Calcium in PDB 6r7v: Tannerella Forsythia Promirolysin Mutant E225A
Protein crystallography data
The structure of Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7v
was solved by
A.Rodriguez-Banqueri,
T.Guevara,
M.Ksiazek,
J.Potempa,
F.X.Gomis-Ruth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.34 /
1.40
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.330,
67.250,
79.640,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.1 /
18.8
|
Other elements in 6r7v:
The structure of Tannerella Forsythia Promirolysin Mutant E225A also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Tannerella Forsythia Promirolysin Mutant E225A
(pdb code 6r7v). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7v:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 6r7v
Go back to
Calcium Binding Sites List in 6r7v
Calcium binding site 1 out
of 2 in the Tannerella Forsythia Promirolysin Mutant E225A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:18.2
occ:1.00
|
O
|
A:TRP236
|
2.3
|
17.9
|
1.0
|
O
|
A:SER242
|
2.3
|
20.7
|
1.0
|
OD2
|
A:ASP239
|
2.4
|
20.9
|
1.0
|
O
|
A:GLY256
|
2.4
|
19.2
|
1.0
|
O
|
A:HOH562
|
2.4
|
19.3
|
1.0
|
O
|
A:GLN255
|
2.4
|
20.0
|
1.0
|
OD1
|
A:ASP239
|
2.4
|
19.0
|
1.0
|
CG
|
A:ASP239
|
2.7
|
18.8
|
1.0
|
C
|
A:GLY256
|
3.3
|
20.1
|
1.0
|
C
|
A:SER242
|
3.4
|
23.8
|
1.0
|
C
|
A:TRP236
|
3.5
|
18.9
|
1.0
|
C
|
A:GLN255
|
3.5
|
20.0
|
1.0
|
CA
|
A:GLY256
|
3.6
|
17.9
|
1.0
|
N
|
A:GLY256
|
4.0
|
18.9
|
1.0
|
N
|
A:SER242
|
4.2
|
22.8
|
1.0
|
CA
|
A:TRP236
|
4.2
|
16.4
|
1.0
|
CB
|
A:TRP236
|
4.2
|
15.6
|
1.0
|
CB
|
A:ASP239
|
4.3
|
19.4
|
1.0
|
CA
|
A:CYS243
|
4.3
|
24.8
|
1.0
|
N
|
A:CYS243
|
4.3
|
25.0
|
1.0
|
C
|
A:GLY241
|
4.3
|
23.8
|
1.0
|
O
|
A:HOH637
|
4.4
|
22.3
|
1.0
|
CA
|
A:SER242
|
4.4
|
23.2
|
1.0
|
N
|
A:GLY237
|
4.5
|
17.4
|
1.0
|
N
|
A:GLY257
|
4.6
|
19.1
|
1.0
|
CD1
|
A:TRP236
|
4.6
|
18.5
|
1.0
|
O
|
A:GLY245
|
4.7
|
23.6
|
1.0
|
CA
|
A:GLY237
|
4.7
|
17.9
|
1.0
|
OD1
|
A:ASN254
|
4.7
|
35.0
|
1.0
|
O
|
A:GLY241
|
4.7
|
23.2
|
1.0
|
CA
|
A:GLN255
|
4.8
|
18.2
|
1.0
|
N
|
A:GLY245
|
4.8
|
22.2
|
1.0
|
C
|
A:CYS243
|
4.8
|
31.6
|
1.0
|
CA
|
A:GLY241
|
4.8
|
20.4
|
1.0
|
OG
|
A:SER242
|
4.8
|
31.8
|
1.0
|
SG
|
A:CYS271
|
4.8
|
29.2
|
1.0
|
CG
|
A:TRP236
|
4.8
|
15.5
|
1.0
|
N
|
A:GLY241
|
4.9
|
21.0
|
1.0
|
N
|
A:GLN255
|
4.9
|
19.6
|
1.0
|
N
|
A:SER244
|
4.9
|
26.7
|
1.0
|
N
|
A:ASP239
|
4.9
|
17.6
|
1.0
|
|
Calcium binding site 2 out
of 2 in 6r7v
Go back to
Calcium Binding Sites List in 6r7v
Calcium binding site 2 out
of 2 in the Tannerella Forsythia Promirolysin Mutant E225A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:17.8
occ:0.97
|
O
|
A:HOH642
|
2.4
|
28.7
|
1.0
|
OD1
|
A:ASP247
|
2.4
|
18.0
|
1.0
|
O
|
A:ILE249
|
2.4
|
18.1
|
1.0
|
O
|
A:THR252
|
2.5
|
16.8
|
1.0
|
O
|
A:HOH594
|
2.5
|
17.7
|
1.0
|
OG1
|
A:THR252
|
2.5
|
16.8
|
1.0
|
O
|
A:HOH601
|
2.6
|
21.3
|
1.0
|
O
|
A:HOH722
|
2.6
|
22.2
|
1.0
|
CG
|
A:ASP247
|
3.4
|
17.6
|
1.0
|
C
|
A:THR252
|
3.5
|
18.6
|
1.0
|
C
|
A:ILE249
|
3.6
|
18.8
|
1.0
|
CB
|
A:THR252
|
3.6
|
16.5
|
1.0
|
OD2
|
A:ASP247
|
3.8
|
16.0
|
1.0
|
CA
|
A:THR252
|
3.9
|
14.8
|
1.0
|
N
|
A:THR252
|
4.1
|
16.7
|
1.0
|
N
|
A:ILE249
|
4.1
|
17.9
|
1.0
|
CA
|
A:ILE249
|
4.2
|
15.5
|
1.0
|
O
|
A:PRO253
|
4.4
|
19.6
|
1.0
|
CB
|
A:ILE249
|
4.4
|
16.8
|
1.0
|
C
|
A:PRO253
|
4.5
|
21.1
|
1.0
|
O
|
A:HOH672
|
4.5
|
30.2
|
0.5
|
N
|
A:ASP247
|
4.6
|
17.8
|
1.0
|
N
|
A:PRO253
|
4.6
|
18.3
|
1.0
|
N
|
A:ALA250
|
4.6
|
17.7
|
1.0
|
N
|
A:ASN254
|
4.7
|
19.7
|
1.0
|
CB
|
A:ASP247
|
4.7
|
17.2
|
1.0
|
O
|
A:HOH637
|
4.7
|
22.3
|
1.0
|
CA
|
A:ALA250
|
4.8
|
19.1
|
1.0
|
OG1
|
A:THR246
|
4.8
|
23.0
|
1.0
|
C
|
A:ALA250
|
4.8
|
23.1
|
1.0
|
O
|
A:ALA250
|
4.9
|
24.1
|
1.0
|
O
|
A:ILE235
|
4.9
|
17.9
|
1.0
|
CG2
|
A:THR252
|
4.9
|
15.3
|
1.0
|
CA
|
A:ASN254
|
5.0
|
20.0
|
1.0
|
O
|
A:HOH740
|
5.0
|
32.4
|
1.0
|
|
Reference:
T.Guevara,
A.Rodriguez-Banqueri,
M.Ksiazek,
J.Potempa,
F.X.Gomis-Ruth.
Structure-Based Mechanism of Cysteine-Switch Latency and of Catalysis By Pappalysin-Family Metallopeptidases Iucrj 2019.
ISSN: ESSN 2052-2525
Page generated: Sat Dec 12 07:29:51 2020
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