Zinc in PDB 5oiu: Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
Protein crystallography data
The structure of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus, PDB code: 5oiu
was solved by
V.Karuppiah,
J.P.Derrick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
95.11 /
2.44
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
220.390,
107.660,
137.830,
90.00,
112.95,
90.00
|
R / Rfree (%)
|
19 /
24.6
|
Other elements in 5oiu:
The structure of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
(pdb code 5oiu). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus, PDB code: 5oiu:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5oiu
Go back to
Zinc Binding Sites List in 5oiu
Zinc binding site 1 out
of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn503
b:39.2
occ:1.00
|
SG
|
A:CYS295
|
2.3
|
37.3
|
1.0
|
SG
|
A:CYS330
|
2.3
|
34.7
|
1.0
|
SG
|
A:CYS327
|
2.4
|
37.6
|
1.0
|
SG
|
A:CYS292
|
2.4
|
37.6
|
1.0
|
CB
|
A:CYS292
|
3.2
|
34.0
|
1.0
|
CB
|
A:CYS295
|
3.3
|
36.7
|
1.0
|
CB
|
A:CYS327
|
3.4
|
32.9
|
1.0
|
CB
|
A:CYS330
|
3.4
|
34.3
|
1.0
|
N
|
A:CYS327
|
3.4
|
25.1
|
1.0
|
CA
|
A:CYS327
|
3.9
|
34.8
|
1.0
|
N
|
A:CYS295
|
3.9
|
37.6
|
1.0
|
N
|
A:CYS330
|
3.9
|
43.9
|
1.0
|
CA
|
A:CYS295
|
4.2
|
38.9
|
1.0
|
C
|
A:GLY326
|
4.2
|
37.9
|
1.0
|
CA
|
A:CYS330
|
4.3
|
33.8
|
1.0
|
C
|
A:CYS327
|
4.3
|
39.0
|
1.0
|
O
|
A:CYS327
|
4.3
|
35.5
|
1.0
|
CA
|
A:GLY326
|
4.4
|
38.1
|
1.0
|
N
|
A:GLY326
|
4.5
|
34.3
|
1.0
|
CA
|
A:CYS292
|
4.6
|
33.4
|
1.0
|
C
|
A:HIS294
|
4.8
|
37.4
|
1.0
|
CB
|
A:ARG329
|
4.8
|
45.0
|
1.0
|
C
|
A:ARG329
|
4.8
|
44.6
|
1.0
|
CB
|
A:HIS294
|
4.8
|
37.8
|
1.0
|
CA
|
A:GLY334
|
4.8
|
32.0
|
1.0
|
N
|
A:ARG329
|
4.8
|
40.6
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5oiu
Go back to
Zinc Binding Sites List in 5oiu
Zinc binding site 2 out
of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn503
b:33.8
occ:1.00
|
SG
|
B:CYS292
|
2.3
|
38.0
|
1.0
|
SG
|
B:CYS295
|
2.3
|
34.6
|
1.0
|
SG
|
B:CYS327
|
2.4
|
34.2
|
1.0
|
SG
|
B:CYS330
|
2.4
|
34.6
|
1.0
|
CB
|
B:CYS292
|
3.1
|
32.0
|
1.0
|
N
|
B:CYS327
|
3.4
|
30.9
|
1.0
|
CB
|
B:CYS295
|
3.4
|
35.0
|
1.0
|
CB
|
B:CYS330
|
3.4
|
32.5
|
1.0
|
CB
|
B:CYS327
|
3.4
|
35.2
|
1.0
|
CA
|
B:CYS327
|
3.8
|
36.3
|
1.0
|
N
|
B:CYS295
|
3.9
|
32.4
|
1.0
|
N
|
B:CYS330
|
3.9
|
44.1
|
1.0
|
C
|
B:GLY326
|
4.1
|
36.3
|
1.0
|
CA
|
B:CYS295
|
4.2
|
32.5
|
1.0
|
CA
|
B:CYS330
|
4.2
|
34.9
|
1.0
|
CA
|
B:GLY326
|
4.3
|
38.6
|
1.0
|
C
|
B:CYS327
|
4.3
|
36.7
|
1.0
|
O
|
B:CYS327
|
4.4
|
35.7
|
1.0
|
N
|
B:GLY326
|
4.5
|
35.5
|
1.0
|
CA
|
B:CYS292
|
4.6
|
34.3
|
1.0
|
CB
|
B:HIS294
|
4.6
|
44.0
|
1.0
|
C
|
B:HIS294
|
4.6
|
34.7
|
1.0
|
C
|
B:ARG329
|
4.7
|
40.0
|
1.0
|
CB
|
B:ARG329
|
4.7
|
44.6
|
1.0
|
N
|
B:ARG329
|
4.8
|
36.5
|
1.0
|
CA
|
B:GLY334
|
4.8
|
35.6
|
1.0
|
N
|
B:HIS294
|
4.9
|
35.1
|
1.0
|
CA
|
B:ARG329
|
5.0
|
40.4
|
1.0
|
CA
|
B:HIS294
|
5.0
|
41.0
|
1.0
|
C
|
B:CYS292
|
5.0
|
33.6
|
1.0
|
|
Zinc binding site 3 out
of 6 in 5oiu
Go back to
Zinc Binding Sites List in 5oiu
Zinc binding site 3 out
of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn503
b:60.0
occ:1.00
|
SG
|
C:CYS330
|
2.3
|
54.8
|
1.0
|
SG
|
C:CYS295
|
2.4
|
58.4
|
1.0
|
SG
|
C:CYS292
|
2.4
|
60.7
|
1.0
|
SG
|
C:CYS327
|
2.7
|
72.2
|
1.0
|
CB
|
C:CYS292
|
3.1
|
52.6
|
1.0
|
CB
|
C:CYS330
|
3.3
|
57.0
|
1.0
|
N
|
C:CYS327
|
3.4
|
60.3
|
1.0
|
CB
|
C:CYS295
|
3.5
|
61.4
|
1.0
|
CB
|
C:CYS327
|
3.6
|
62.4
|
1.0
|
N
|
C:CYS295
|
3.9
|
63.7
|
1.0
|
CA
|
C:CYS327
|
3.9
|
64.9
|
1.0
|
C
|
C:GLY326
|
4.1
|
63.5
|
1.0
|
O
|
C:CYS327
|
4.2
|
63.3
|
1.0
|
N
|
C:CYS330
|
4.2
|
65.9
|
1.0
|
C
|
C:CYS327
|
4.3
|
67.0
|
1.0
|
CA
|
C:GLY326
|
4.3
|
61.8
|
1.0
|
CA
|
C:CYS295
|
4.3
|
56.2
|
1.0
|
CA
|
C:CYS330
|
4.4
|
59.5
|
1.0
|
N
|
C:GLY326
|
4.5
|
62.4
|
1.0
|
CA
|
C:CYS292
|
4.6
|
46.3
|
1.0
|
CA
|
C:GLY334
|
4.7
|
50.2
|
1.0
|
C
|
C:HIS294
|
4.7
|
66.8
|
1.0
|
C
|
C:ARG329
|
4.8
|
65.4
|
1.0
|
N
|
C:HIS294
|
4.9
|
62.5
|
1.0
|
CB
|
C:HIS294
|
4.9
|
71.6
|
1.0
|
C
|
C:CYS292
|
4.9
|
52.8
|
1.0
|
O
|
C:GLY326
|
5.0
|
63.0
|
1.0
|
N
|
C:ARG329
|
5.0
|
70.7
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5oiu
Go back to
Zinc Binding Sites List in 5oiu
Zinc binding site 4 out
of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn503
b:53.8
occ:1.00
|
SG
|
D:CYS330
|
2.4
|
48.9
|
1.0
|
SG
|
D:CYS292
|
2.4
|
50.8
|
1.0
|
SG
|
D:CYS295
|
2.5
|
53.5
|
1.0
|
SG
|
D:CYS327
|
2.6
|
67.8
|
1.0
|
CB
|
D:CYS292
|
3.0
|
43.4
|
1.0
|
N
|
D:CYS327
|
3.2
|
60.8
|
1.0
|
CB
|
D:CYS330
|
3.3
|
51.1
|
1.0
|
CB
|
D:CYS327
|
3.5
|
57.8
|
1.0
|
CB
|
D:CYS295
|
3.5
|
53.8
|
1.0
|
CA
|
D:CYS327
|
3.8
|
58.8
|
1.0
|
N
|
D:CYS330
|
3.9
|
55.0
|
1.0
|
C
|
D:GLY326
|
4.0
|
62.1
|
1.0
|
N
|
D:CYS295
|
4.1
|
66.0
|
1.0
|
C
|
D:CYS327
|
4.2
|
61.5
|
1.0
|
CA
|
D:CYS330
|
4.2
|
53.5
|
1.0
|
O
|
D:CYS327
|
4.2
|
59.5
|
1.0
|
CA
|
D:GLY326
|
4.3
|
57.7
|
1.0
|
CA
|
D:CYS295
|
4.4
|
57.4
|
1.0
|
CA
|
D:CYS292
|
4.5
|
45.5
|
1.0
|
N
|
D:GLY326
|
4.6
|
55.8
|
1.0
|
CA
|
D:GLY334
|
4.6
|
43.6
|
1.0
|
C
|
D:ARG329
|
4.6
|
58.0
|
1.0
|
N
|
D:GLY334
|
4.8
|
49.4
|
1.0
|
N
|
D:ARG329
|
4.8
|
61.7
|
1.0
|
CB
|
D:ARG329
|
4.8
|
53.4
|
1.0
|
C
|
D:CYS292
|
4.9
|
54.1
|
1.0
|
O
|
D:GLY326
|
5.0
|
61.3
|
1.0
|
CA
|
D:ARG329
|
5.0
|
55.4
|
1.0
|
C
|
D:GLY334
|
5.0
|
42.4
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5oiu
Go back to
Zinc Binding Sites List in 5oiu
Zinc binding site 5 out
of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn503
b:59.1
occ:1.00
|
SG
|
E:CYS292
|
2.1
|
49.9
|
1.0
|
SG
|
E:CYS295
|
2.3
|
52.4
|
1.0
|
SG
|
E:CYS330
|
2.5
|
54.0
|
1.0
|
SG
|
E:CYS327
|
2.6
|
66.3
|
1.0
|
CB
|
E:CYS292
|
3.0
|
50.0
|
1.0
|
CB
|
E:CYS330
|
3.2
|
46.1
|
1.0
|
N
|
E:CYS327
|
3.4
|
61.5
|
1.0
|
CB
|
E:CYS295
|
3.5
|
64.9
|
1.0
|
CB
|
E:CYS327
|
3.5
|
56.9
|
1.0
|
N
|
E:CYS295
|
3.9
|
59.1
|
1.0
|
CA
|
E:CYS327
|
3.9
|
58.8
|
1.0
|
N
|
E:CYS330
|
4.0
|
57.8
|
1.0
|
C
|
E:GLY326
|
4.2
|
63.4
|
1.0
|
CA
|
E:CYS330
|
4.2
|
51.6
|
1.0
|
O
|
E:CYS327
|
4.3
|
61.1
|
1.0
|
CA
|
E:CYS295
|
4.3
|
64.8
|
1.0
|
C
|
E:CYS327
|
4.4
|
60.6
|
1.0
|
CA
|
E:GLY326
|
4.4
|
59.5
|
1.0
|
CA
|
E:CYS292
|
4.4
|
51.5
|
1.0
|
N
|
E:GLY326
|
4.5
|
59.4
|
1.0
|
C
|
E:HIS294
|
4.7
|
67.9
|
1.0
|
CB
|
E:ARG329
|
4.7
|
66.0
|
1.0
|
CA
|
E:GLY334
|
4.7
|
40.3
|
1.0
|
C
|
E:CYS292
|
4.8
|
55.2
|
1.0
|
C
|
E:ARG329
|
4.9
|
60.2
|
1.0
|
C
|
E:GLY334
|
4.9
|
48.6
|
1.0
|
O
|
E:CYS292
|
4.9
|
50.3
|
1.0
|
N
|
E:GLY334
|
4.9
|
42.8
|
1.0
|
|
Zinc binding site 6 out
of 6 in 5oiu
Go back to
Zinc Binding Sites List in 5oiu
Zinc binding site 6 out
of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn503
b:61.4
occ:1.00
|
SG
|
F:CYS292
|
2.1
|
52.0
|
1.0
|
SG
|
F:CYS295
|
2.2
|
52.0
|
1.0
|
SG
|
F:CYS327
|
2.5
|
75.9
|
1.0
|
SG
|
F:CYS330
|
2.6
|
57.8
|
1.0
|
CB
|
F:CYS292
|
3.0
|
48.9
|
1.0
|
CB
|
F:CYS327
|
3.3
|
59.7
|
1.0
|
CB
|
F:CYS330
|
3.3
|
48.5
|
1.0
|
N
|
F:CYS327
|
3.5
|
66.5
|
1.0
|
CB
|
F:CYS295
|
3.5
|
69.7
|
1.0
|
CA
|
F:CYS327
|
3.8
|
62.5
|
1.0
|
O
|
F:CYS327
|
3.8
|
70.0
|
1.0
|
N
|
F:CYS295
|
3.8
|
60.4
|
1.0
|
C
|
F:CYS327
|
4.0
|
70.5
|
1.0
|
N
|
F:CYS330
|
4.1
|
65.5
|
1.0
|
CA
|
F:CYS295
|
4.3
|
62.1
|
1.0
|
CA
|
F:CYS330
|
4.3
|
54.0
|
1.0
|
CA
|
F:CYS292
|
4.4
|
52.4
|
1.0
|
C
|
F:GLY326
|
4.5
|
66.7
|
1.0
|
CA
|
F:GLY334
|
4.5
|
45.4
|
1.0
|
C
|
F:HIS294
|
4.6
|
66.2
|
1.0
|
CB
|
F:HIS294
|
4.7
|
67.0
|
1.0
|
N
|
F:GLY334
|
4.7
|
43.2
|
1.0
|
C
|
F:CYS292
|
4.8
|
58.3
|
1.0
|
CA
|
F:GLY326
|
4.8
|
55.0
|
1.0
|
N
|
F:HIS294
|
4.9
|
67.7
|
1.0
|
C
|
F:ARG329
|
4.9
|
67.0
|
1.0
|
C
|
F:GLY334
|
4.9
|
52.6
|
1.0
|
N
|
F:GLY326
|
4.9
|
57.6
|
1.0
|
O
|
F:CYS292
|
4.9
|
61.0
|
1.0
|
CA
|
F:HIS294
|
4.9
|
66.5
|
1.0
|
|
Reference:
R.Collins,
V.Karuppiah,
C.A.Siebert,
R.Dajani,
A.Thistlethwaite,
J.P.Derrick.
Structural Cycle of the Thermus Thermophilus Pilf Atpase: the Powering of Type Iva Pilus Assembly. Sci Rep V. 8 14022 2018.
ISSN: ESSN 2045-2322
PubMed: 30232337
DOI: 10.1038/S41598-018-32218-3
Page generated: Sun Oct 27 23:39:04 2024
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