Calcium in PDB 5fss: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure
Enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure
All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 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 40 Bar of Krypton Pressure, PDB code: 5fss
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)
|
46.38 /
1.50
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.749,
92.749,
128.995,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.2 /
18
|
Other elements in 5fss:
The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure
(pdb code 5fss). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure, PDB code: 5fss:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 5fss
Go back to
Calcium Binding Sites List in 5fss
Calcium binding site 1 out
of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:12.5
occ:1.00
|
O
|
A:GLU187
|
2.3
|
12.8
|
1.0
|
OD1
|
A:ASP185
|
2.4
|
14.2
|
1.0
|
OD2
|
A:ASP138
|
2.4
|
12.2
|
1.0
|
OE2
|
A:GLU190
|
2.5
|
15.1
|
1.0
|
OE1
|
A:GLU177
|
2.5
|
13.3
|
1.0
|
O
|
A:HOH2217
|
2.5
|
13.9
|
1.0
|
OE1
|
A:GLU190
|
2.6
|
13.1
|
1.0
|
OE2
|
A:GLU177
|
2.7
|
14.2
|
1.0
|
CD
|
A:GLU190
|
2.8
|
13.0
|
1.0
|
CD
|
A:GLU177
|
2.9
|
14.0
|
1.0
|
C
|
A:GLU187
|
3.4
|
10.7
|
1.0
|
CG
|
A:ASP138
|
3.4
|
11.3
|
1.0
|
CG
|
A:ASP185
|
3.4
|
16.5
|
1.0
|
CA
|
A:CA402
|
3.8
|
16.0
|
0.5
|
OD2
|
A:ASP185
|
3.8
|
19.0
|
1.0
|
CB
|
A:ASP138
|
4.0
|
9.2
|
1.0
|
O
|
A:ASP185
|
4.0
|
14.0
|
1.0
|
N
|
A:GLU187
|
4.1
|
14.2
|
1.0
|
CA
|
A:GLU187
|
4.3
|
13.2
|
1.0
|
N
|
A:ILE188
|
4.3
|
11.2
|
1.0
|
O
|
A:HOH2194
|
4.3
|
14.5
|
1.0
|
OD1
|
A:ASP138
|
4.3
|
13.4
|
1.0
|
CG
|
A:GLU190
|
4.3
|
13.8
|
1.0
|
CA
|
A:ILE188
|
4.3
|
11.9
|
1.0
|
CG
|
A:GLU177
|
4.4
|
12.4
|
1.0
|
N
|
A:GLY189
|
4.4
|
10.7
|
1.0
|
C
|
A:ASP185
|
4.5
|
14.7
|
1.0
|
CB
|
A:GLU187
|
4.6
|
15.3
|
1.0
|
O
|
A:HOH2220
|
4.6
|
25.3
|
1.0
|
N
|
A:ASP185
|
4.7
|
14.9
|
1.0
|
CB
|
A:ASP185
|
4.7
|
13.8
|
1.0
|
C
|
A:ILE188
|
4.8
|
11.9
|
1.0
|
CA
|
A:ASP185
|
4.9
|
12.6
|
1.0
|
CB
|
A:GLU177
|
4.9
|
11.5
|
1.0
|
N
|
A:GLU190
|
5.0
|
12.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 5fss
Go back to
Calcium Binding Sites List in 5fss
Calcium binding site 2 out
of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:16.0
occ:0.50
|
OE2
|
A:GLU190
|
2.3
|
15.1
|
1.0
|
O
|
A:HOH2220
|
2.4
|
25.3
|
1.0
|
O
|
A:HOH2223
|
2.4
|
32.9
|
1.0
|
O
|
A:ASN183
|
2.5
|
23.0
|
1.0
|
OD2
|
A:ASP185
|
2.7
|
19.0
|
1.0
|
OE2
|
A:GLU177
|
2.7
|
14.2
|
1.0
|
CD
|
A:GLU190
|
3.3
|
13.0
|
1.0
|
CD
|
A:GLU177
|
3.3
|
14.0
|
1.0
|
CG
|
A:ASP185
|
3.4
|
16.5
|
1.0
|
C
|
A:ASN183
|
3.7
|
18.1
|
1.0
|
OD1
|
A:ASP185
|
3.7
|
14.2
|
1.0
|
OE1
|
A:GLU177
|
3.7
|
13.3
|
1.0
|
CG
|
A:GLU190
|
3.7
|
13.8
|
1.0
|
CA
|
A:CA401
|
3.8
|
12.5
|
1.0
|
O
|
A:HOH2222
|
4.0
|
32.2
|
1.0
|
CA
|
A:PRO184
|
4.1
|
15.7
|
1.0
|
N
|
A:ASP185
|
4.2
|
14.9
|
1.0
|
OD2
|
A:ASP191
|
4.2
|
18.1
|
1.0
|
OD1
|
A:ASP191
|
4.2
|
18.0
|
1.0
|
OE1
|
A:GLU190
|
4.3
|
13.1
|
1.0
|
C
|
A:PRO184
|
4.3
|
18.0
|
1.0
|
CG
|
A:GLU177
|
4.3
|
12.4
|
1.0
|
CB
|
A:ASN183
|
4.4
|
31.1
|
1.0
|
CB
|
A:ASP185
|
4.4
|
13.8
|
1.0
|
N
|
A:PRO184
|
4.4
|
17.3
|
1.0
|
O
|
A:LYS182
|
4.5
|
29.3
|
1.0
|
CG
|
A:ASP191
|
4.5
|
17.2
|
1.0
|
CA
|
A:ASN183
|
4.7
|
25.5
|
1.0
|
O
|
A:HOH2194
|
4.8
|
14.5
|
1.0
|
O
|
A:HOH2224
|
4.9
|
34.4
|
1.0
|
CA
|
A:ASP185
|
4.9
|
12.6
|
1.0
|
|
Calcium binding site 3 out
of 4 in 5fss
Go back to
Calcium Binding Sites List in 5fss
Calcium binding site 3 out
of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:12.6
occ:1.00
|
O
|
A:GLN61
|
2.3
|
12.4
|
1.0
|
OD1
|
A:ASP59
|
2.4
|
12.5
|
1.0
|
OD2
|
A:ASP57
|
2.4
|
12.9
|
1.0
|
O
|
A:HOH2109
|
2.4
|
15.5
|
1.0
|
O
|
A:HOH2112
|
2.4
|
14.8
|
1.0
|
O
|
A:HOH2110
|
2.5
|
13.9
|
1.0
|
OD1
|
A:ASP57
|
2.6
|
12.2
|
1.0
|
CG
|
A:ASP57
|
2.8
|
13.7
|
1.0
|
CG
|
A:ASP59
|
3.4
|
13.9
|
1.0
|
C
|
A:GLN61
|
3.5
|
10.4
|
1.0
|
OD2
|
A:ASP59
|
3.8
|
16.6
|
1.0
|
N
|
A:GLN61
|
3.9
|
12.1
|
1.0
|
O
|
A:HOH2116
|
4.0
|
16.2
|
1.0
|
CA
|
A:GLN61
|
4.1
|
11.1
|
1.0
|
N
|
A:ASP59
|
4.3
|
12.3
|
1.0
|
CB
|
A:GLN61
|
4.3
|
13.3
|
1.0
|
CB
|
A:ASP57
|
4.3
|
11.7
|
1.0
|
O
|
A:HOH2043
|
4.4
|
21.8
|
1.0
|
O
|
A:HOH2111
|
4.5
|
16.2
|
1.0
|
N
|
A:PHE62
|
4.6
|
10.7
|
1.0
|
O
|
A:HOH2042
|
4.6
|
29.4
|
1.0
|
CB
|
A:ASP59
|
4.6
|
11.6
|
1.0
|
OD2
|
A:ASP67
|
4.6
|
11.8
|
1.0
|
N
|
A:ASN60
|
4.6
|
12.2
|
1.0
|
O
|
A:HOH2105
|
4.6
|
11.9
|
1.0
|
O
|
A:HOH2044
|
4.7
|
32.7
|
1.0
|
N
|
A:ALA58
|
4.7
|
11.9
|
1.0
|
CA
|
A:ASP59
|
4.8
|
11.8
|
1.0
|
CA
|
A:PHE62
|
4.8
|
10.4
|
1.0
|
C
|
A:ASP59
|
4.9
|
13.5
|
1.0
|
|
Calcium binding site 4 out
of 4 in 5fss
Go back to
Calcium Binding Sites List in 5fss
Calcium binding site 4 out
of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:15.5
occ:1.00
|
O
|
A:ILE197
|
2.3
|
20.2
|
1.0
|
O
|
A:TYR193
|
2.3
|
15.8
|
1.0
|
O
|
A:THR194
|
2.4
|
17.8
|
1.0
|
OD1
|
A:ASP200
|
2.4
|
16.5
|
1.0
|
OG1
|
A:THR194
|
2.4
|
18.6
|
1.0
|
O
|
A:HOH2228
|
2.4
|
15.9
|
1.0
|
O
|
A:HOH2231
|
2.5
|
22.2
|
1.0
|
C
|
A:THR194
|
3.2
|
17.1
|
1.0
|
C
|
A:TYR193
|
3.3
|
15.8
|
1.0
|
C
|
A:ILE197
|
3.4
|
25.5
|
1.0
|
CG
|
A:ASP200
|
3.5
|
13.4
|
1.0
|
CB
|
A:THR194
|
3.5
|
16.1
|
1.0
|
CA
|
A:THR194
|
3.7
|
16.1
|
1.0
|
OD2
|
A:ASP200
|
3.8
|
17.6
|
1.0
|
N
|
A:THR194
|
3.9
|
15.2
|
1.0
|
CA
|
A:ILE197
|
4.2
|
24.1
|
1.0
|
CB
|
A:ILE197
|
4.2
|
22.1
|
1.0
|
N
|
A:ILE197
|
4.3
|
26.5
|
1.0
|
N
|
A:PRO195
|
4.3
|
16.4
|
1.0
|
O
|
A:HOH2234
|
4.4
|
30.0
|
1.0
|
O
|
A:ASP200
|
4.5
|
16.2
|
1.0
|
N
|
A:SER198
|
4.5
|
27.4
|
1.0
|
CA
|
A:TYR193
|
4.5
|
14.9
|
1.0
|
O
|
A:GLU190
|
4.6
|
15.2
|
1.0
|
O
|
A:HOH2229
|
4.6
|
23.9
|
1.0
|
N
|
A:ASP200
|
4.6
|
18.3
|
1.0
|
CA
|
A:SER198
|
4.6
|
25.9
|
1.0
|
CA
|
A:PRO195
|
4.7
|
18.2
|
1.0
|
CD2
|
A:TYR193
|
4.7
|
16.4
|
1.0
|
CB
|
A:TYR193
|
4.7
|
14.5
|
1.0
|
CG2
|
A:THR194
|
4.7
|
19.1
|
1.0
|
CB
|
A:ASP200
|
4.8
|
17.5
|
1.0
|
C
|
A:ASP200
|
4.8
|
13.1
|
1.0
|
CG2
|
A:ILE197
|
4.8
|
23.1
|
1.0
|
N
|
A:GLY199
|
4.9
|
23.9
|
1.0
|
C
|
A:SER198
|
4.9
|
23.5
|
1.0
|
CA
|
A:ASP200
|
5.0
|
17.7
|
1.0
|
C
|
A:PRO195
|
5.0
|
23.0
|
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: Sun Jul 14 19:20:39 2024
|