.0
|
CB
|
A:SER92
|
4.0
|
9.5
|
1.0
|
CA
|
A:GLY36
|
4.0
|
12.4
|
1.0
|
N
|
A:ILE100
|
4.1
|
8.2
|
1.0
|
C
|
A:ALA98
|
4.1
|
11.6
|
1.0
|
O
|
A:ASN97
|
4.2
|
11.4
|
1.0
|
CA
|
A:ALA99
|
4.3
|
9.6
|
1.0
|
CG1
|
A:ILE39
|
4.3
|
10.3
|
1.0
|
N
|
A:GLY36
|
4.3
|
9.8
|
1.0
|
C
|
A:GLY36
|
4.4
|
13.6
|
1.0
|
C
|
A:ASN97
|
4.4
|
9.5
|
1.0
|
C
|
A:ALA99
|
4.5
|
10.3
|
1.0
|
N
|
A:ALA99
|
4.6
|
12.2
|
1.0
|
CA
|
A:GLY38
|
4.6
|
6.9
|
1.0
|
CB
|
A:ILE100
|
4.6
|
6.0
|
1.0
|
CB
|
A:ARG35
|
4.8
|
8.0
|
1.0
|
C
|
A:ASN37
|
4.8
|
11.8
|
1.0
|
CZ
|
A:TYR81
|
4.8
|
13.0
|
1.0
|
N
|
A:ILE39
|
4.8
|
7.4
|
1.0
|
CA
|
A:ASN97
|
4.8
|
11.4
|
1.0
|
CG
|
A:TYR81
|
4.8
|
6.5
|
1.0
|
CB
|
A:ASN97
|
4.9
|
20.6
|
1.0
|
CA
|
A:ASN37
|
4.9
|
12.4
|
1.0
|
CA
|
A:ILE100
|
5.0
|
6.1
|
1.0
|
|
Krypton binding site 3 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 3 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 3 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1320
b:20.6
occ:0.34
|
O
|
A:TYR193
|
3.3
|
12.5
|
1.0
|
CA
|
A:PRO195
|
3.4
|
19.8
|
1.0
|
O
|
A:ASP191
|
3.4
|
13.6
|
1.0
|
O
|
A:HOH2201
|
3.5
|
19.3
|
1.0
|
C
|
A:VAL192
|
3.5
|
12.1
|
1.0
|
N
|
A:PRO195
|
3.6
|
14.4
|
1.0
|
N
|
A:TYR193
|
3.7
|
11.2
|
1.0
|
CB
|
A:PRO195
|
3.7
|
18.7
|
1.0
|
C
|
A:TYR193
|
3.8
|
14.6
|
1.0
|
CA
|
A:VAL192
|
3.8
|
10.7
|
1.0
|
O
|
A:VAL192
|
3.8
|
13.1
|
1.0
|
CD1
|
A:ILE131
|
3.9
|
12.9
|
1.0
|
C
|
A:ASP191
|
3.9
|
12.4
|
1.0
|
C
|
A:THR194
|
4.0
|
13.7
|
1.0
|
CD
|
A:PRO195
|
4.0
|
21.9
|
1.0
|
N
|
A:VAL192
|
4.1
|
10.9
|
1.0
|
CG1
|
A:ILE131
|
4.1
|
8.6
|
1.0
|
O
|
A:THR194
|
4.3
|
19.5
|
1.0
|
CA
|
A:TYR193
|
4.3
|
9.7
|
1.0
|
N
|
A:THR194
|
4.4
|
14.0
|
1.0
|
O
|
A:GLU190
|
4.4
|
13.5
|
1.0
|
CG
|
A:PRO195
|
4.4
|
20.1
|
1.0
|
CG2
|
A:ILE131
|
4.6
|
16.3
|
1.0
|
CA
|
A:CA1326
|
4.7
|
13.9
|
1.0
|
C
|
A:PRO195
|
4.7
|
22.1
|
1.0
|
CA
|
A:THR194
|
4.8
|
15.3
|
1.0
|
|
Krypton binding site 4 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 4 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 4 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1321
b:17.6
occ:0.20
|
CE2
|
A:PHE281
|
3.3
|
13.6
|
1.0
|
O
|
A:HOH2186
|
3.4
|
23.3
|
1.0
|
ND2
|
A:ASN233
|
3.6
|
14.4
|
1.0
|
CG
|
A:GLU160
|
3.6
|
12.2
|
1.0
|
CZ
|
A:PHE281
|
3.6
|
13.4
|
1.0
|
CG
|
A:ASN233
|
3.6
|
13.6
|
1.0
|
CB
|
A:ARG220
|
3.7
|
17.8
|
1.0
|
OE2
|
A:GLU160
|
3.7
|
17.1
|
1.0
|
CB
|
A:ASN233
|
3.8
|
12.1
|
1.0
|
CD
|
A:ARG220
|
3.8
|
16.7
|
1.0
|
CD
|
A:GLU160
|
3.9
|
12.1
|
1.0
|
CE1
|
A:TYR217
|
3.9
|
17.7
|
1.0
|
CD2
|
A:PHE281
|
3.9
|
12.7
|
1.0
|
OD1
|
A:ASN233
|
4.2
|
12.8
|
1.0
|
CG
|
A:ARG220
|
4.3
|
15.4
|
1.0
|
CE1
|
A:PHE281
|
4.4
|
10.9
|
1.0
|
CD1
|
A:ILE236
|
4.4
|
9.3
|
1.0
|
CD1
|
A:TYR217
|
4.4
|
14.2
|
1.0
|
O
|
A:HOH2079
|
4.5
|
33.5
|
1.0
|
CG
|
A:PHE281
|
4.7
|
13.0
|
1.0
|
CB
|
A:GLU160
|
4.7
|
12.9
|
1.0
|
OE1
|
A:GLU160
|
4.8
|
13.6
|
1.0
|
CZ
|
A:TYR217
|
4.8
|
15.5
|
1.0
|
O
|
A:HOH2181
|
4.8
|
17.5
|
1.0
|
CD1
|
A:PHE281
|
4.9
|
12.0
|
1.0
|
CA
|
A:ARG220
|
4.9
|
13.5
|
1.0
|
CA
|
A:GLU160
|
5.0
|
9.9
|
1.0
|
OH
|
A:TYR217
|
5.0
|
15.7
|
1.0
|
NE
|
A:ARG220
|
5.0
|
20.6
|
1.0
|
|
Krypton binding site 5 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 5 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 5 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1322
b:27.1
occ:0.28
|
OE1
|
A:GLN119
|
3.4
|
10.3
|
1.0
|
O
|
A:HOH2156
|
3.9
|
30.3
|
0.5
|
CD
|
A:ARG101
|
3.9
|
16.2
|
1.0
|
CD
|
A:GLN119
|
3.9
|
10.2
|
1.0
|
CB
|
A:GLN119
|
4.1
|
5.7
|
1.0
|
CB
|
A:PRO51
|
4.1
|
8.3
|
1.0
|
CG
|
A:GLN119
|
4.1
|
6.7
|
1.0
|
CG
|
A:PRO51
|
4.1
|
12.1
|
1.0
|
O
|
A:HOH2153
|
4.2
|
31.7
|
1.0
|
CD
|
A:PRO51
|
4.3
|
12.8
|
1.0
|
CB
|
A:ARG101
|
4.5
|
8.3
|
1.0
|
O
|
A:SER118
|
4.6
|
10.5
|
1.0
|
CB
|
A:SER118
|
4.7
|
11.2
|
1.0
|
CG
|
A:ARG101
|
4.7
|
12.1
|
1.0
|
NE
|
A:ARG101
|
4.8
|
24.3
|
1.0
|
NE2
|
A:GLN119
|
4.8
|
13.5
|
1.0
|
N
|
A:PRO51
|
4.9
|
11.0
|
1.0
|
C
|
A:SER118
|
5.0
|
11.6
|
1.0
|
|
Krypton binding site 6 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 6 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 6 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1323
b:23.6
occ:0.24
|
O
|
A:HOH2212
|
2.8
|
27.2
|
1.0
|
N
|
A:PRO214
|
3.6
|
11.5
|
1.0
|
O
|
A:GLY212
|
3.6
|
16.5
|
1.0
|
CA
|
A:PRO214
|
3.7
|
14.0
|
1.0
|
C
|
A:ASP213
|
3.9
|
11.9
|
1.0
|
CD
|
A:PRO214
|
4.0
|
12.6
|
1.0
|
CB
|
A:PRO214
|
4.1
|
12.8
|
1.0
|
O
|
A:ASP213
|
4.1
|
13.7
|
1.0
|
O
|
A:LYS219
|
4.3
|
16.0
|
1.0
|
C
|
A:GLY212
|
4.3
|
17.5
|
1.0
|
CB
|
A:LYS219
|
4.4
|
20.5
|
1.0
|
CA
|
A:ASP213
|
4.5
|
11.8
|
1.0
|
CD
|
A:LYS219
|
4.7
|
35.6
|
1.0
|
N
|
A:ASP213
|
4.7
|
13.1
|
1.0
|
CG
|
A:PRO214
|
4.7
|
10.7
|
1.0
|
O
|
A:HOH2220
|
4.8
|
24.5
|
1.0
|
|
Krypton binding site 7 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 7 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 7 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1324
b:22.5
occ:0.22
|
O
|
A:HOH2032
|
2.8
|
26.3
|
1.0
|
ND2
|
A:ASN21
|
3.3
|
10.2
|
1.0
|
CG
|
A:ASN21
|
3.6
|
9.7
|
1.0
|
CG1
|
A:VAL7
|
3.6
|
9.9
|
1.0
|
OD1
|
A:ASN21
|
3.6
|
14.9
|
1.0
|
O
|
A:HOH2039
|
3.6
|
22.0
|
1.0
|
O
|
A:HOH2037
|
3.8
|
20.3
|
1.0
|
C
|
A:ILE20
|
3.9
|
11.6
|
0.4
|
C
|
A:ILE20
|
3.9
|
11.6
|
0.6
|
N
|
A:ASN21
|
3.9
|
9.2
|
1.0
|
CB
|
A:ASN19
|
4.0
|
12.5
|
1.0
|
C
|
A:ASN19
|
4.1
|
10.5
|
1.0
|
CG2
|
A:VAL7
|
4.1
|
12.6
|
1.0
|
N
|
A:ILE20
|
4.1
|
10.7
|
0.4
|
N
|
A:ILE20
|
4.1
|
10.8
|
0.6
|
O
|
A:ASN19
|
4.1
|
11.0
|
1.0
|
O
|
A:ILE20
|
4.2
|
11.1
|
0.4
|
O
|
A:ILE20
|
4.2
|
11.2
|
0.6
|
CA
|
A:ILE20
|
4.2
|
10.5
|
0.4
|
CA
|
A:ILE20
|
4.2
|
10.5
|
0.6
|
CA
|
A:ASN21
|
4.3
|
8.3
|
1.0
|
CB
|
A:VAL7
|
4.4
|
9.8
|
1.0
|
O
|
A:HOH2038
|
4.5
|
18.7
|
1.0
|
CB
|
A:ASN21
|
4.6
|
9.7
|
1.0
|
O
|
A:HOH2015
|
4.6
|
33.8
|
1.0
|
CA
|
A:ASN19
|
4.7
|
11.6
|
1.0
|
O
|
A:HOH2036
|
5.0
|
12.4
|
1.0
|
|
Krypton binding site 8 out
of 8 in 5fsp
Go back to
Krypton Binding Sites List in 5fsp
Krypton binding site 8 out
of 8 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 8 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr1325
b:22.5
occ:0.23
|
CG1
|
A:VAL2318
|
3.1
|
40.7
|
1.0
|
CA
|
A:VAL2318
|
3.4
|
25.7
|
1.0
|
CG
|
A:HIS142
|
3.4
|
9.9
|
1.0
|
NH2
|
A:ARG203
|
3.6
|
10.9
|
1.0
|
ND1
|
A:HIS142
|
3.6
|
8.3
|
1.0
|
CD2
|
A:HIS142
|
3.7
|
6.7
|
1.0
|
O
|
A:VAL2318
|
3.7
|
23.6
|
1.0
|
CB
|
A:VAL2318
|
3.8
|
32.4
|
1.0
|
CB
|
A:HIS142
|
3.8
|
8.1
|
1.0
|
CG2
|
A:ILE188
|
3.8
|
13.0
|
1.0
|
C
|
A:VAL2318
|
4.0
|
28.8
|
1.0
|
CE1
|
A:HIS142
|
4.0
|
10.3
|
1.0
|
NE2
|
A:HIS142
|
4.0
|
10.0
|
1.0
|
CA
|
A:VAL139
|
4.1
|
6.7
|
1.0
|
CG1
|
A:VAL139
|
4.2
|
10.1
|
1.0
|
CG2
|
A:VAL139
|
4.3
|
10.4
|
1.0
|
OE2
|
A:GLU143
|
4.3
|
18.1
|
1.0
|
N
|
A:VAL2318
|
4.4
|
24.1
|
1.0
|
CB
|
A:VAL139
|
4.4
|
10.2
|
1.0
|
O
|
A:VAL139
|
4.7
|
8.4
|
1.0
|
OD1
|
A:ASP170
|
4.7
|
11.2
|
1.0
|
CZ
|
A:ARG203
|
4.8
|
13.8
|
1.0
|
O
|
A:ASP138
|
4.9
|
10.9
|
1.0
|
O
|
A:HOH2165
|
4.9
|
36.9
|
1.0
|
CD2
|
A:LEU202
|
5.0
|
23.3
|
1.0
|
C
|
A:VAL139
|
5.0
|
9.6
|
1.0
|
|
Reference:
B.Lafumat,
C.Mueller-Dieckmann,
N.Colloc'h,
T.Prange,
A.Royant,
P.Van Der Linden,
P.Carpentier.
Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using A Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. V. 49 1478 2016.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576716010992
Page generated: Tue Aug 13 01:25:53 2024
|