Krypton in PDB 5fst: Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
Enzymatic activity of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
All present enzymatic activity of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure:
3.2.1.17;
Protein crystallography data
The structure of Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fst
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)
|
55.86 /
1.20
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.001,
79.001,
37.053,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
10.9 /
13.4
|
Other elements in 5fst:
The structure of Structure of Lysozyme 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 Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure
(pdb code 5fst). This binding sites where shown within
5.0 Angstroms radius around Krypton atom.
In total 5 binding sites of Krypton where determined in the
Structure of Lysozyme Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure, PDB code: 5fst:
Jump to Krypton binding site number:
1;
2;
3;
4;
5;
Krypton binding site 1 out
of 5 in 5fst
Go back to
Krypton Binding Sites List in 5fst
Krypton binding site 1 out
of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1130
b:37.4
occ:0.33
|
HA
|
A:HIS15
|
3.0
|
14.4
|
1.0
|
CD2
|
A:HIS15
|
3.4
|
21.0
|
1.0
|
HG2
|
A:ARG14
|
3.4
|
26.1
|
1.0
|
HH12
|
A:ARG14
|
3.4
|
47.2
|
1.0
|
NH1
|
A:ARG14
|
3.4
|
58.5
|
1.0
|
HD2
|
A:HIS15
|
3.5
|
21.0
|
1.0
|
O
|
A:HOH2027
|
3.5
|
38.3
|
1.0
|
NE2
|
A:HIS15
|
3.6
|
24.8
|
1.0
|
HH11
|
A:ARG14
|
3.6
|
47.2
|
1.0
|
O
|
A:ARG14
|
3.6
|
17.2
|
1.0
|
CG
|
A:HIS15
|
3.7
|
14.5
|
1.0
|
HE2
|
A:HIS15
|
3.8
|
24.8
|
1.0
|
CZ
|
A:ARG14
|
3.8
|
45.8
|
1.0
|
CA
|
A:HIS15
|
3.9
|
14.4
|
1.0
|
CE1
|
A:HIS15
|
4.1
|
17.9
|
1.0
|
HH22
|
A:ARG14
|
4.1
|
58.5
|
1.0
|
ND1
|
A:HIS15
|
4.1
|
17.5
|
1.0
|
NH2
|
A:ARG14
|
4.1
|
47.2
|
1.0
|
C
|
A:ARG14
|
4.1
|
14.5
|
1.0
|
O
|
A:HOH2024
|
4.2
|
33.5
|
1.0
|
N
|
A:HIS15
|
4.3
|
13.2
|
1.0
|
CG
|
A:ARG14
|
4.3
|
26.1
|
1.0
|
CB
|
A:HIS15
|
4.3
|
14.5
|
1.0
|
O
|
A:HOH2151
|
4.4
|
60.1
|
1.0
|
NE
|
A:ARG14
|
4.4
|
41.1
|
1.0
|
HE1
|
A:HIS15
|
4.6
|
17.9
|
1.0
|
HH21
|
A:ARG14
|
4.6
|
58.5
|
1.0
|
HD1
|
A:HIS15
|
4.7
|
17.5
|
1.0
|
HB3
|
A:HIS15
|
4.7
|
14.5
|
1.0
|
O
|
A:HOH2155
|
4.7
|
29.0
|
1.0
|
HG3
|
A:ARG14
|
4.8
|
26.1
|
1.0
|
CD
|
A:ARG14
|
4.9
|
32.8
|
1.0
|
HB3
|
A:ARG14
|
4.9
|
20.4
|
1.0
|
HE
|
A:ARG14
|
4.9
|
41.1
|
1.0
|
|
Krypton binding site 2 out
of 5 in 5fst
Go back to
Krypton Binding Sites List in 5fst
Krypton binding site 2 out
of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1131
b:17.5
occ:0.50
|
HD12
|
A:ILE55
|
1.5
|
14.5
|
0.5
|
CD1
|
A:ILE55
|
2.4
|
14.5
|
0.5
|
HD13
|
A:ILE55
|
2.5
|
14.5
|
0.5
|
HG22
|
A:ILE55
|
2.9
|
19.8
|
0.5
|
HD11
|
A:ILE55
|
3.0
|
14.5
|
0.5
|
HG23
|
A:VAL92
|
3.1
|
11.9
|
1.0
|
HG21
|
A:VAL92
|
3.2
|
11.9
|
1.0
|
HG13
|
A:ILE55
|
3.2
|
8.8
|
0.5
|
HG21
|
A:ILE55
|
3.2
|
19.8
|
0.5
|
HD13
|
A:LEU56
|
3.2
|
11.9
|
1.0
|
HE3
|
A:MET12
|
3.2
|
11.9
|
1.0
|
HB3
|
A:SER91
|
3.3
|
9.5
|
1.0
|
HD13
|
A:ILE88
|
3.3
|
13.6
|
1.0
|
CG1
|
A:ILE55
|
3.4
|
8.8
|
0.5
|
CG2
|
A:ILE55
|
3.4
|
19.8
|
0.5
|
HG23
|
A:ILE55
|
3.4
|
19.8
|
0.5
|
HB
|
A:ILE88
|
3.4
|
11.0
|
1.0
|
HD12
|
A:LEU56
|
3.4
|
11.9
|
1.0
|
HE1
|
A:MET12
|
3.5
|
11.9
|
1.0
|
CG2
|
A:VAL92
|
3.6
|
11.9
|
1.0
|
HB2
|
A:SER91
|
3.6
|
9.5
|
1.0
|
HG12
|
A:ILE55
|
3.6
|
8.8
|
0.5
|
HG
|
A:LEU56
|
3.6
|
9.6
|
1.0
|
CD1
|
A:LEU56
|
3.7
|
11.9
|
1.0
|
HG2
|
A:MET12
|
3.8
|
9.3
|
1.0
|
CE
|
A:MET12
|
3.8
|
11.9
|
1.0
|
HA
|
A:VAL92
|
3.8
|
10.1
|
1.0
|
CB
|
A:SER91
|
3.9
|
9.5
|
1.0
|
HD12
|
A:LEU17
|
4.0
|
14.1
|
1.0
|
N
|
A:VAL92
|
4.1
|
9.7
|
1.0
|
H
|
A:VAL92
|
4.2
|
9.7
|
1.0
|
CD1
|
A:ILE88
|
4.2
|
13.6
|
1.0
|
HG22
|
A:VAL92
|
4.2
|
11.9
|
1.0
|
CG
|
A:LEU56
|
4.2
|
9.6
|
1.0
|
HD12
|
A:LEU8
|
4.3
|
11.1
|
1.0
|
C
|
A:SER91
|
4.3
|
8.9
|
1.0
|
CB
|
A:ILE88
|
4.3
|
11.0
|
1.0
|
CA
|
A:VAL92
|
4.3
|
10.1
|
1.0
|
HD13
|
A:LEU17
|
4.4
|
14.1
|
1.0
|
HD11
|
A:ILE88
|
4.4
|
13.6
|
1.0
|
HE2
|
A:MET12
|
4.4
|
11.9
|
1.0
|
HG22
|
A:ILE88
|
4.5
|
12.2
|
1.0
|
O
|
A:ILE88
|
4.6
|
10.2
|
1.0
|
CG
|
A:MET12
|
4.6
|
9.3
|
1.0
|
HD11
|
A:LEU56
|
4.6
|
11.9
|
1.0
|
CB
|
A:VAL92
|
4.6
|
12.0
|
1.0
|
CD1
|
A:LEU17
|
4.6
|
14.1
|
1.0
|
O
|
A:SER91
|
4.7
|
9.6
|
1.0
|
CG1
|
A:ILE88
|
4.7
|
11.8
|
1.0
|
CB
|
A:ILE55
|
4.7
|
11.0
|
0.5
|
HG3
|
A:MET12
|
4.7
|
9.3
|
1.0
|
HG23
|
A:ILE88
|
4.8
|
12.2
|
1.0
|
CA
|
A:SER91
|
4.8
|
9.2
|
1.0
|
CG2
|
A:ILE88
|
4.8
|
12.2
|
1.0
|
HG13
|
A:ILE88
|
4.8
|
11.8
|
1.0
|
HG22
|
A:ILE55
|
4.8
|
11.3
|
0.5
|
HG
|
A:SER91
|
4.8
|
9.6
|
0.0
|
CB
|
A:ILE55
|
4.8
|
14.4
|
0.5
|
HD11
|
A:ILE55
|
4.8
|
12.9
|
0.5
|
HB2
|
A:LEU56
|
4.9
|
9.2
|
1.0
|
HB
|
A:ILE55
|
4.9
|
11.0
|
0.5
|
HD12
|
A:ILE88
|
4.9
|
13.6
|
1.0
|
HD11
|
A:LEU17
|
5.0
|
14.1
|
1.0
|
OG
|
A:SER91
|
5.0
|
9.6
|
1.0
|
|
Krypton binding site 3 out
of 5 in 5fst
Go back to
Krypton Binding Sites List in 5fst
Krypton binding site 3 out
of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1132
b:24.8
occ:0.25
|
O
|
A:HOH2096
|
2.3
|
15.7
|
0.5
|
HG1
|
A:THR43
|
2.9
|
13.0
|
0.0
|
OG1
|
A:THR43
|
3.1
|
13.0
|
1.0
|
HB
|
A:THR43
|
3.2
|
11.1
|
1.0
|
CB
|
A:THR43
|
3.7
|
11.1
|
1.0
|
HB2
|
A:ARG45
|
3.7
|
8.2
|
0.2
|
HE
|
A:ARG45
|
3.8
|
20.0
|
0.2
|
HG21
|
A:THR51
|
3.8
|
8.8
|
1.0
|
H
|
A:ARG45
|
3.9
|
11.9
|
0.5
|
HH22
|
A:ARG68
|
3.9
|
11.9
|
0.5
|
HB2
|
A:ARG45
|
3.9
|
14.5
|
0.2
|
HA
|
A:ASN44
|
4.0
|
10.3
|
1.0
|
H
|
A:ARG45
|
4.0
|
11.2
|
0.5
|
HB2
|
A:ARG45
|
4.0
|
18.6
|
0.5
|
HG22
|
A:THR51
|
4.1
|
8.8
|
1.0
|
O
|
A:HOH2092
|
4.2
|
24.0
|
1.0
|
NH2
|
A:ARG45
|
4.2
|
37.0
|
0.5
|
HH21
|
A:ARG45
|
4.2
|
19.2
|
0.2
|
CZ
|
A:ARG45
|
4.2
|
15.5
|
0.5
|
C
|
A:THR43
|
4.2
|
11.0
|
1.0
|
N
|
A:ASN44
|
4.2
|
9.3
|
1.0
|
N
|
A:ARG45
|
4.2
|
11.9
|
0.5
|
HH22
|
A:ARG45
|
4.2
|
37.0
|
0.5
|
N
|
A:ARG45
|
4.3
|
11.2
|
0.5
|
O
|
A:THR43
|
4.3
|
14.7
|
1.0
|
CA
|
A:ASN44
|
4.4
|
10.3
|
1.0
|
HH21
|
A:ARG45
|
4.4
|
37.0
|
0.5
|
CG2
|
A:THR51
|
4.4
|
8.8
|
1.0
|
C
|
A:ASN44
|
4.4
|
9.4
|
1.0
|
H
|
A:ASN44
|
4.5
|
9.3
|
1.0
|
NH2
|
A:ARG68
|
4.6
|
11.9
|
0.5
|
NE
|
A:ARG45
|
4.6
|
14.0
|
0.5
|
HD3
|
A:ARG45
|
4.6
|
8.7
|
0.5
|
HH21
|
A:ARG68
|
4.6
|
11.9
|
0.5
|
CB
|
A:ARG45
|
4.6
|
8.2
|
0.2
|
CA
|
A:THR43
|
4.6
|
9.9
|
1.0
|
NH1
|
A:ARG45
|
4.7
|
22.7
|
0.5
|
HG22
|
A:THR43
|
4.7
|
11.0
|
1.0
|
NE
|
A:ARG45
|
4.7
|
20.0
|
0.2
|
HH12
|
A:ARG45
|
4.7
|
22.7
|
0.5
|
CB
|
A:ARG45
|
4.8
|
14.5
|
0.2
|
CG2
|
A:THR43
|
4.8
|
11.0
|
1.0
|
HE
|
A:ARG45
|
4.9
|
14.0
|
0.5
|
CB
|
A:ARG45
|
4.9
|
18.6
|
0.5
|
HG23
|
A:THR51
|
4.9
|
8.8
|
1.0
|
CA
|
A:ARG45
|
4.9
|
13.0
|
0.5
|
HA
|
A:ARG45
|
4.9
|
10.1
|
0.2
|
CA
|
A:ARG45
|
4.9
|
10.1
|
0.2
|
NH2
|
A:ARG45
|
4.9
|
19.2
|
0.2
|
CA
|
A:ARG45
|
5.0
|
12.0
|
0.2
|
HB3
|
A:ARG45
|
5.0
|
8.2
|
0.2
|
HD3
|
A:ARG45
|
5.0
|
12.2
|
0.2
|
|
Krypton binding site 4 out
of 5 in 5fst
Go back to
Krypton Binding Sites List in 5fst
Krypton binding site 4 out
of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1133
b:19.1
occ:0.20
|
HD11
|
A:LEU84
|
2.4
|
15.6
|
1.0
|
HB3
|
A:GLN41
|
2.9
|
8.3
|
1.0
|
CD1
|
A:LEU84
|
3.2
|
15.6
|
1.0
|
OE1
|
A:GLN41
|
3.3
|
11.3
|
1.0
|
HD13
|
A:LEU84
|
3.4
|
15.6
|
1.0
|
HB3
|
A:LEU84
|
3.6
|
9.5
|
1.0
|
CB
|
A:GLN41
|
3.6
|
8.3
|
1.0
|
HA
|
A:GLN41
|
3.6
|
7.9
|
1.0
|
HG2
|
A:GLN41
|
3.7
|
9.0
|
1.0
|
O
|
A:GLN41
|
3.7
|
10.6
|
1.0
|
HD12
|
A:LEU84
|
3.7
|
15.6
|
1.0
|
CG
|
A:GLN41
|
4.0
|
9.0
|
1.0
|
CD
|
A:GLN41
|
4.0
|
8.6
|
1.0
|
CA
|
A:GLN41
|
4.1
|
7.9
|
1.0
|
HD23
|
A:LEU84
|
4.1
|
9.7
|
1.0
|
CG
|
A:LEU84
|
4.3
|
10.4
|
1.0
|
CB
|
A:LEU84
|
4.3
|
9.5
|
1.0
|
HG21
|
A:THR43
|
4.3
|
11.0
|
1.0
|
C
|
A:GLN41
|
4.4
|
8.7
|
1.0
|
HB2
|
A:GLN41
|
4.4
|
8.3
|
1.0
|
HB2
|
A:LEU84
|
4.5
|
9.5
|
1.0
|
O
|
A:HOH2089
|
4.6
|
9.9
|
1.0
|
CD2
|
A:LEU84
|
4.7
|
9.7
|
1.0
|
HG22
|
A:THR43
|
4.7
|
11.0
|
1.0
|
HG3
|
A:GLN41
|
4.9
|
9.0
|
1.0
|
CG2
|
A:THR43
|
5.0
|
11.0
|
1.0
|
|
Krypton binding site 5 out
of 5 in 5fst
Go back to
Krypton Binding Sites List in 5fst
Krypton binding site 5 out
of 5 in the Structure of Lysozyme 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 Lysozyme 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:Kr1134
b:27.9
occ:0.25
|
HG2
|
A:LYS13
|
3.2
|
18.1
|
1.0
|
HB2
|
A:ARG14
|
3.3
|
20.4
|
1.0
|
HB3
|
A:LYS13
|
3.3
|
14.2
|
1.0
|
HD3
|
A:LYS13
|
3.4
|
20.4
|
1.0
|
HA
|
A:ARG14
|
3.4
|
15.1
|
1.0
|
N
|
A:ARG14
|
3.7
|
13.6
|
1.0
|
H
|
A:ARG14
|
3.7
|
13.6
|
1.0
|
CG
|
A:LYS13
|
3.8
|
18.1
|
1.0
|
O
|
A:ALA10
|
3.9
|
13.1
|
1.0
|
CA
|
A:ARG14
|
3.9
|
15.1
|
1.0
|
CB
|
A:LYS13
|
4.0
|
14.2
|
1.0
|
CB
|
A:ARG14
|
4.0
|
20.4
|
1.0
|
CD
|
A:LYS13
|
4.0
|
20.4
|
1.0
|
C
|
A:LYS13
|
4.1
|
12.8
|
1.0
|
OXT
|
A:LEU129
|
4.2
|
24.8
|
1.0
|
HE2
|
A:LYS13
|
4.4
|
27.0
|
1.0
|
HG3
|
A:ARG14
|
4.4
|
26.1
|
1.0
|
HA
|
A:ALA10
|
4.4
|
12.8
|
1.0
|
HB2
|
A:ALA10
|
4.6
|
14.0
|
1.0
|
O
|
A:LYS13
|
4.7
|
15.2
|
1.0
|
CA
|
A:LYS13
|
4.7
|
13.2
|
1.0
|
HG3
|
A:LYS13
|
4.7
|
18.1
|
1.0
|
HB3
|
A:ARG14
|
4.7
|
20.4
|
1.0
|
HB2
|
A:LYS13
|
4.8
|
14.2
|
1.0
|
CE
|
A:LYS13
|
4.8
|
27.0
|
1.0
|
CG
|
A:ARG14
|
4.8
|
26.1
|
1.0
|
HD2
|
A:LYS13
|
4.8
|
20.4
|
1.0
|
C
|
A:ALA10
|
4.8
|
12.4
|
1.0
|
HA
|
A:LEU129
|
5.0
|
21.9
|
1.0
|
HZ1
|
A:LYS13
|
5.0
|
32.6
|
1.0
|
HD3
|
A:ARG14
|
5.0
|
32.8
|
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 01:26:32 2024
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