Iron in PDB 7owi: Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425
Protein crystallography data
The structure of Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425, PDB code: 7owi
was solved by
D.Schmidt,
G.Mlynek,
K.Djinovic-Carugo,
C.Obinger,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.29 /
1.70
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.447,
72.675,
112.12,
90,
94.84,
90
|
|
R / Rfree (%)
|
17.3 /
19.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425
(pdb code 7owi). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425, PDB code: 7owi:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7owi
Go back to
Iron Binding Sites List in 7owi
Iron binding site 1 out
of 4 in the Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:19.8
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
19.8
|
1.0
|
|
ND
|
A:HEM501
|
2.0
|
20.0
|
1.0
|
|
NC
|
A:HEM501
|
2.1
|
21.6
|
1.0
|
|
NA
|
A:HEM501
|
2.1
|
20.4
|
1.0
|
|
NB
|
A:HEM501
|
2.1
|
22.2
|
1.0
|
|
NE2
|
A:HIS114
|
2.1
|
23.9
|
1.0
|
|
O
|
A:HOH681
|
2.5
|
26.8
|
1.0
|
|
CE1
|
A:HIS114
|
3.1
|
29.2
|
1.0
|
|
C4D
|
A:HEM501
|
3.1
|
21.4
|
1.0
|
|
C1C
|
A:HEM501
|
3.1
|
23.1
|
1.0
|
|
C4A
|
A:HEM501
|
3.1
|
22.9
|
1.0
|
|
C4C
|
A:HEM501
|
3.1
|
21.8
|
1.0
|
|
C1A
|
A:HEM501
|
3.1
|
22.4
|
1.0
|
|
C1D
|
A:HEM501
|
3.1
|
20.5
|
1.0
|
|
C4B
|
A:HEM501
|
3.1
|
22.9
|
1.0
|
|
C1B
|
A:HEM501
|
3.1
|
23.6
|
1.0
|
|
CD2
|
A:HIS114
|
3.1
|
23.9
|
1.0
|
|
HE1
|
A:HIS114
|
3.2
|
35.1
|
1.0
|
|
HD2
|
A:HIS114
|
3.3
|
28.7
|
1.0
|
|
CHA
|
A:HEM501
|
3.4
|
21.5
|
1.0
|
|
CHD
|
A:HEM501
|
3.4
|
21.1
|
1.0
|
|
CHC
|
A:HEM501
|
3.4
|
23.7
|
1.0
|
|
CHB
|
A:HEM501
|
3.4
|
23.9
|
1.0
|
|
HO4
|
A:MPD503
|
3.7
|
31.6
|
1.0
|
|
HE1
|
A:MET162
|
4.1
|
46.6
|
1.0
|
|
ND1
|
A:HIS114
|
4.2
|
27.9
|
1.0
|
|
CG
|
A:HIS114
|
4.3
|
25.5
|
1.0
|
|
C2C
|
A:HEM501
|
4.3
|
22.6
|
1.0
|
|
C2A
|
A:HEM501
|
4.3
|
21.6
|
1.0
|
|
C3A
|
A:HEM501
|
4.3
|
23.2
|
1.0
|
|
C3D
|
A:HEM501
|
4.3
|
20.3
|
1.0
|
|
C3B
|
A:HEM501
|
4.3
|
23.2
|
1.0
|
|
C2B
|
A:HEM501
|
4.3
|
24.2
|
1.0
|
|
C3C
|
A:HEM501
|
4.3
|
22.1
|
1.0
|
|
C2D
|
A:HEM501
|
4.3
|
20.5
|
1.0
|
|
HHA
|
A:HEM501
|
4.4
|
25.9
|
1.0
|
|
HHB
|
A:HEM501
|
4.4
|
28.6
|
1.0
|
|
HHC
|
A:HEM501
|
4.4
|
28.5
|
1.0
|
|
HHD
|
A:HEM501
|
4.4
|
25.3
|
1.0
|
|
H51
|
A:MPD503
|
4.5
|
32.9
|
1.0
|
|
O
|
A:HOH708
|
4.5
|
26.0
|
1.0
|
|
O4
|
A:MPD503
|
4.7
|
26.3
|
1.0
|
|
HE1
|
A:PHE108
|
4.7
|
29.9
|
1.0
|
|
H53
|
A:MPD503
|
4.8
|
32.9
|
1.0
|
|
H4
|
A:MPD503
|
4.9
|
32.3
|
1.0
|
|
HZ
|
A:PHE108
|
5.0
|
29.0
|
1.0
|
|
HD1
|
A:HIS114
|
5.0
|
33.5
|
1.0
|
|
CE
|
A:MET162
|
5.0
|
38.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 7owi
Go back to
Iron Binding Sites List in 7owi
Iron binding site 2 out
of 4 in the Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe203
b:22.6
occ:1.00
|
FE
|
B:HEM203
|
0.0
|
22.6
|
1.0
|
|
ND
|
B:HEM203
|
2.0
|
20.8
|
1.0
|
|
NB
|
B:HEM203
|
2.0
|
23.1
|
1.0
|
|
H53
|
B:MPD204
|
2.1
|
29.1
|
1.0
|
|
NC
|
B:HEM203
|
2.1
|
23.2
|
1.0
|
|
NA
|
B:HEM203
|
2.1
|
22.9
|
1.0
|
|
H51
|
B:MPD204
|
2.1
|
29.1
|
1.0
|
|
NE2
|
B:HIS114
|
2.2
|
23.5
|
1.0
|
|
C5
|
B:MPD204
|
2.5
|
24.2
|
1.0
|
|
C4D
|
B:HEM203
|
3.0
|
22.8
|
1.0
|
|
C4B
|
B:HEM203
|
3.0
|
24.4
|
1.0
|
|
C1C
|
B:HEM203
|
3.1
|
24.1
|
1.0
|
|
C4C
|
B:HEM203
|
3.1
|
23.8
|
1.0
|
|
C1B
|
B:HEM203
|
3.1
|
26.5
|
1.0
|
|
C1D
|
B:HEM203
|
3.1
|
22.5
|
1.0
|
|
C1A
|
B:HEM203
|
3.1
|
23.6
|
1.0
|
|
C4A
|
B:HEM203
|
3.1
|
24.4
|
1.0
|
|
H52
|
B:MPD204
|
3.2
|
29.1
|
1.0
|
|
CE1
|
B:HIS114
|
3.2
|
25.1
|
1.0
|
|
CD2
|
B:HIS114
|
3.2
|
25.0
|
1.0
|
|
HE1
|
B:HIS114
|
3.3
|
30.1
|
1.0
|
|
HD2
|
B:HIS114
|
3.4
|
30.0
|
1.0
|
|
CHA
|
B:HEM203
|
3.4
|
22.4
|
1.0
|
|
CHC
|
B:HEM203
|
3.4
|
24.4
|
1.0
|
|
HE1
|
B:MET162
|
3.4
|
33.1
|
0.4
|
|
CHD
|
B:HEM203
|
3.5
|
23.8
|
1.0
|
|
CHB
|
B:HEM203
|
3.5
|
26.2
|
1.0
|
|
C4
|
B:MPD204
|
3.7
|
26.3
|
1.0
|
|
H4
|
B:MPD204
|
3.8
|
31.6
|
1.0
|
|
H13
|
B:MPD204
|
4.1
|
31.9
|
1.0
|
|
HO4
|
B:MPD204
|
4.2
|
47.8
|
1.0
|
|
H12
|
B:MPD204
|
4.2
|
31.9
|
1.0
|
|
C3B
|
B:HEM203
|
4.3
|
24.8
|
1.0
|
|
C3D
|
B:HEM203
|
4.3
|
20.9
|
1.0
|
|
C2B
|
B:HEM203
|
4.3
|
25.1
|
1.0
|
|
C2D
|
B:HEM203
|
4.3
|
21.6
|
1.0
|
|
C2C
|
B:HEM203
|
4.3
|
24.2
|
1.0
|
|
C2A
|
B:HEM203
|
4.3
|
23.6
|
1.0
|
|
C3C
|
B:HEM203
|
4.3
|
23.6
|
1.0
|
|
C3A
|
B:HEM203
|
4.3
|
24.6
|
1.0
|
|
ND1
|
B:HIS114
|
4.3
|
26.9
|
1.0
|
|
CG
|
B:HIS114
|
4.4
|
25.8
|
1.0
|
|
CE
|
B:MET162
|
4.4
|
27.6
|
0.4
|
|
HHA
|
B:HEM203
|
4.4
|
26.9
|
1.0
|
|
HHC
|
B:HEM203
|
4.4
|
29.2
|
1.0
|
|
O4
|
B:MPD204
|
4.4
|
39.8
|
1.0
|
|
HHD
|
B:HEM203
|
4.4
|
28.6
|
1.0
|
|
HHB
|
B:HEM203
|
4.4
|
31.5
|
1.0
|
|
HZ
|
B:PHE145
|
4.5
|
28.5
|
1.0
|
|
C1
|
B:MPD204
|
4.6
|
26.6
|
1.0
|
|
HE1
|
B:MET162
|
4.6
|
33.6
|
0.6
|
|
HE3
|
B:MET162
|
4.6
|
33.1
|
0.4
|
|
HE3
|
B:MET162
|
4.7
|
33.6
|
0.6
|
|
HE1
|
B:PHE108
|
4.7
|
28.7
|
1.0
|
|
HE1
|
B:PHE145
|
4.7
|
28.8
|
1.0
|
|
C3
|
B:MPD204
|
4.8
|
27.0
|
1.0
|
|
HO2
|
B:MPD204
|
4.9
|
43.6
|
1.0
|
|
O2
|
B:MPD204
|
4.9
|
36.4
|
1.0
|
|
HE2
|
B:MET162
|
4.9
|
33.1
|
0.4
|
|
C2
|
B:MPD204
|
5.0
|
28.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 7owi
Go back to
Iron Binding Sites List in 7owi
Iron binding site 3 out
of 4 in the Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe502
b:18.7
occ:1.00
|
FE
|
C:HEM502
|
0.0
|
18.7
|
1.0
|
|
NC
|
C:HEM502
|
2.0
|
19.7
|
1.0
|
|
NB
|
C:HEM502
|
2.0
|
21.1
|
1.0
|
|
ND
|
C:HEM502
|
2.0
|
18.1
|
1.0
|
|
NA
|
C:HEM502
|
2.0
|
19.0
|
1.0
|
|
NE2
|
C:HIS114
|
2.1
|
20.7
|
1.0
|
|
O
|
C:HOH719
|
2.5
|
25.2
|
1.0
|
|
CE1
|
C:HIS114
|
3.0
|
21.9
|
1.0
|
|
C4C
|
C:HEM502
|
3.0
|
20.8
|
1.0
|
|
C4A
|
C:HEM502
|
3.0
|
21.6
|
1.0
|
|
C1C
|
C:HEM502
|
3.1
|
21.2
|
1.0
|
|
C1B
|
C:HEM502
|
3.1
|
21.4
|
1.0
|
|
C1D
|
C:HEM502
|
3.1
|
19.0
|
1.0
|
|
C4B
|
C:HEM502
|
3.1
|
21.8
|
1.0
|
|
C1A
|
C:HEM502
|
3.1
|
21.4
|
1.0
|
|
C4D
|
C:HEM502
|
3.1
|
19.2
|
1.0
|
|
HE1
|
C:HIS114
|
3.1
|
26.4
|
1.0
|
|
CD2
|
C:HIS114
|
3.2
|
22.4
|
1.0
|
|
CHD
|
C:HEM502
|
3.4
|
19.3
|
1.0
|
|
CHB
|
C:HEM502
|
3.4
|
21.7
|
1.0
|
|
CHC
|
C:HEM502
|
3.4
|
22.2
|
1.0
|
|
CHA
|
C:HEM502
|
3.4
|
20.1
|
1.0
|
|
HD2
|
C:HIS114
|
3.5
|
26.8
|
1.0
|
|
HE1
|
C:MET162
|
3.6
|
30.4
|
1.0
|
|
HO4
|
C:MPD504
|
3.8
|
34.9
|
1.0
|
|
ND1
|
C:HIS114
|
4.2
|
22.7
|
1.0
|
|
C2C
|
C:HEM502
|
4.2
|
21.6
|
1.0
|
|
C3C
|
C:HEM502
|
4.3
|
19.9
|
1.0
|
|
C3A
|
C:HEM502
|
4.3
|
21.6
|
1.0
|
|
C3B
|
C:HEM502
|
4.3
|
22.2
|
1.0
|
|
C3D
|
C:HEM502
|
4.3
|
19.2
|
1.0
|
|
C2A
|
C:HEM502
|
4.3
|
20.1
|
1.0
|
|
C2D
|
C:HEM502
|
4.3
|
18.8
|
1.0
|
|
C2B
|
C:HEM502
|
4.3
|
22.0
|
1.0
|
|
CG
|
C:HIS114
|
4.3
|
22.3
|
1.0
|
|
H51
|
C:MPD504
|
4.3
|
32.1
|
1.0
|
|
HHD
|
C:HEM502
|
4.4
|
23.1
|
1.0
|
|
HHB
|
C:HEM502
|
4.4
|
26.1
|
1.0
|
|
HHC
|
C:HEM502
|
4.4
|
26.6
|
1.0
|
|
HHA
|
C:HEM502
|
4.4
|
24.1
|
1.0
|
|
CE
|
C:MET162
|
4.6
|
25.3
|
1.0
|
|
O
|
C:HOH738
|
4.6
|
28.5
|
1.0
|
|
HE1
|
C:PHE108
|
4.7
|
27.6
|
1.0
|
|
O4
|
C:MPD504
|
4.7
|
29.0
|
1.0
|
|
H52
|
C:MPD504
|
4.8
|
32.1
|
1.0
|
|
HE3
|
C:MET162
|
4.9
|
30.4
|
1.0
|
|
H4
|
C:MPD504
|
4.9
|
38.3
|
1.0
|
|
HD1
|
C:HIS114
|
4.9
|
27.3
|
1.0
|
|
C5
|
C:MPD504
|
4.9
|
26.8
|
1.0
|
|
HE1
|
C:PHE145
|
4.9
|
27.6
|
1.0
|
|
HZ
|
C:PHE108
|
5.0
|
25.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 7owi
Go back to
Iron Binding Sites List in 7owi
Iron binding site 4 out
of 4 in the Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425
 Mono view
 Stereo pair view
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A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Dimeric Chlorite Dismutase Variant R127A (Ccld R127A) From Cyanothece Sp. PCC7425 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe505
b:19.8
occ:1.00
|
FE
|
D:HEM505
|
0.0
|
19.8
|
1.0
|
|
ND
|
D:HEM505
|
2.0
|
19.4
|
1.0
|
|
NB
|
D:HEM505
|
2.0
|
20.0
|
1.0
|
|
NA
|
D:HEM505
|
2.0
|
19.4
|
1.0
|
|
NC
|
D:HEM505
|
2.1
|
21.1
|
1.0
|
|
H52
|
D:MPD506
|
2.1
|
28.1
|
1.0
|
|
H51
|
D:MPD506
|
2.2
|
28.1
|
1.0
|
|
NE2
|
D:HIS114
|
2.2
|
21.6
|
1.0
|
|
C5
|
D:MPD506
|
2.6
|
23.4
|
1.0
|
|
C1D
|
D:HEM505
|
3.0
|
20.7
|
1.0
|
|
C4D
|
D:HEM505
|
3.0
|
21.7
|
1.0
|
|
C4C
|
D:HEM505
|
3.1
|
21.6
|
1.0
|
|
C1A
|
D:HEM505
|
3.1
|
22.1
|
1.0
|
|
C1B
|
D:HEM505
|
3.1
|
21.8
|
1.0
|
|
C4A
|
D:HEM505
|
3.1
|
21.8
|
1.0
|
|
C4B
|
D:HEM505
|
3.1
|
22.0
|
1.0
|
|
C1C
|
D:HEM505
|
3.1
|
21.9
|
1.0
|
|
CE1
|
D:HIS114
|
3.1
|
23.4
|
1.0
|
|
H53
|
D:MPD506
|
3.2
|
28.1
|
1.0
|
|
CD2
|
D:HIS114
|
3.2
|
23.2
|
1.0
|
|
HE1
|
D:HIS114
|
3.2
|
28.1
|
1.0
|
|
HD2
|
D:HIS114
|
3.4
|
27.8
|
1.0
|
|
CHA
|
D:HEM505
|
3.4
|
21.3
|
1.0
|
|
CHD
|
D:HEM505
|
3.4
|
21.0
|
1.0
|
|
CHC
|
D:HEM505
|
3.4
|
22.1
|
1.0
|
|
CHB
|
D:HEM505
|
3.4
|
22.0
|
1.0
|
|
C4
|
D:MPD506
|
3.8
|
31.3
|
1.0
|
|
H11
|
D:MPD506
|
3.9
|
31.2
|
1.0
|
|
H4
|
D:MPD506
|
3.9
|
37.5
|
1.0
|
|
HM3
|
D:MPD506
|
4.0
|
29.4
|
1.0
|
|
HE1
|
D:MET162
|
4.2
|
42.9
|
1.0
|
|
ND1
|
D:HIS114
|
4.2
|
23.2
|
1.0
|
|
C2D
|
D:HEM505
|
4.3
|
20.1
|
1.0
|
|
C3D
|
D:HEM505
|
4.3
|
20.5
|
1.0
|
|
C2A
|
D:HEM505
|
4.3
|
19.9
|
1.0
|
|
C3A
|
D:HEM505
|
4.3
|
20.9
|
1.0
|
|
C3B
|
D:HEM505
|
4.3
|
21.4
|
1.0
|
|
C2C
|
D:HEM505
|
4.3
|
21.5
|
1.0
|
|
C3C
|
D:HEM505
|
4.3
|
22.4
|
1.0
|
|
HO4
|
D:MPD506
|
4.3
|
47.0
|
1.0
|
|
C2B
|
D:HEM505
|
4.3
|
22.1
|
1.0
|
|
CG
|
D:HIS114
|
4.3
|
24.0
|
1.0
|
|
HM2
|
D:MPD506
|
4.4
|
29.4
|
1.0
|
|
HHA
|
D:HEM505
|
4.4
|
25.6
|
1.0
|
|
HHD
|
D:HEM505
|
4.4
|
25.2
|
1.0
|
|
HHB
|
D:HEM505
|
4.4
|
26.4
|
1.0
|
|
HHC
|
D:HEM505
|
4.4
|
26.5
|
1.0
|
|
O4
|
D:MPD506
|
4.5
|
39.1
|
1.0
|
|
CM
|
D:MPD506
|
4.6
|
24.5
|
1.0
|
|
HE2
|
D:MET162
|
4.6
|
42.9
|
1.0
|
|
HZ
|
D:PHE145
|
4.6
|
27.1
|
1.0
|
|
HE1
|
D:PHE108
|
4.7
|
26.2
|
1.0
|
|
HE1
|
D:PHE145
|
4.7
|
27.3
|
1.0
|
|
C1
|
D:MPD506
|
4.8
|
26.0
|
1.0
|
|
CE
|
D:MET162
|
4.8
|
35.8
|
1.0
|
|
C3
|
D:MPD506
|
4.9
|
27.1
|
1.0
|
|
HZ
|
D:PHE108
|
4.9
|
25.9
|
1.0
|
|
C2
|
D:MPD506
|
5.0
|
27.6
|
1.0
|
|
HD1
|
D:HIS114
|
5.0
|
27.8
|
1.0
|
|
Reference:
D.Schmidt,
C.Obinger.
Impact of the Dynamics of the Catalytic Arginine on Nitrite and Chlorite Binding By Dimeric Chlorite Dismutase J.Inorg.Biochem. 2021.
ISSN: ISSN 0162-0134
DOI: 10.1016/J.JINORGBIO.2021.111689
Page generated: Thu Aug 8 14:49:05 2024
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