Calcium in PDB 2g4z: Anomalous Substructure of Thermolysin
Enzymatic activity of Anomalous Substructure of Thermolysin
All present enzymatic activity of Anomalous Substructure of Thermolysin:
3.4.24.27;
Protein crystallography data
The structure of Anomalous Substructure of Thermolysin, PDB code: 2g4z
was solved by
C.Mueller-Dieckmann,
M.S.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.98
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.487,
92.487,
127.529,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19 /
23.7
|
Other elements in 2g4z:
The structure of Anomalous Substructure of Thermolysin also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Anomalous Substructure of Thermolysin
(pdb code 2g4z). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Anomalous Substructure of Thermolysin, PDB code: 2g4z:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 2g4z
Go back to
Calcium Binding Sites List in 2g4z
Calcium binding site 1 out
of 3 in the Anomalous Substructure of Thermolysin
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Anomalous Substructure of Thermolysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca322
b:35.5
occ:1.00
|
O
|
A:GLN61
|
2.3
|
35.4
|
1.0
|
OD1
|
A:ASP57
|
2.3
|
34.6
|
1.0
|
OD1
|
A:ASP59
|
2.4
|
37.6
|
1.0
|
O
|
A:HOH367
|
2.4
|
35.2
|
1.0
|
O
|
A:HOH395
|
2.4
|
32.6
|
1.0
|
O
|
A:HOH382
|
2.4
|
34.2
|
1.0
|
OD2
|
A:ASP57
|
2.6
|
32.2
|
1.0
|
CG
|
A:ASP57
|
2.8
|
38.5
|
1.0
|
CG
|
A:ASP59
|
3.4
|
32.6
|
1.0
|
C
|
A:GLN61
|
3.4
|
34.4
|
1.0
|
OD2
|
A:ASP59
|
3.8
|
36.2
|
1.0
|
N
|
A:GLN61
|
3.9
|
36.1
|
1.0
|
O
|
A:HOH365
|
4.0
|
36.4
|
1.0
|
CA
|
A:GLN61
|
4.1
|
37.5
|
1.0
|
CB
|
A:ASP57
|
4.3
|
36.2
|
1.0
|
N
|
A:ASP59
|
4.4
|
35.6
|
1.0
|
CB
|
A:GLN61
|
4.4
|
38.3
|
1.0
|
N
|
A:PHE62
|
4.5
|
34.9
|
1.0
|
O
|
A:HOH346
|
4.5
|
33.5
|
1.0
|
OD2
|
A:ASP67
|
4.6
|
35.3
|
1.0
|
CB
|
A:ASP59
|
4.6
|
36.9
|
1.0
|
CA
|
A:PHE62
|
4.7
|
33.7
|
1.0
|
N
|
A:ASN60
|
4.7
|
35.7
|
1.0
|
N
|
A:ALA58
|
4.8
|
33.4
|
1.0
|
CA
|
A:ASP59
|
4.9
|
36.4
|
1.0
|
C
|
A:ASP59
|
4.9
|
36.6
|
1.0
|
|
Calcium binding site 2 out
of 3 in 2g4z
Go back to
Calcium Binding Sites List in 2g4z
Calcium binding site 2 out
of 3 in the Anomalous Substructure of Thermolysin
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Anomalous Substructure of Thermolysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca323
b:36.0
occ:1.00
|
O
|
A:GLU187
|
2.3
|
34.4
|
1.0
|
OE2
|
A:GLU190
|
2.4
|
35.4
|
1.0
|
OD2
|
A:ASP138
|
2.4
|
37.3
|
1.0
|
O
|
A:HOH358
|
2.4
|
33.5
|
1.0
|
OD1
|
A:ASP185
|
2.5
|
35.3
|
1.0
|
OE1
|
A:GLU177
|
2.5
|
32.7
|
1.0
|
OE1
|
A:GLU190
|
2.6
|
39.7
|
1.0
|
OE2
|
A:GLU177
|
2.8
|
36.5
|
1.0
|
CD
|
A:GLU190
|
2.8
|
35.2
|
1.0
|
CD
|
A:GLU177
|
3.0
|
38.3
|
1.0
|
CG
|
A:ASP138
|
3.4
|
37.5
|
1.0
|
C
|
A:GLU187
|
3.4
|
35.5
|
1.0
|
CG
|
A:ASP185
|
3.5
|
42.9
|
1.0
|
OD2
|
A:ASP185
|
3.8
|
40.3
|
1.0
|
CB
|
A:ASP138
|
3.9
|
33.7
|
1.0
|
O
|
A:ASP185
|
4.1
|
37.0
|
1.0
|
N
|
A:GLU187
|
4.2
|
36.7
|
1.0
|
O
|
A:HOH402
|
4.3
|
36.1
|
1.0
|
OD1
|
A:ASP138
|
4.3
|
34.4
|
1.0
|
N
|
A:ILE188
|
4.3
|
37.0
|
1.0
|
CA
|
A:GLU187
|
4.3
|
37.3
|
1.0
|
CA
|
A:ILE188
|
4.3
|
35.8
|
1.0
|
CG
|
A:GLU190
|
4.4
|
38.5
|
1.0
|
CG
|
A:GLU177
|
4.4
|
35.7
|
1.0
|
N
|
A:GLY189
|
4.5
|
36.9
|
1.0
|
C
|
A:ASP185
|
4.5
|
37.9
|
1.0
|
CB
|
A:GLU187
|
4.5
|
37.9
|
1.0
|
N
|
A:ASP185
|
4.6
|
38.0
|
1.0
|
CB
|
A:ASP185
|
4.8
|
38.4
|
1.0
|
C
|
A:ILE188
|
4.8
|
37.6
|
1.0
|
CA
|
A:ASP185
|
4.8
|
37.8
|
1.0
|
CB
|
A:GLU177
|
4.9
|
34.0
|
1.0
|
|
Calcium binding site 3 out
of 3 in 2g4z
Go back to
Calcium Binding Sites List in 2g4z
Calcium binding site 3 out
of 3 in the Anomalous Substructure of Thermolysin
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Anomalous Substructure of Thermolysin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca324
b:40.9
occ:1.00
|
O
|
A:HOH356
|
2.1
|
48.0
|
1.0
|
OG1
|
A:THR194
|
2.2
|
42.8
|
1.0
|
OD1
|
A:ASP200
|
2.3
|
38.7
|
1.0
|
O
|
A:ILE197
|
2.3
|
47.7
|
1.0
|
O
|
A:THR194
|
2.4
|
45.4
|
1.0
|
O
|
A:HOH339
|
2.4
|
38.7
|
1.0
|
O
|
A:TYR193
|
2.4
|
35.8
|
1.0
|
C
|
A:THR194
|
3.2
|
43.9
|
1.0
|
CB
|
A:THR194
|
3.3
|
43.5
|
1.0
|
C
|
A:TYR193
|
3.4
|
39.3
|
1.0
|
CG
|
A:ASP200
|
3.4
|
37.6
|
1.0
|
C
|
A:ILE197
|
3.5
|
50.5
|
1.0
|
CA
|
A:THR194
|
3.6
|
43.0
|
1.0
|
OD2
|
A:ASP200
|
3.8
|
37.3
|
1.0
|
N
|
A:THR194
|
3.9
|
41.1
|
1.0
|
N
|
A:PRO195
|
4.2
|
45.2
|
1.0
|
CA
|
A:ILE197
|
4.2
|
51.1
|
1.0
|
N
|
A:ILE197
|
4.3
|
52.6
|
1.0
|
CB
|
A:ILE197
|
4.3
|
51.6
|
1.0
|
O
|
A:ASP200
|
4.4
|
40.6
|
1.0
|
CA
|
A:TYR193
|
4.5
|
38.9
|
1.0
|
CG2
|
A:THR194
|
4.5
|
44.6
|
1.0
|
N
|
A:SER198
|
4.5
|
47.9
|
1.0
|
O
|
A:GLU190
|
4.6
|
38.0
|
1.0
|
N
|
A:ASP200
|
4.6
|
42.7
|
1.0
|
CB
|
A:TYR193
|
4.6
|
40.0
|
1.0
|
CA
|
A:PRO195
|
4.6
|
47.3
|
1.0
|
O
|
A:HOH418
|
4.7
|
48.5
|
1.0
|
CA
|
A:SER198
|
4.7
|
49.8
|
1.0
|
CB
|
A:ASP200
|
4.7
|
42.2
|
1.0
|
CD2
|
A:TYR193
|
4.7
|
45.5
|
1.0
|
C
|
A:ASP200
|
4.8
|
41.4
|
1.0
|
C
|
A:PRO195
|
4.9
|
48.6
|
1.0
|
C
|
A:SER198
|
4.9
|
49.1
|
1.0
|
CA
|
A:ASP200
|
4.9
|
41.3
|
1.0
|
N
|
A:TYR193
|
4.9
|
37.2
|
1.0
|
N
|
A:GLY199
|
5.0
|
48.7
|
1.0
|
CG
|
A:TYR193
|
5.0
|
42.9
|
1.0
|
|
Reference:
C.Mueller-Dieckmann,
S.Panjikar,
A.Schmidt,
S.Mueller,
J.Kuper,
A.Geerlof,
M.Wilmanns,
R.K.Singh,
P.A.Tucker,
M.S.Weiss.
On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part IV. Efficient Determination of Anomalous Substructures in Biomacromolecules Using Longer X-Ray Wavelengths. Acta Crystallogr.,Sect.D V. 63 366 2007.
ISSN: ISSN 0907-4449
PubMed: 17327674
DOI: 10.1107/S0907444906055624
Page generated: Fri Jul 12 10:41:54 2024
|