Aluminium in PDB 6t66: Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
Enzymatic activity of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
All present enzymatic activity of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4:
3.6.4.12;
Protein crystallography data
The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66
was solved by
P.Legrand,
S.Quevillon-Cheruel,
I.Li De La Sierra-Gallay,
H.Walbott,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.63 /
3.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.978,
123.292,
263.493,
90,
90,
90
|
R / Rfree (%)
|
25.5 /
27.6
|
Other elements in 6t66:
The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 also contains other interesting chemical elements:
Aluminium Binding Sites:
The binding sites of Aluminium atom in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
(pdb code 6t66). This binding sites where shown within
5.0 Angstroms radius around Aluminium atom.
In total 6 binding sites of Aluminium where determined in the
Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66:
Jump to Aluminium binding site number:
1;
2;
3;
4;
5;
6;
Aluminium binding site 1 out
of 6 in 6t66
Go back to
Aluminium Binding Sites List in 6t66
Aluminium binding site 1 out
of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
Mono view
Stereo pair view
|
A full contact list of Aluminium with other atoms in the Al binding
site number 1 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Al503
b:175.6
occ:1.00
|
AL
|
A:ALF503
|
0.0
|
175.6
|
1.0
|
F1
|
A:ALF503
|
1.8
|
175.6
|
1.0
|
F2
|
A:ALF503
|
1.8
|
175.2
|
1.0
|
F4
|
A:ALF503
|
1.8
|
176.0
|
1.0
|
F3
|
A:ALF503
|
1.8
|
175.5
|
1.0
|
O3B
|
A:GDP501
|
2.0
|
151.9
|
1.0
|
OE1
|
A:GLU259
|
3.1
|
176.5
|
1.0
|
PB
|
A:GDP501
|
3.2
|
152.1
|
1.0
|
O2B
|
A:GDP501
|
3.5
|
151.4
|
1.0
|
MG
|
A:MG502
|
3.8
|
63.7
|
1.0
|
NH1
|
B:ARG439
|
3.9
|
183.1
|
1.0
|
O3A
|
A:GDP501
|
4.0
|
153.0
|
1.0
|
CD
|
A:GLU259
|
4.0
|
184.8
|
1.0
|
OE2
|
A:GLU259
|
4.0
|
177.3
|
1.0
|
NZ
|
A:LYS234
|
4.1
|
170.7
|
1.0
|
CE
|
A:LYS234
|
4.3
|
164.3
|
1.0
|
O
|
B:GLN407
|
4.3
|
149.3
|
1.0
|
NE
|
B:ARG439
|
4.4
|
180.4
|
1.0
|
N
|
A:SER231
|
4.4
|
144.5
|
1.0
|
O1B
|
A:GDP501
|
4.4
|
152.4
|
1.0
|
CE1
|
A:TYR341
|
4.4
|
159.2
|
1.0
|
CZ
|
B:ARG439
|
4.4
|
194.6
|
1.0
|
NZ
|
B:LYS437
|
4.5
|
177.6
|
1.0
|
CA
|
A:PRO230
|
4.6
|
145.4
|
1.0
|
CE
|
B:LYS437
|
4.7
|
171.5
|
1.0
|
NE2
|
A:GLN381
|
4.7
|
185.1
|
1.0
|
CB
|
A:PRO230
|
4.8
|
147.2
|
1.0
|
OH
|
A:TYR341
|
4.9
|
166.0
|
1.0
|
CA
|
B:GLN407
|
4.9
|
147.6
|
1.0
|
O
|
B:GLU406
|
4.9
|
152.0
|
1.0
|
|
Aluminium binding site 2 out
of 6 in 6t66
Go back to
Aluminium Binding Sites List in 6t66
Aluminium binding site 2 out
of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
Mono view
Stereo pair view
|
A full contact list of Aluminium with other atoms in the Al binding
site number 2 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Al503
b:160.6
occ:1.00
|
AL
|
B:ALF503
|
0.0
|
160.6
|
1.0
|
F1
|
B:ALF503
|
1.8
|
160.2
|
1.0
|
F4
|
B:ALF503
|
1.8
|
161.0
|
1.0
|
F3
|
B:ALF503
|
1.8
|
160.5
|
1.0
|
F2
|
B:ALF503
|
1.8
|
160.8
|
1.0
|
O3B
|
B:GDP501
|
2.0
|
146.2
|
1.0
|
OE1
|
B:GLU259
|
3.2
|
160.7
|
1.0
|
PB
|
B:GDP501
|
3.2
|
146.1
|
1.0
|
O2B
|
B:GDP501
|
3.5
|
145.8
|
1.0
|
MG
|
B:MG502
|
3.9
|
52.1
|
1.0
|
NH1
|
C:ARG439
|
3.9
|
190.4
|
1.0
|
O3A
|
B:GDP501
|
4.0
|
145.3
|
1.0
|
CD
|
B:GLU259
|
4.0
|
171.8
|
1.0
|
OE2
|
B:GLU259
|
4.0
|
165.3
|
1.0
|
NZ
|
B:LYS234
|
4.1
|
160.1
|
1.0
|
O
|
C:GLN407
|
4.1
|
158.8
|
1.0
|
CE
|
B:LYS234
|
4.3
|
151.9
|
1.0
|
N
|
B:SER231
|
4.4
|
129.8
|
1.0
|
O1B
|
B:GDP501
|
4.4
|
146.7
|
1.0
|
CE1
|
B:TYR341
|
4.4
|
144.8
|
1.0
|
CZ
|
C:ARG439
|
4.5
|
202.7
|
1.0
|
NZ
|
C:LYS437
|
4.6
|
196.7
|
1.0
|
NE
|
C:ARG439
|
4.6
|
187.6
|
1.0
|
CA
|
C:GLN407
|
4.6
|
156.9
|
1.0
|
CE
|
C:LYS437
|
4.6
|
188.0
|
1.0
|
CA
|
B:PRO230
|
4.7
|
130.6
|
1.0
|
O
|
C:GLU406
|
4.7
|
161.3
|
1.0
|
NE2
|
B:GLN381
|
4.7
|
177.7
|
1.0
|
CB
|
B:PRO230
|
4.8
|
132.3
|
1.0
|
C
|
C:GLN407
|
4.8
|
159.3
|
1.0
|
OH
|
B:TYR341
|
4.9
|
152.3
|
1.0
|
|
Aluminium binding site 3 out
of 6 in 6t66
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Aluminium Binding Sites List in 6t66
Aluminium binding site 3 out
of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
Mono view
Stereo pair view
|
A full contact list of Aluminium with other atoms in the Al binding
site number 3 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Al503
b:161.9
occ:1.00
|
AL
|
C:ALF503
|
0.0
|
161.9
|
1.0
|
F1
|
C:ALF503
|
1.8
|
161.8
|
1.0
|
F2
|
C:ALF503
|
1.8
|
161.8
|
1.0
|
F4
|
C:ALF503
|
1.8
|
161.8
|
1.0
|
F3
|
C:ALF503
|
1.8
|
162.0
|
1.0
|
O1B
|
C:GDP501
|
2.0
|
142.9
|
1.0
|
OE1
|
C:GLU259
|
3.2
|
177.6
|
1.0
|
PB
|
C:GDP501
|
3.2
|
142.3
|
1.0
|
O3B
|
C:GDP501
|
3.5
|
142.2
|
1.0
|
NH1
|
D:ARG439
|
3.7
|
200.1
|
1.0
|
MG
|
C:MG502
|
3.9
|
34.8
|
1.0
|
O3A
|
C:GDP501
|
4.0
|
142.3
|
1.0
|
CD
|
C:GLU259
|
4.0
|
186.5
|
1.0
|
OE2
|
C:GLU259
|
4.0
|
178.6
|
1.0
|
O
|
D:GLN407
|
4.1
|
175.7
|
1.0
|
NZ
|
C:LYS234
|
4.1
|
162.3
|
1.0
|
CE
|
C:LYS234
|
4.3
|
155.6
|
1.0
|
CZ
|
D:ARG439
|
4.4
|
212.2
|
1.0
|
N
|
C:SER231
|
4.4
|
135.9
|
1.0
|
CE1
|
C:TYR341
|
4.4
|
156.3
|
1.0
|
O2B
|
C:GDP501
|
4.4
|
142.2
|
1.0
|
NE
|
D:ARG439
|
4.4
|
198.4
|
1.0
|
NZ
|
D:LYS437
|
4.5
|
204.2
|
1.0
|
CA
|
D:GLN407
|
4.6
|
173.3
|
1.0
|
CE
|
D:LYS437
|
4.6
|
196.2
|
1.0
|
CA
|
C:PRO230
|
4.7
|
137.3
|
1.0
|
O
|
D:GLU406
|
4.7
|
176.9
|
1.0
|
NE2
|
C:GLN381
|
4.7
|
181.2
|
1.0
|
C
|
D:GLN407
|
4.8
|
176.1
|
1.0
|
CB
|
C:PRO230
|
4.8
|
139.2
|
1.0
|
OH
|
C:TYR341
|
4.8
|
163.3
|
1.0
|
|
Aluminium binding site 4 out
of 6 in 6t66
Go back to
Aluminium Binding Sites List in 6t66
Aluminium binding site 4 out
of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
Mono view
Stereo pair view
|
A full contact list of Aluminium with other atoms in the Al binding
site number 4 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Al503
b:272.6
occ:1.00
|
AL
|
D:ALF503
|
0.0
|
272.6
|
1.0
|
F4
|
D:ALF503
|
1.8
|
272.7
|
1.0
|
F3
|
D:ALF503
|
1.8
|
272.6
|
1.0
|
F1
|
D:ALF503
|
1.8
|
271.5
|
1.0
|
F2
|
D:ALF503
|
1.8
|
272.9
|
1.0
|
O1B
|
D:GDP501
|
2.1
|
220.4
|
1.0
|
OE1
|
D:GLU259
|
3.2
|
199.3
|
1.0
|
PB
|
D:GDP501
|
3.2
|
220.2
|
1.0
|
O3B
|
D:GDP501
|
3.5
|
220.8
|
1.0
|
MG
|
D:MG502
|
3.9
|
74.6
|
1.0
|
O3A
|
D:GDP501
|
4.0
|
219.1
|
1.0
|
CD
|
D:GLU259
|
4.0
|
206.1
|
1.0
|
OE2
|
D:GLU259
|
4.0
|
200.4
|
1.0
|
NZ
|
D:LYS234
|
4.1
|
205.2
|
1.0
|
CE
|
D:LYS234
|
4.3
|
197.6
|
1.0
|
N
|
D:SER231
|
4.4
|
177.3
|
1.0
|
O2B
|
D:GDP501
|
4.4
|
220.2
|
1.0
|
CE1
|
D:TYR341
|
4.4
|
166.8
|
1.0
|
CA
|
D:PRO230
|
4.7
|
177.1
|
1.0
|
NE2
|
D:GLN381
|
4.7
|
207.1
|
1.0
|
CB
|
D:PRO230
|
4.8
|
178.9
|
1.0
|
OH
|
D:TYR341
|
4.9
|
174.4
|
1.0
|
|
Aluminium binding site 5 out
of 6 in 6t66
Go back to
Aluminium Binding Sites List in 6t66
Aluminium binding site 5 out
of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
Mono view
Stereo pair view
|
A full contact list of Aluminium with other atoms in the Al binding
site number 5 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Al503
b:218.5
occ:1.00
|
AL
|
E:ALF503
|
0.0
|
218.5
|
1.0
|
F3
|
E:ALF503
|
1.8
|
218.6
|
1.0
|
F1
|
E:ALF503
|
1.8
|
218.1
|
1.0
|
F4
|
E:ALF503
|
1.8
|
218.4
|
1.0
|
F2
|
E:ALF503
|
1.8
|
218.7
|
1.0
|
O3B
|
E:GDP501
|
2.0
|
187.7
|
1.0
|
OE1
|
E:GLU259
|
3.2
|
229.7
|
1.0
|
PB
|
E:GDP501
|
3.2
|
187.7
|
1.0
|
O2B
|
E:GDP501
|
3.5
|
187.7
|
1.0
|
MG
|
E:MG502
|
3.9
|
74.6
|
1.0
|
O3A
|
E:GDP501
|
4.0
|
187.0
|
1.0
|
CD
|
E:GLU259
|
4.0
|
235.3
|
1.0
|
NH1
|
F:ARG439
|
4.0
|
255.4
|
1.0
|
OE2
|
E:GLU259
|
4.0
|
232.1
|
1.0
|
NZ
|
E:LYS234
|
4.1
|
239.7
|
1.0
|
O
|
F:GLN407
|
4.3
|
227.2
|
1.0
|
CE
|
E:LYS234
|
4.3
|
230.6
|
1.0
|
N
|
E:SER231
|
4.4
|
200.0
|
1.0
|
O1B
|
E:GDP501
|
4.4
|
187.9
|
1.0
|
CE1
|
E:TYR341
|
4.4
|
229.9
|
1.0
|
CZ
|
F:ARG439
|
4.6
|
267.0
|
1.0
|
NE
|
F:ARG439
|
4.6
|
252.1
|
1.0
|
CA
|
E:PRO230
|
4.7
|
201.9
|
1.0
|
NE2
|
E:GLN381
|
4.7
|
259.0
|
1.0
|
CB
|
E:PRO230
|
4.8
|
203.7
|
1.0
|
OH
|
E:TYR341
|
4.9
|
236.2
|
1.0
|
NZ
|
F:LYS437
|
4.9
|
264.0
|
1.0
|
CA
|
F:GLN407
|
4.9
|
225.0
|
1.0
|
|
Aluminium binding site 6 out
of 6 in 6t66
Go back to
Aluminium Binding Sites List in 6t66
Aluminium binding site 6 out
of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4
Mono view
Stereo pair view
|
A full contact list of Aluminium with other atoms in the Al binding
site number 6 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Al503
b:287.8
occ:1.00
|
AL
|
F:ALF503
|
0.0
|
287.8
|
1.0
|
F1
|
F:ALF503
|
1.8
|
287.7
|
1.0
|
F4
|
F:ALF503
|
1.8
|
288.0
|
1.0
|
F2
|
F:ALF503
|
1.8
|
287.2
|
1.0
|
F3
|
F:ALF503
|
1.8
|
287.9
|
1.0
|
O3B
|
F:GDP501
|
2.0
|
216.0
|
1.0
|
OE1
|
F:GLU259
|
3.2
|
221.3
|
1.0
|
PB
|
F:GDP501
|
3.2
|
215.3
|
1.0
|
O2B
|
F:GDP501
|
3.5
|
215.6
|
1.0
|
MG
|
F:MG502
|
3.9
|
92.1
|
1.0
|
O3A
|
F:GDP501
|
4.0
|
214.3
|
1.0
|
CD
|
F:GLU259
|
4.0
|
224.9
|
1.0
|
OE2
|
F:GLU259
|
4.0
|
219.5
|
1.0
|
NZ
|
F:LYS234
|
4.1
|
233.4
|
1.0
|
CE
|
F:LYS234
|
4.3
|
224.9
|
1.0
|
N
|
F:SER231
|
4.4
|
199.5
|
1.0
|
O1B
|
F:GDP501
|
4.4
|
215.1
|
1.0
|
CE1
|
F:TYR341
|
4.4
|
204.1
|
1.0
|
CA
|
F:PRO230
|
4.7
|
200.3
|
1.0
|
NE2
|
F:GLN381
|
4.7
|
241.7
|
1.0
|
CB
|
F:PRO230
|
4.8
|
202.2
|
1.0
|
OH
|
F:TYR341
|
4.9
|
212.3
|
1.0
|
|
Reference:
S.Marsin,
Y.Adam,
C.Cargemel,
J.Andreani,
S.Baconnais,
P.Legrand,
I.Li De La Sierra-Gallay,
A.Humbert,
M.Aumont-Nicaise,
C.Velours,
F.Ochsenbein,
D.Durand,
E.Le Cam,
H.Walbott,
C.Possoz,
S.Quevillon-Cheruel,
J.-L.Ferat.
Study of the Dnab:Dcia Interplay Reveals Insights Into the Primary Mode of Loading of the Bacterial Replicative Helicase To Be Published.
Page generated: Wed Jul 10 09:55:19 2024
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