Iron in PDB 8acw: X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 A Resolution
Enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 A Resolution
All present enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 A Resolution:
7.2.1.1;
Protein crystallography data
The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 A Resolution, PDB code: 8acw
was solved by
G.Fritz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.60 /
3.40
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.72,
142.94,
103.39,
90,
109.93,
90
|
|
R / Rfree (%)
|
27 /
30.6
|
Other elements in 8acw:
The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 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 3.4 A Resolution
(pdb code 8acw). 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 3.4 A Resolution, PDB code: 8acw:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8acw
Go back to
Iron Binding Sites List in 8acw
Iron binding site 1 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 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 3.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe202
b:123.4
occ:1.00
|
FE1
|
E:FES202
|
0.0
|
123.4
|
1.0
|
|
SG
|
D:CYS112
|
2.2
|
150.8
|
1.0
|
|
S1
|
E:FES202
|
2.2
|
163.2
|
1.0
|
|
S2
|
E:FES202
|
2.2
|
173.1
|
1.0
|
|
SG
|
E:CYS26
|
2.3
|
181.8
|
1.0
|
|
HB2
|
E:CYS26
|
2.5
|
129.9
|
1.0
|
|
FE2
|
E:FES202
|
2.7
|
376.1
|
1.0
|
|
CB
|
E:CYS26
|
2.9
|
108.0
|
1.0
|
|
HB2
|
D:CYS112
|
3.1
|
194.3
|
1.0
|
|
H
|
D:CYS112
|
3.2
|
228.0
|
1.0
|
|
CB
|
D:CYS112
|
3.3
|
161.7
|
1.0
|
|
HB3
|
E:CYS26
|
3.5
|
129.9
|
1.0
|
|
H
|
D:GLY27
|
3.5
|
187.7
|
1.0
|
|
H
|
E:CYS26
|
3.5
|
178.4
|
1.0
|
|
N
|
D:CYS112
|
3.9
|
189.7
|
1.0
|
|
H
|
D:CYS29
|
4.0
|
324.0
|
1.0
|
|
H
|
E:CYS120
|
4.0
|
314.7
|
1.0
|
|
HB3
|
D:CYS112
|
4.0
|
194.3
|
1.0
|
|
HA
|
E:ASN119
|
4.1
|
243.4
|
1.0
|
|
HB2
|
D:CYS29
|
4.1
|
216.8
|
1.0
|
|
CA
|
E:CYS26
|
4.1
|
106.1
|
1.0
|
|
SG
|
D:CYS29
|
4.2
|
178.6
|
1.0
|
|
N
|
E:CYS26
|
4.2
|
148.4
|
1.0
|
|
CA
|
D:CYS112
|
4.2
|
171.3
|
1.0
|
|
H
|
D:VAL28
|
4.2
|
117.0
|
1.0
|
|
N
|
D:GLY27
|
4.2
|
156.2
|
1.0
|
|
HA2
|
D:GLY27
|
4.3
|
210.8
|
1.0
|
|
O
|
D:THR110
|
4.3
|
212.6
|
1.0
|
|
HA
|
D:LEU26
|
4.4
|
206.0
|
1.0
|
|
O
|
E:VAL118
|
4.4
|
246.9
|
1.0
|
|
HA
|
D:CYS112
|
4.5
|
205.9
|
1.0
|
|
HA
|
D:ASN111
|
4.6
|
211.4
|
1.0
|
|
CB
|
D:CYS29
|
4.7
|
180.4
|
1.0
|
|
H
|
E:THR27
|
4.7
|
161.5
|
1.0
|
|
CA
|
D:GLY27
|
4.7
|
175.4
|
1.0
|
|
HA
|
E:CYS26
|
4.7
|
127.7
|
1.0
|
|
N
|
D:VAL28
|
4.7
|
97.3
|
1.0
|
|
HA2
|
E:GLY24
|
4.8
|
193.9
|
1.0
|
|
N
|
E:CYS120
|
4.8
|
262.0
|
1.0
|
|
SG
|
E:CYS120
|
4.8
|
226.8
|
1.0
|
|
N
|
D:CYS29
|
4.8
|
269.8
|
1.0
|
|
HB2
|
E:CYS120
|
4.9
|
282.9
|
1.0
|
|
HG23
|
E:THR27
|
4.9
|
183.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 8acw
Go back to
Iron Binding Sites List in 8acw
Iron binding site 2 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 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 3.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe202
b:376.1
occ:1.00
|
FE2
|
E:FES202
|
0.0
|
376.1
|
1.0
|
|
HB2
|
D:CYS29
|
2.1
|
216.8
|
1.0
|
|
S2
|
E:FES202
|
2.2
|
173.1
|
1.0
|
|
S1
|
E:FES202
|
2.2
|
163.2
|
1.0
|
|
SG
|
D:CYS29
|
2.3
|
178.6
|
1.0
|
|
SG
|
E:CYS120
|
2.3
|
226.8
|
1.0
|
|
HB2
|
E:CYS120
|
2.4
|
282.9
|
1.0
|
|
H
|
E:CYS120
|
2.6
|
314.7
|
1.0
|
|
CB
|
D:CYS29
|
2.6
|
180.4
|
1.0
|
|
FE1
|
E:FES202
|
2.7
|
123.4
|
1.0
|
|
CB
|
E:CYS120
|
2.8
|
235.4
|
1.0
|
|
HB3
|
D:CYS29
|
3.1
|
216.8
|
1.0
|
|
N
|
E:CYS120
|
3.3
|
262.0
|
1.0
|
|
H
|
E:GLY24
|
3.5
|
222.6
|
1.0
|
|
H
|
D:CYS29
|
3.5
|
324.0
|
1.0
|
|
HB3
|
E:CYS120
|
3.6
|
282.9
|
1.0
|
|
CA
|
E:CYS120
|
3.6
|
207.8
|
1.0
|
|
HA2
|
E:GLY24
|
3.9
|
193.9
|
1.0
|
|
CA
|
D:CYS29
|
3.9
|
214.7
|
1.0
|
|
HA
|
E:CYS120
|
4.1
|
249.6
|
1.0
|
|
N
|
D:CYS29
|
4.1
|
269.8
|
1.0
|
|
SG
|
E:CYS26
|
4.1
|
181.8
|
1.0
|
|
H
|
E:CYS26
|
4.1
|
178.4
|
1.0
|
|
H
|
E:MET25
|
4.2
|
183.4
|
1.0
|
|
N
|
E:GLY24
|
4.2
|
185.2
|
1.0
|
|
HA
|
E:ASN119
|
4.2
|
243.4
|
1.0
|
|
O
|
D:THR110
|
4.4
|
212.6
|
1.0
|
|
CA
|
E:GLY24
|
4.4
|
161.3
|
1.0
|
|
C
|
E:ASN119
|
4.4
|
186.4
|
1.0
|
|
HA
|
D:CYS29
|
4.5
|
257.9
|
1.0
|
|
HB
|
D:THR110
|
4.5
|
238.1
|
1.0
|
|
SG
|
D:CYS112
|
4.6
|
150.8
|
1.0
|
|
HB2
|
E:CYS26
|
4.6
|
129.9
|
1.0
|
|
N
|
E:MET25
|
4.7
|
152.6
|
1.0
|
|
H
|
D:CYS112
|
4.7
|
228.0
|
1.0
|
|
H
|
D:SER30
|
4.7
|
189.8
|
1.0
|
|
HA
|
D:ASN111
|
4.8
|
211.4
|
1.0
|
|
CA
|
E:ASN119
|
4.9
|
202.6
|
1.0
|
|
HA
|
E:LEU23
|
4.9
|
185.6
|
1.0
|
|
C
|
E:GLY24
|
4.9
|
95.8
|
1.0
|
|
C
|
D:CYS29
|
4.9
|
168.5
|
1.0
|
|
H
|
E:ALA121
|
4.9
|
197.2
|
1.0
|
|
C
|
E:CYS120
|
4.9
|
202.1
|
1.0
|
|
N
|
E:CYS26
|
5.0
|
148.4
|
1.0
|
|
CB
|
E:CYS26
|
5.0
|
108.0
|
1.0
|
|
Iron binding site 3 out
of 4 in 8acw
Go back to
Iron Binding Sites List in 8acw
Iron binding site 3 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 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 3.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1502
b:371.3
occ:1.00
|
FE1
|
F:FES1502
|
0.0
|
371.3
|
1.0
|
|
S1
|
F:FES1502
|
2.2
|
350.4
|
1.0
|
|
S2
|
F:FES1502
|
2.2
|
308.8
|
1.0
|
|
SG
|
F:CYS70
|
2.3
|
368.9
|
1.0
|
|
SG
|
F:CYS76
|
2.3
|
245.5
|
1.0
|
|
FE2
|
F:FES1502
|
2.7
|
329.6
|
1.0
|
|
H
|
F:CYS76
|
2.7
|
403.1
|
1.0
|
|
H
|
F:GLY77
|
2.8
|
436.8
|
1.0
|
|
H
|
F:CYS70
|
3.1
|
365.7
|
1.0
|
|
H
|
F:SER75
|
3.3
|
320.9
|
1.0
|
|
H
|
F:GLY71
|
3.3
|
410.5
|
1.0
|
|
N
|
F:CYS76
|
3.4
|
335.6
|
1.0
|
|
CB
|
F:CYS70
|
3.5
|
327.9
|
1.0
|
|
CB
|
F:CYS76
|
3.6
|
289.7
|
1.0
|
|
HB3
|
F:CYS70
|
3.6
|
393.8
|
1.0
|
|
N
|
F:GLY77
|
3.6
|
363.7
|
1.0
|
|
HB3
|
F:CYS76
|
3.7
|
347.9
|
1.0
|
|
N
|
F:CYS70
|
3.8
|
304.5
|
1.0
|
|
H
|
F:ALA69
|
3.8
|
314.9
|
1.0
|
|
N
|
F:GLY71
|
3.8
|
341.9
|
1.0
|
|
CA
|
F:CYS76
|
3.9
|
329.8
|
1.0
|
|
O
|
F:GLY71
|
3.9
|
256.8
|
1.0
|
|
N
|
F:SER75
|
3.9
|
267.2
|
1.0
|
|
HA2
|
F:GLY74
|
3.9
|
325.1
|
1.0
|
|
H
|
F:GLN78
|
4.0
|
381.1
|
1.0
|
|
H
|
F:GLY74
|
4.0
|
275.2
|
1.0
|
|
CA
|
F:CYS70
|
4.0
|
311.9
|
1.0
|
|
C
|
F:CYS76
|
4.3
|
321.0
|
1.0
|
|
C
|
F:CYS70
|
4.3
|
306.4
|
1.0
|
|
HB2
|
F:CYS70
|
4.3
|
393.8
|
1.0
|
|
HB2
|
F:CYS76
|
4.4
|
347.9
|
1.0
|
|
SG
|
F:CYS111
|
4.4
|
256.6
|
1.0
|
|
C
|
F:SER75
|
4.4
|
289.1
|
1.0
|
|
H
|
F:CYS79
|
4.4
|
325.8
|
1.0
|
|
SG
|
F:CYS79
|
4.5
|
256.9
|
1.0
|
|
HB3
|
F:CYS79
|
4.5
|
298.6
|
1.0
|
|
N
|
F:GLY74
|
4.5
|
229.1
|
1.0
|
|
HA2
|
F:GLY77
|
4.5
|
423.6
|
1.0
|
|
CA
|
F:GLY74
|
4.5
|
270.7
|
1.0
|
|
N
|
F:ALA69
|
4.6
|
262.2
|
1.0
|
|
CA
|
F:GLY77
|
4.6
|
352.8
|
1.0
|
|
HA
|
F:SER68
|
4.6
|
296.0
|
1.0
|
|
C
|
F:GLY74
|
4.6
|
299.9
|
1.0
|
|
N
|
F:GLN78
|
4.6
|
317.3
|
1.0
|
|
HB2
|
F:SER68
|
4.7
|
276.4
|
1.0
|
|
CA
|
F:SER75
|
4.7
|
271.4
|
1.0
|
|
H
|
F:GLY73
|
4.7
|
311.5
|
1.0
|
|
C
|
F:GLY71
|
4.7
|
241.7
|
1.0
|
|
CA
|
F:GLY71
|
4.8
|
291.1
|
1.0
|
|
HA
|
F:CYS76
|
4.8
|
396.1
|
1.0
|
|
C
|
F:ALA69
|
4.9
|
268.5
|
1.0
|
|
HB3
|
F:SER75
|
4.9
|
341.7
|
1.0
|
|
HB3
|
F:ALA69
|
4.9
|
295.0
|
1.0
|
|
HA
|
F:CYS70
|
5.0
|
374.5
|
1.0
|
|
HD13
|
F:LEU109
|
5.0
|
361.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 8acw
Go back to
Iron Binding Sites List in 8acw
Iron binding site 4 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae at 3.4 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 3.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1502
b:329.6
occ:1.00
|
FE2
|
F:FES1502
|
0.0
|
329.6
|
1.0
|
|
S2
|
F:FES1502
|
2.2
|
308.8
|
1.0
|
|
S1
|
F:FES1502
|
2.2
|
350.4
|
1.0
|
|
SG
|
F:CYS79
|
2.3
|
256.9
|
1.0
|
|
SG
|
F:CYS111
|
2.3
|
256.6
|
1.0
|
|
FE1
|
F:FES1502
|
2.7
|
371.3
|
1.0
|
|
HB3
|
F:CYS111
|
3.3
|
302.0
|
1.0
|
|
HB3
|
F:LEU109
|
3.4
|
353.4
|
1.0
|
|
HB3
|
F:CYS79
|
3.4
|
298.6
|
1.0
|
|
CB
|
F:CYS111
|
3.5
|
251.4
|
1.0
|
|
HA2
|
F:GLY74
|
3.5
|
325.1
|
1.0
|
|
CB
|
F:CYS79
|
3.5
|
248.6
|
1.0
|
|
H
|
F:CYS111
|
3.6
|
349.6
|
1.0
|
|
O
|
F:GLY71
|
3.8
|
256.8
|
1.0
|
|
HD22
|
F:LEU109
|
3.9
|
336.8
|
1.0
|
|
HD13
|
F:LEU109
|
3.9
|
361.1
|
1.0
|
|
H
|
F:CYS79
|
3.9
|
325.8
|
1.0
|
|
HD22
|
F:LEU56
|
4.0
|
309.2
|
1.0
|
|
H
|
F:GLY74
|
4.0
|
275.2
|
1.0
|
|
HB2
|
F:CYS79
|
4.1
|
298.6
|
1.0
|
|
HB2
|
F:CYS111
|
4.1
|
302.0
|
1.0
|
|
H
|
F:GLY77
|
4.1
|
436.8
|
1.0
|
|
N
|
F:CYS111
|
4.3
|
291.1
|
1.0
|
|
CB
|
F:LEU109
|
4.3
|
294.2
|
1.0
|
|
SG
|
F:CYS70
|
4.4
|
368.9
|
1.0
|
|
H
|
F:GLN112
|
4.4
|
291.2
|
1.0
|
|
CA
|
F:GLY74
|
4.4
|
270.7
|
1.0
|
|
SG
|
F:CYS76
|
4.5
|
245.5
|
1.0
|
|
CA
|
F:CYS111
|
4.5
|
266.3
|
1.0
|
|
N
|
F:GLY74
|
4.6
|
229.1
|
1.0
|
|
N
|
F:CYS79
|
4.6
|
271.3
|
1.0
|
|
HA2
|
F:GLY77
|
4.6
|
423.6
|
1.0
|
|
CA
|
F:CYS79
|
4.6
|
266.2
|
1.0
|
|
H
|
F:GLY71
|
4.7
|
410.5
|
1.0
|
|
H
|
F:SER75
|
4.7
|
320.9
|
1.0
|
|
HB3
|
F:SER68
|
4.7
|
276.4
|
1.0
|
|
CD2
|
F:LEU109
|
4.8
|
280.4
|
1.0
|
|
HD13
|
F:LEU56
|
4.8
|
244.0
|
1.0
|
|
HB2
|
F:LEU109
|
4.8
|
353.4
|
1.0
|
|
CD1
|
F:LEU109
|
4.8
|
300.7
|
1.0
|
|
H
|
F:ALA110
|
4.8
|
301.2
|
1.0
|
|
HA
|
F:LEU109
|
4.8
|
346.9
|
1.0
|
|
N
|
F:GLY77
|
4.9
|
363.7
|
1.0
|
|
CG
|
F:LEU109
|
4.9
|
287.8
|
1.0
|
|
C
|
F:GLY71
|
4.9
|
241.7
|
1.0
|
|
CD2
|
F:LEU56
|
4.9
|
257.4
|
1.0
|
|
N
|
F:GLN112
|
5.0
|
242.4
|
1.0
|
|
HB2
|
F:SER68
|
5.0
|
276.4
|
1.0
|
|
HA3
|
F:GLY74
|
5.0
|
325.1
|
1.0
|
|
Reference:
G.Fritz,
G.Fritz.
N/A N/A.
ISSN: ESSN 1545-9985
Page generated: Fri Aug 9 17:25:24 2024
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