Iron in PDB 8ad0: X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A
Enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A
All present enzymatic activity of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A:
7.2.1.1;
Protein crystallography data
The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A, PDB code: 8ad0
was solved by
G.Fritz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.12 /
3.11
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.31,
142.15,
105.93,
90,
109.83,
90
|
|
R / Rfree (%)
|
24.9 /
28.8
|
Other elements in 8ad0:
The structure of X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A 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 in Different Conformation at 3.1 A
(pdb code 8ad0). 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 in Different Conformation at 3.1 A, PDB code: 8ad0:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8ad0
Go back to
Iron Binding Sites List in 8ad0
Iron binding site 1 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A
 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 in Different Conformation at 3.1 A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe302
b:115.0
occ:1.00
|
FE1
|
D:FES302
|
0.0
|
115.0
|
1.0
|
|
S1
|
D:FES302
|
2.2
|
117.4
|
1.0
|
|
S2
|
D:FES302
|
2.2
|
118.6
|
1.0
|
|
SG
|
E:CYS26
|
2.3
|
107.9
|
1.0
|
|
SG
|
D:CYS112
|
2.3
|
121.3
|
1.0
|
|
FE2
|
D:FES302
|
2.7
|
115.6
|
1.0
|
|
HB2
|
E:CYS26
|
2.9
|
127.5
|
1.0
|
|
H
|
D:CYS112
|
3.0
|
156.5
|
1.0
|
|
CB
|
E:CYS26
|
3.2
|
105.6
|
1.0
|
|
HB2
|
D:CYS112
|
3.3
|
147.7
|
1.0
|
|
H
|
D:GLY27
|
3.3
|
155.8
|
1.0
|
|
CB
|
D:CYS112
|
3.4
|
122.5
|
1.0
|
|
HB3
|
E:CYS26
|
3.7
|
127.5
|
1.0
|
|
H
|
E:CYS26
|
3.7
|
126.0
|
1.0
|
|
N
|
D:CYS112
|
3.7
|
129.8
|
1.0
|
|
O
|
D:THR110
|
3.8
|
123.3
|
1.0
|
|
N
|
D:GLY27
|
4.1
|
129.2
|
1.0
|
|
HA
|
D:LEU26
|
4.1
|
141.4
|
1.0
|
|
CA
|
D:CYS112
|
4.2
|
129.9
|
1.0
|
|
H
|
D:VAL28
|
4.2
|
133.2
|
1.0
|
|
HB3
|
D:CYS112
|
4.2
|
147.7
|
1.0
|
|
HA
|
D:ASN111
|
4.2
|
159.5
|
1.0
|
|
H
|
D:CYS29
|
4.3
|
129.2
|
1.0
|
|
HA2
|
D:GLY27
|
4.3
|
141.2
|
1.0
|
|
N
|
E:CYS26
|
4.4
|
104.3
|
1.0
|
|
O
|
E:VAL118
|
4.4
|
122.9
|
1.0
|
|
CA
|
E:CYS26
|
4.4
|
104.7
|
1.0
|
|
SG
|
D:CYS29
|
4.4
|
106.7
|
1.0
|
|
HG23
|
E:VAL118
|
4.5
|
148.3
|
1.0
|
|
HA
|
E:ASN119
|
4.5
|
147.3
|
1.0
|
|
HA
|
D:CYS112
|
4.6
|
156.7
|
1.0
|
|
HB2
|
D:CYS29
|
4.6
|
128.6
|
1.0
|
|
CA
|
D:GLY27
|
4.7
|
117.0
|
1.0
|
|
SG
|
E:CYS120
|
4.7
|
117.1
|
1.0
|
|
C
|
D:ASN111
|
4.7
|
133.7
|
1.0
|
|
H
|
E:CYS120
|
4.8
|
161.1
|
1.0
|
|
N
|
D:VAL28
|
4.8
|
110.4
|
1.0
|
|
HA2
|
E:GLY24
|
4.9
|
145.6
|
1.0
|
|
CA
|
D:ASN111
|
4.9
|
132.3
|
1.0
|
|
C
|
D:THR110
|
5.0
|
122.4
|
1.0
|
|
HA
|
E:CYS26
|
5.0
|
126.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 8ad0
Go back to
Iron Binding Sites List in 8ad0
Iron binding site 2 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A
 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 in Different Conformation at 3.1 A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe302
b:115.6
occ:1.00
|
FE2
|
D:FES302
|
0.0
|
115.6
|
1.0
|
|
S1
|
D:FES302
|
2.2
|
117.4
|
1.0
|
|
S2
|
D:FES302
|
2.2
|
118.6
|
1.0
|
|
SG
|
E:CYS120
|
2.3
|
117.1
|
1.0
|
|
SG
|
D:CYS29
|
2.3
|
106.7
|
1.0
|
|
HB2
|
D:CYS29
|
2.4
|
128.6
|
1.0
|
|
FE1
|
D:FES302
|
2.7
|
115.0
|
1.0
|
|
CB
|
D:CYS29
|
2.8
|
106.5
|
1.0
|
|
H
|
E:CYS120
|
3.3
|
161.1
|
1.0
|
|
H
|
D:CYS29
|
3.3
|
129.2
|
1.0
|
|
HB3
|
D:CYS29
|
3.4
|
128.6
|
1.0
|
|
H
|
E:GLY24
|
3.5
|
138.0
|
1.0
|
|
HB2
|
E:CYS120
|
3.6
|
158.1
|
1.0
|
|
CB
|
E:CYS120
|
3.6
|
131.1
|
1.0
|
|
SG
|
E:CYS26
|
3.9
|
107.9
|
1.0
|
|
HA2
|
E:GLY24
|
4.0
|
145.6
|
1.0
|
|
N
|
E:CYS120
|
4.0
|
133.6
|
1.0
|
|
N
|
D:CYS29
|
4.0
|
107.0
|
1.0
|
|
CA
|
D:CYS29
|
4.0
|
106.2
|
1.0
|
|
H
|
E:MET25
|
4.1
|
126.9
|
1.0
|
|
O
|
D:THR110
|
4.1
|
123.3
|
1.0
|
|
H
|
E:CYS26
|
4.2
|
126.0
|
1.0
|
|
N
|
E:GLY24
|
4.2
|
114.3
|
1.0
|
|
HB
|
D:THR110
|
4.3
|
146.6
|
1.0
|
|
HB3
|
E:CYS120
|
4.3
|
158.1
|
1.0
|
|
HA
|
D:ASN111
|
4.4
|
159.5
|
1.0
|
|
HA
|
E:ASN119
|
4.4
|
147.3
|
1.0
|
|
CA
|
E:CYS120
|
4.4
|
126.8
|
1.0
|
|
O
|
E:VAL118
|
4.4
|
122.9
|
1.0
|
|
CA
|
E:GLY24
|
4.5
|
120.7
|
1.0
|
|
HA
|
D:CYS29
|
4.6
|
128.3
|
1.0
|
|
H
|
D:CYS112
|
4.7
|
156.5
|
1.0
|
|
N
|
E:MET25
|
4.7
|
105.1
|
1.0
|
|
HG1
|
D:THR110
|
4.7
|
148.9
|
1.0
|
|
HA
|
E:CYS120
|
4.7
|
153.0
|
1.0
|
|
H
|
D:SER30
|
4.8
|
130.6
|
1.0
|
|
HB2
|
E:CYS26
|
4.8
|
127.5
|
1.0
|
|
SG
|
D:CYS112
|
4.8
|
121.3
|
1.0
|
|
HA
|
E:LEU23
|
4.8
|
129.4
|
1.0
|
|
C
|
D:THR110
|
4.9
|
122.4
|
1.0
|
|
H
|
D:VAL28
|
4.9
|
133.2
|
1.0
|
|
HA2
|
D:GLY27
|
4.9
|
141.2
|
1.0
|
|
HB2
|
E:MET25
|
5.0
|
123.7
|
1.0
|
|
C
|
E:GLY24
|
5.0
|
107.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 8ad0
Go back to
Iron Binding Sites List in 8ad0
Iron binding site 3 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A
 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 in Different Conformation at 3.1 A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1502
b:193.9
occ:1.00
|
FE1
|
F:FES1502
|
0.0
|
193.9
|
1.0
|
|
S1
|
F:FES1502
|
2.2
|
161.3
|
1.0
|
|
S2
|
F:FES1502
|
2.2
|
162.1
|
1.0
|
|
SG
|
F:CYS76
|
2.3
|
167.7
|
1.0
|
|
SG
|
F:CYS70
|
2.4
|
181.0
|
1.0
|
|
FE2
|
F:FES1502
|
2.7
|
162.2
|
1.0
|
|
H
|
F:CYS76
|
2.8
|
195.3
|
1.0
|
|
H
|
F:GLY77
|
2.9
|
193.5
|
1.0
|
|
H
|
F:GLY72
|
3.3
|
192.7
|
1.0
|
|
H
|
F:CYS70
|
3.5
|
209.0
|
1.0
|
|
H
|
F:SER75
|
3.5
|
199.7
|
1.0
|
|
N
|
F:CYS76
|
3.5
|
162.1
|
1.0
|
|
CB
|
F:CYS76
|
3.5
|
167.3
|
1.0
|
|
HB3
|
F:CYS76
|
3.6
|
201.6
|
1.0
|
|
N
|
F:GLY77
|
3.7
|
160.6
|
1.0
|
|
CB
|
F:CYS70
|
3.7
|
176.0
|
1.0
|
|
HB3
|
F:CYS70
|
3.7
|
212.0
|
1.0
|
|
H
|
F:GLY71
|
3.7
|
204.8
|
1.0
|
|
HA
|
F:SER68
|
3.9
|
195.5
|
1.0
|
|
CA
|
F:CYS76
|
3.9
|
162.4
|
1.0
|
|
H
|
F:GLN78
|
4.0
|
216.9
|
1.0
|
|
H
|
F:GLY74
|
4.1
|
202.6
|
1.0
|
|
N
|
F:CYS70
|
4.1
|
173.5
|
1.0
|
|
N
|
F:GLY72
|
4.1
|
159.9
|
1.0
|
|
N
|
F:SER75
|
4.2
|
165.7
|
1.0
|
|
SG
|
F:CYS111
|
4.3
|
149.0
|
1.0
|
|
HB3
|
F:CYS79
|
4.3
|
192.4
|
1.0
|
|
HA2
|
F:GLY72
|
4.3
|
192.8
|
1.0
|
|
HB2
|
F:CYS76
|
4.3
|
201.6
|
1.0
|
|
N
|
F:GLY71
|
4.3
|
170.0
|
1.0
|
|
C
|
F:CYS76
|
4.3
|
163.2
|
1.0
|
|
H
|
F:CYS79
|
4.3
|
193.6
|
1.0
|
|
CA
|
F:CYS70
|
4.4
|
171.8
|
1.0
|
|
HA2
|
F:GLY74
|
4.4
|
203.2
|
1.0
|
|
HB2
|
F:CYS70
|
4.4
|
212.0
|
1.0
|
|
HA2
|
F:GLY77
|
4.5
|
193.1
|
1.0
|
|
SG
|
F:CYS79
|
4.5
|
195.6
|
1.0
|
|
C
|
F:SER75
|
4.6
|
160.2
|
1.0
|
|
CA
|
F:GLY72
|
4.6
|
160.0
|
1.0
|
|
CA
|
F:GLY77
|
4.6
|
160.3
|
1.0
|
|
O
|
F:GLY72
|
4.6
|
168.8
|
1.0
|
|
HB3
|
F:SER75
|
4.6
|
191.4
|
1.0
|
|
N
|
F:GLN78
|
4.6
|
180.1
|
1.0
|
|
C
|
F:GLY72
|
4.6
|
167.7
|
1.0
|
|
N
|
F:GLY74
|
4.7
|
168.1
|
1.0
|
|
C
|
F:CYS70
|
4.7
|
168.5
|
1.0
|
|
CA
|
F:SER68
|
4.7
|
162.2
|
1.0
|
|
HA
|
F:CYS76
|
4.8
|
195.7
|
1.0
|
|
CA
|
F:GLY74
|
4.9
|
168.6
|
1.0
|
|
C
|
F:SER68
|
4.9
|
167.3
|
1.0
|
|
CA
|
F:SER75
|
4.9
|
161.4
|
1.0
|
|
CB
|
F:CYS79
|
4.9
|
159.7
|
1.0
|
|
HB2
|
F:SER68
|
4.9
|
190.6
|
1.0
|
|
HB3
|
F:CYS111
|
4.9
|
173.7
|
1.0
|
|
H
|
F:ALA69
|
5.0
|
207.5
|
1.0
|
|
N
|
F:CYS79
|
5.0
|
160.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 8ad0
Go back to
Iron Binding Sites List in 8ad0
Iron binding site 4 out
of 4 in the X-Ray Structure of Na+-Nqr From Vibrio Cholerae in Different Conformation at 3.1 A
 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 in Different Conformation at 3.1 A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1502
b:162.2
occ:1.00
|
FE2
|
F:FES1502
|
0.0
|
162.2
|
1.0
|
|
SG
|
F:CYS111
|
2.2
|
149.0
|
1.0
|
|
S2
|
F:FES1502
|
2.2
|
162.1
|
1.0
|
|
S1
|
F:FES1502
|
2.2
|
161.3
|
1.0
|
|
SG
|
F:CYS79
|
2.3
|
195.6
|
1.0
|
|
FE1
|
F:FES1502
|
2.7
|
193.9
|
1.0
|
|
HB3
|
F:CYS111
|
2.9
|
173.7
|
1.0
|
|
CB
|
F:CYS111
|
3.2
|
144.1
|
1.0
|
|
HB3
|
F:CYS79
|
3.3
|
192.4
|
1.0
|
|
CB
|
F:CYS79
|
3.5
|
159.7
|
1.0
|
|
H
|
F:CYS111
|
3.5
|
172.3
|
1.0
|
|
HA2
|
F:GLY72
|
3.6
|
192.8
|
1.0
|
|
HB3
|
F:LEU109
|
3.7
|
166.7
|
1.0
|
|
HB2
|
F:CYS111
|
3.8
|
173.7
|
1.0
|
|
H
|
F:GLY74
|
3.8
|
202.6
|
1.0
|
|
HD12
|
F:LEU56
|
3.9
|
196.1
|
1.0
|
|
H
|
F:CYS79
|
3.9
|
193.6
|
1.0
|
|
H
|
F:GLY72
|
3.9
|
192.7
|
1.0
|
|
HA2
|
F:GLY74
|
4.0
|
203.2
|
1.0
|
|
HB2
|
F:CYS79
|
4.1
|
192.4
|
1.0
|
|
H
|
F:GLY77
|
4.1
|
193.5
|
1.0
|
|
N
|
F:CYS111
|
4.2
|
142.9
|
1.0
|
|
CA
|
F:CYS111
|
4.3
|
141.5
|
1.0
|
|
HD13
|
F:LEU109
|
4.3
|
171.0
|
1.0
|
|
HD13
|
F:LEU56
|
4.4
|
196.1
|
1.0
|
|
CA
|
F:GLY72
|
4.4
|
160.0
|
1.0
|
|
SG
|
F:CYS76
|
4.4
|
167.7
|
1.0
|
|
SG
|
F:CYS70
|
4.5
|
181.0
|
1.0
|
|
HG2
|
F:GLN112
|
4.5
|
165.2
|
1.0
|
|
CD1
|
F:LEU56
|
4.5
|
162.8
|
1.0
|
|
N
|
F:GLY72
|
4.5
|
159.9
|
1.0
|
|
HA2
|
F:GLY77
|
4.5
|
193.1
|
1.0
|
|
N
|
F:CYS79
|
4.6
|
160.7
|
1.0
|
|
CA
|
F:CYS79
|
4.6
|
156.4
|
1.0
|
|
HD22
|
F:LEU109
|
4.6
|
170.4
|
1.0
|
|
N
|
F:GLY74
|
4.6
|
168.1
|
1.0
|
|
O
|
F:CYS79
|
4.6
|
149.6
|
1.0
|
|
CB
|
F:LEU109
|
4.7
|
138.2
|
1.0
|
|
HD11
|
F:LEU56
|
4.7
|
196.1
|
1.0
|
|
HA
|
F:SER68
|
4.8
|
195.5
|
1.0
|
|
CA
|
F:GLY74
|
4.8
|
168.6
|
1.0
|
|
H
|
F:SER75
|
4.8
|
199.7
|
1.0
|
|
C
|
F:GLY72
|
4.9
|
167.7
|
1.0
|
|
N
|
F:GLY77
|
4.9
|
160.6
|
1.0
|
|
H
|
F:ALA110
|
5.0
|
166.5
|
1.0
|
|
HA
|
F:CYS111
|
5.0
|
170.6
|
1.0
|
|
HB2
|
F:LEU109
|
5.0
|
166.7
|
1.0
|
|
Reference:
G.Fritz,
G.Fritz.
N/A N/A.
ISSN: ESSN 1545-9985
Page generated: Thu Aug 7 12:57:16 2025
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