Iron in PDB 8acy: X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution
Enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution
All present enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution:
7.2.1.1;
Protein crystallography data
The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution, PDB code: 8acy
was solved by
G.Fritz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.73 /
3.50
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.27,
143.32,
104.37,
90,
110.98,
90
|
|
R / Rfree (%)
|
26.6 /
29
|
Other elements in 8acy:
The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution
(pdb code 8acy). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution, PDB code: 8acy:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8acy
Go back to
Iron Binding Sites List in 8acy
Iron binding site 1 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe1001
b:146.5
occ:1.00
|
FE1
|
E:FES1001
|
0.0
|
146.5
|
1.0
|
|
S1
|
E:FES1001
|
2.2
|
147.4
|
1.0
|
|
S2
|
E:FES1001
|
2.2
|
143.2
|
1.0
|
|
SG
|
D:CYS112
|
2.2
|
134.8
|
1.0
|
|
SG
|
E:CYS26
|
2.3
|
139.0
|
1.0
|
|
HB2
|
E:CYS26
|
2.5
|
158.3
|
1.0
|
|
FE2
|
E:FES1001
|
2.7
|
144.5
|
1.0
|
|
CB
|
E:CYS26
|
2.9
|
131.9
|
1.0
|
|
HB2
|
D:CYS112
|
3.2
|
178.3
|
1.0
|
|
H
|
D:GLY27
|
3.2
|
172.1
|
1.0
|
|
CB
|
D:CYS112
|
3.4
|
148.6
|
1.0
|
|
H
|
D:CYS112
|
3.4
|
180.3
|
1.0
|
|
HB3
|
E:CYS26
|
3.5
|
158.3
|
1.0
|
|
H
|
E:CYS26
|
3.5
|
153.3
|
1.0
|
|
SG
|
D:CYS29
|
3.9
|
127.9
|
1.0
|
|
N
|
D:GLY27
|
4.0
|
143.4
|
1.0
|
|
N
|
D:CYS112
|
4.0
|
150.2
|
1.0
|
|
HB3
|
D:CYS112
|
4.0
|
178.3
|
1.0
|
|
H
|
D:CYS29
|
4.1
|
174.9
|
1.0
|
|
H
|
D:VAL28
|
4.1
|
162.7
|
1.0
|
|
CA
|
E:CYS26
|
4.1
|
131.8
|
1.0
|
|
N
|
E:CYS26
|
4.1
|
127.8
|
1.0
|
|
HA2
|
D:GLY27
|
4.2
|
173.8
|
1.0
|
|
H
|
E:CYS120
|
4.2
|
171.3
|
1.0
|
|
HA
|
D:LEU26
|
4.3
|
171.4
|
1.0
|
|
O
|
D:THR110
|
4.3
|
172.3
|
1.0
|
|
CA
|
D:CYS112
|
4.3
|
144.9
|
1.0
|
|
O
|
E:VAL118
|
4.3
|
157.9
|
1.0
|
|
HA
|
E:ASN119
|
4.4
|
183.7
|
1.0
|
|
CA
|
D:GLY27
|
4.6
|
144.8
|
1.0
|
|
HA
|
D:CYS112
|
4.6
|
173.9
|
1.0
|
|
N
|
D:VAL28
|
4.6
|
135.6
|
1.0
|
|
HA
|
E:CYS26
|
4.7
|
158.2
|
1.0
|
|
HB2
|
D:CYS29
|
4.7
|
156.5
|
1.0
|
|
H
|
E:THR27
|
4.7
|
149.6
|
1.0
|
|
HA
|
D:ASN111
|
4.7
|
185.7
|
1.0
|
|
HA2
|
E:GLY24
|
4.8
|
163.3
|
1.0
|
|
HD23
|
D:LEU26
|
4.8
|
171.3
|
1.0
|
|
SG
|
E:CYS120
|
4.8
|
169.4
|
1.0
|
|
N
|
D:CYS29
|
4.9
|
145.8
|
1.0
|
|
HB
|
D:VAL28
|
5.0
|
151.3
|
1.0
|
|
C
|
D:GLY27
|
5.0
|
139.2
|
1.0
|
|
CB
|
D:CYS29
|
5.0
|
130.4
|
1.0
|
|
N
|
E:CYS120
|
5.0
|
142.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 8acy
Go back to
Iron Binding Sites List in 8acy
Iron binding site 2 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe1001
b:144.5
occ:1.00
|
FE2
|
E:FES1001
|
0.0
|
144.5
|
1.0
|
|
S2
|
E:FES1001
|
2.2
|
143.2
|
1.0
|
|
S1
|
E:FES1001
|
2.2
|
147.4
|
1.0
|
|
SG
|
D:CYS29
|
2.2
|
127.9
|
1.0
|
|
SG
|
E:CYS120
|
2.3
|
169.4
|
1.0
|
|
HB2
|
E:CYS120
|
2.6
|
173.2
|
1.0
|
|
HB2
|
D:CYS29
|
2.6
|
156.5
|
1.0
|
|
H
|
E:CYS120
|
2.7
|
171.3
|
1.0
|
|
FE1
|
E:FES1001
|
2.7
|
146.5
|
1.0
|
|
CB
|
E:CYS120
|
2.9
|
144.3
|
1.0
|
|
CB
|
D:CYS29
|
3.0
|
130.4
|
1.0
|
|
N
|
E:CYS120
|
3.4
|
142.8
|
1.0
|
|
HB3
|
D:CYS29
|
3.5
|
156.5
|
1.0
|
|
H
|
E:GLY24
|
3.5
|
170.1
|
1.0
|
|
H
|
D:CYS29
|
3.6
|
174.9
|
1.0
|
|
HB3
|
E:CYS120
|
3.7
|
173.2
|
1.0
|
|
CA
|
E:CYS120
|
3.7
|
139.4
|
1.0
|
|
HA2
|
E:GLY24
|
4.0
|
163.3
|
1.0
|
|
HA
|
E:CYS120
|
4.1
|
167.3
|
1.0
|
|
H
|
E:CYS26
|
4.2
|
153.3
|
1.0
|
|
CA
|
D:CYS29
|
4.2
|
136.2
|
1.0
|
|
N
|
D:CYS29
|
4.2
|
145.8
|
1.0
|
|
HA
|
E:ASN119
|
4.2
|
183.7
|
1.0
|
|
H
|
E:MET25
|
4.3
|
154.8
|
1.0
|
|
SG
|
E:CYS26
|
4.3
|
139.0
|
1.0
|
|
N
|
E:GLY24
|
4.3
|
141.8
|
1.0
|
|
O
|
D:THR110
|
4.3
|
172.3
|
1.0
|
|
HB
|
D:THR110
|
4.3
|
183.9
|
1.0
|
|
SG
|
D:CYS112
|
4.4
|
134.8
|
1.0
|
|
C
|
E:ASN119
|
4.5
|
142.9
|
1.0
|
|
CA
|
E:GLY24
|
4.6
|
136.1
|
1.0
|
|
HB2
|
E:CYS26
|
4.6
|
158.3
|
1.0
|
|
H
|
D:CYS112
|
4.7
|
180.3
|
1.0
|
|
O
|
E:VAL118
|
4.7
|
157.9
|
1.0
|
|
N
|
E:MET25
|
4.8
|
129.0
|
1.0
|
|
HA
|
D:CYS29
|
4.8
|
163.4
|
1.0
|
|
OD1
|
E:ASN119
|
4.8
|
162.5
|
1.0
|
|
H
|
D:SER30
|
4.8
|
166.5
|
1.0
|
|
HA
|
D:ASN111
|
4.8
|
185.7
|
1.0
|
|
CA
|
E:ASN119
|
4.9
|
153.1
|
1.0
|
|
HA
|
E:LEU23
|
4.9
|
148.8
|
1.0
|
|
H
|
E:ALA121
|
5.0
|
157.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 8acy
Go back to
Iron Binding Sites List in 8acy
Iron binding site 3 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1502
b:274.9
occ:1.00
|
FE1
|
F:FES1502
|
0.0
|
274.9
|
1.0
|
|
S1
|
F:FES1502
|
2.2
|
275.4
|
1.0
|
|
S2
|
F:FES1502
|
2.2
|
261.0
|
1.0
|
|
SG
|
F:CYS70
|
2.3
|
271.1
|
1.0
|
|
SG
|
F:CYS76
|
2.3
|
242.2
|
1.0
|
|
FE2
|
F:FES1502
|
2.7
|
274.2
|
1.0
|
|
H
|
F:CYS76
|
2.7
|
325.5
|
1.0
|
|
H
|
F:GLY77
|
2.9
|
322.1
|
1.0
|
|
H
|
F:CYS70
|
3.1
|
288.0
|
1.0
|
|
H
|
F:SER75
|
3.2
|
317.0
|
1.0
|
|
H
|
F:GLY71
|
3.2
|
277.8
|
1.0
|
|
N
|
F:CYS76
|
3.4
|
271.2
|
1.0
|
|
CB
|
F:CYS70
|
3.5
|
254.3
|
1.0
|
|
HB3
|
F:CYS70
|
3.6
|
305.2
|
1.0
|
|
CB
|
F:CYS76
|
3.6
|
250.0
|
1.0
|
|
N
|
F:GLY77
|
3.7
|
268.4
|
1.0
|
|
N
|
F:CYS70
|
3.7
|
240.0
|
1.0
|
|
HB3
|
F:CYS76
|
3.7
|
300.0
|
1.0
|
|
N
|
F:GLY71
|
3.8
|
231.5
|
1.0
|
|
H
|
F:ALA69
|
3.8
|
285.0
|
1.0
|
|
N
|
F:SER75
|
3.9
|
264.2
|
1.0
|
|
O
|
F:GLY71
|
3.9
|
247.7
|
1.0
|
|
HA2
|
F:GLY74
|
3.9
|
306.0
|
1.0
|
|
CA
|
F:CYS76
|
3.9
|
264.2
|
1.0
|
|
H
|
F:GLY74
|
4.0
|
296.7
|
1.0
|
|
CA
|
F:CYS70
|
4.0
|
243.8
|
1.0
|
|
H
|
F:GLN78
|
4.0
|
306.1
|
1.0
|
|
C
|
F:CYS70
|
4.3
|
237.2
|
1.0
|
|
HB2
|
F:CYS70
|
4.3
|
305.2
|
1.0
|
|
C
|
F:CYS76
|
4.3
|
265.4
|
1.0
|
|
HB2
|
F:CYS76
|
4.4
|
300.0
|
1.0
|
|
SG
|
F:CYS111
|
4.4
|
227.6
|
1.0
|
|
C
|
F:SER75
|
4.4
|
271.8
|
1.0
|
|
N
|
F:GLY74
|
4.5
|
247.3
|
1.0
|
|
SG
|
F:CYS79
|
4.5
|
221.9
|
1.0
|
|
CA
|
F:GLY74
|
4.5
|
255.0
|
1.0
|
|
H
|
F:CYS79
|
4.5
|
293.5
|
1.0
|
|
HB3
|
F:CYS79
|
4.5
|
288.1
|
1.0
|
|
HA2
|
F:GLY77
|
4.5
|
310.2
|
1.0
|
|
N
|
F:ALA69
|
4.6
|
237.5
|
1.0
|
|
C
|
F:GLY74
|
4.6
|
266.9
|
1.0
|
|
HA
|
F:SER68
|
4.6
|
284.2
|
1.0
|
|
CA
|
F:GLY77
|
4.6
|
258.5
|
1.0
|
|
HB2
|
F:SER68
|
4.7
|
281.0
|
1.0
|
|
CA
|
F:SER75
|
4.7
|
268.2
|
1.0
|
|
N
|
F:GLN78
|
4.7
|
255.1
|
1.0
|
|
H
|
F:GLY73
|
4.7
|
290.9
|
1.0
|
|
C
|
F:GLY71
|
4.7
|
236.4
|
1.0
|
|
CA
|
F:GLY71
|
4.7
|
227.8
|
1.0
|
|
C
|
F:ALA69
|
4.8
|
231.4
|
1.0
|
|
HB3
|
F:SER75
|
4.8
|
332.7
|
1.0
|
|
HA
|
F:CYS76
|
4.9
|
317.1
|
1.0
|
|
HB3
|
F:ALA69
|
4.9
|
270.5
|
1.0
|
|
HA
|
F:CYS70
|
4.9
|
292.5
|
1.0
|
|
HA2
|
F:GLY71
|
5.0
|
273.4
|
1.0
|
|
HD13
|
F:LEU109
|
5.0
|
286.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 8acy
Go back to
Iron Binding Sites List in 8acy
Iron binding site 4 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.5 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1502
b:274.2
occ:1.00
|
FE2
|
F:FES1502
|
0.0
|
274.2
|
1.0
|
|
S2
|
F:FES1502
|
2.2
|
261.0
|
1.0
|
|
S1
|
F:FES1502
|
2.2
|
275.4
|
1.0
|
|
SG
|
F:CYS111
|
2.3
|
227.6
|
1.0
|
|
SG
|
F:CYS79
|
2.3
|
221.9
|
1.0
|
|
FE1
|
F:FES1502
|
2.7
|
274.9
|
1.0
|
|
HB3
|
F:CYS111
|
3.3
|
278.5
|
1.0
|
|
HB3
|
F:CYS79
|
3.4
|
288.1
|
1.0
|
|
HB3
|
F:LEU109
|
3.5
|
278.8
|
1.0
|
|
HA2
|
F:GLY74
|
3.5
|
306.0
|
1.0
|
|
CB
|
F:CYS111
|
3.5
|
232.1
|
1.0
|
|
CB
|
F:CYS79
|
3.6
|
240.1
|
1.0
|
|
H
|
F:CYS111
|
3.6
|
272.2
|
1.0
|
|
O
|
F:GLY71
|
3.7
|
247.7
|
1.0
|
|
HD13
|
F:LEU109
|
3.9
|
286.5
|
1.0
|
|
H
|
F:GLY74
|
3.9
|
296.7
|
1.0
|
|
H
|
F:CYS79
|
4.0
|
293.5
|
1.0
|
|
HD22
|
F:LEU109
|
4.0
|
273.1
|
1.0
|
|
H
|
F:GLY77
|
4.1
|
322.1
|
1.0
|
|
HD22
|
F:LEU56
|
4.1
|
261.9
|
1.0
|
|
HB2
|
F:CYS79
|
4.1
|
288.1
|
1.0
|
|
HB2
|
F:CYS111
|
4.1
|
278.5
|
1.0
|
|
SG
|
F:CYS70
|
4.3
|
271.1
|
1.0
|
|
CA
|
F:GLY74
|
4.4
|
255.0
|
1.0
|
|
N
|
F:CYS111
|
4.4
|
226.9
|
1.0
|
|
CB
|
F:LEU109
|
4.4
|
232.3
|
1.0
|
|
H
|
F:GLN112
|
4.5
|
273.1
|
1.0
|
|
SG
|
F:CYS76
|
4.5
|
242.2
|
1.0
|
|
N
|
F:GLY74
|
4.6
|
247.3
|
1.0
|
|
CA
|
F:CYS111
|
4.6
|
230.6
|
1.0
|
|
H
|
F:GLY71
|
4.6
|
277.8
|
1.0
|
|
HA2
|
F:GLY77
|
4.6
|
310.2
|
1.0
|
|
N
|
F:CYS79
|
4.6
|
244.6
|
1.0
|
|
CA
|
F:CYS79
|
4.7
|
240.8
|
1.0
|
|
H
|
F:SER75
|
4.7
|
317.0
|
1.0
|
|
HB3
|
F:SER68
|
4.7
|
281.0
|
1.0
|
|
CD1
|
F:LEU109
|
4.8
|
238.7
|
1.0
|
|
C
|
F:GLY71
|
4.8
|
236.4
|
1.0
|
|
N
|
F:GLY77
|
4.9
|
268.4
|
1.0
|
|
HB2
|
F:LEU109
|
4.9
|
278.8
|
1.0
|
|
HD13
|
F:LEU56
|
4.9
|
265.4
|
1.0
|
|
CD2
|
F:LEU109
|
4.9
|
227.6
|
1.0
|
|
HB2
|
F:SER68
|
4.9
|
281.0
|
1.0
|
|
H
|
F:ALA110
|
4.9
|
263.5
|
1.0
|
|
CG
|
F:LEU109
|
4.9
|
229.0
|
1.0
|
|
H
|
F:GLY73
|
5.0
|
290.9
|
1.0
|
|
HA
|
F:LEU109
|
5.0
|
271.8
|
1.0
|
|
HA3
|
F:GLY74
|
5.0
|
306.0
|
1.0
|
|
Reference:
G.Fritz,
G.Fritz.
N/A N/A.
ISSN: ESSN 1545-9985
Page generated: Fri Aug 9 17:25:23 2024
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