Iron in PDB 4rsz: The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
Protein crystallography data
The structure of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C, PDB code: 4rsz
was solved by
A.Merlino,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
104.22 /
2.19
|
Space group
|
P 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.344,
120.344,
36.673,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.1 /
28.2
|
Other elements in 4rsz:
The structure of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
(pdb code 4rsz). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C, PDB code: 4rsz:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4rsz
Go back to
Iron Binding Sites List in 4rsz
Iron binding site 1 out
of 6 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:23.1
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
23.1
|
1.0
|
ND
|
A:HEM201
|
1.9
|
23.1
|
1.0
|
NE2
|
A:HIS18
|
1.9
|
22.8
|
1.0
|
NA
|
A:HEM201
|
2.0
|
23.3
|
1.0
|
NC
|
A:HEM201
|
2.1
|
22.6
|
1.0
|
NB
|
A:HEM201
|
2.1
|
23.2
|
1.0
|
SD
|
A:MET80
|
2.3
|
24.9
|
1.0
|
CE1
|
A:HIS18
|
2.9
|
22.8
|
1.0
|
C4D
|
A:HEM201
|
3.0
|
23.2
|
1.0
|
C1D
|
A:HEM201
|
3.0
|
23.1
|
1.0
|
CD2
|
A:HIS18
|
3.0
|
22.7
|
1.0
|
C1B
|
A:HEM201
|
3.0
|
23.5
|
1.0
|
C4A
|
A:HEM201
|
3.0
|
23.4
|
1.0
|
C1A
|
A:HEM201
|
3.0
|
23.4
|
1.0
|
C4B
|
A:HEM201
|
3.1
|
23.4
|
1.0
|
C4C
|
A:HEM201
|
3.1
|
22.8
|
1.0
|
C1C
|
A:HEM201
|
3.1
|
22.9
|
1.0
|
CE
|
A:MET80
|
3.3
|
25.1
|
1.0
|
CHB
|
A:HEM201
|
3.4
|
23.5
|
1.0
|
CHA
|
A:HEM201
|
3.4
|
23.3
|
1.0
|
CHD
|
A:HEM201
|
3.4
|
22.9
|
1.0
|
CG
|
A:MET80
|
3.4
|
26.1
|
1.0
|
CHC
|
A:HEM201
|
3.5
|
23.2
|
1.0
|
ND1
|
A:HIS18
|
4.0
|
22.9
|
1.0
|
CG
|
A:HIS18
|
4.1
|
22.7
|
1.0
|
C3A
|
A:HEM201
|
4.2
|
23.4
|
1.0
|
C2A
|
A:HEM201
|
4.2
|
23.5
|
1.0
|
CB
|
A:MET80
|
4.2
|
26.6
|
1.0
|
C3D
|
A:HEM201
|
4.2
|
23.5
|
1.0
|
C2D
|
A:HEM201
|
4.2
|
23.2
|
1.0
|
C2B
|
A:HEM201
|
4.2
|
23.9
|
1.0
|
C2C
|
A:HEM201
|
4.3
|
22.8
|
1.0
|
C3B
|
A:HEM201
|
4.3
|
23.8
|
1.0
|
C3C
|
A:HEM201
|
4.3
|
22.8
|
1.0
|
OH
|
A:TYR67
|
4.5
|
33.9
|
1.0
|
|
Iron binding site 2 out
of 6 in 4rsz
Go back to
Iron Binding Sites List in 4rsz
Iron binding site 2 out
of 6 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:27.5
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
27.5
|
1.0
|
NE2
|
B:HIS18
|
1.9
|
26.5
|
1.0
|
ND
|
B:HEM201
|
1.9
|
26.7
|
1.0
|
NA
|
B:HEM201
|
2.0
|
26.9
|
1.0
|
NC
|
B:HEM201
|
2.1
|
27.3
|
1.0
|
NB
|
B:HEM201
|
2.1
|
28.1
|
1.0
|
SD
|
B:MET80
|
2.3
|
29.5
|
1.0
|
CE1
|
B:HIS18
|
2.9
|
26.2
|
1.0
|
C1D
|
B:HEM201
|
2.9
|
26.6
|
1.0
|
C4D
|
B:HEM201
|
3.0
|
26.6
|
1.0
|
CD2
|
B:HIS18
|
3.0
|
26.1
|
1.0
|
C4A
|
B:HEM201
|
3.0
|
27.6
|
1.0
|
C1A
|
B:HEM201
|
3.0
|
26.9
|
1.0
|
C4C
|
B:HEM201
|
3.0
|
27.4
|
1.0
|
C1B
|
B:HEM201
|
3.0
|
28.4
|
1.0
|
C4B
|
B:HEM201
|
3.1
|
28.3
|
1.0
|
C1C
|
B:HEM201
|
3.1
|
27.8
|
1.0
|
CE
|
B:MET80
|
3.3
|
30.5
|
1.0
|
CHD
|
B:HEM201
|
3.3
|
26.9
|
1.0
|
CHB
|
B:HEM201
|
3.4
|
28.1
|
1.0
|
CHA
|
B:HEM201
|
3.4
|
26.8
|
1.0
|
CG
|
B:MET80
|
3.5
|
30.1
|
1.0
|
CHC
|
B:HEM201
|
3.5
|
28.2
|
1.0
|
ND1
|
B:HIS18
|
4.0
|
25.9
|
1.0
|
CG
|
B:HIS18
|
4.1
|
25.8
|
1.0
|
C3A
|
B:HEM201
|
4.2
|
27.5
|
1.0
|
C2D
|
B:HEM201
|
4.2
|
26.4
|
1.0
|
C2A
|
B:HEM201
|
4.2
|
27.0
|
1.0
|
C3D
|
B:HEM201
|
4.2
|
26.4
|
1.0
|
CB
|
B:MET80
|
4.3
|
30.3
|
1.0
|
C2B
|
B:HEM201
|
4.3
|
29.3
|
1.0
|
C2C
|
B:HEM201
|
4.3
|
27.9
|
1.0
|
C3C
|
B:HEM201
|
4.3
|
27.6
|
1.0
|
C3B
|
B:HEM201
|
4.3
|
28.8
|
1.0
|
OH
|
B:TYR67
|
4.6
|
41.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 4rsz
Go back to
Iron Binding Sites List in 4rsz
Iron binding site 3 out
of 6 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:28.2
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
28.2
|
1.0
|
ND
|
C:HEM201
|
1.9
|
27.6
|
1.0
|
NE2
|
C:HIS18
|
1.9
|
29.2
|
1.0
|
NA
|
C:HEM201
|
2.0
|
29.3
|
1.0
|
NB
|
C:HEM201
|
2.1
|
29.0
|
1.0
|
NC
|
C:HEM201
|
2.1
|
27.6
|
1.0
|
SD
|
C:MET80
|
2.4
|
30.2
|
1.0
|
C1D
|
C:HEM201
|
2.9
|
26.8
|
1.0
|
CE1
|
C:HIS18
|
2.9
|
28.9
|
1.0
|
C4D
|
C:HEM201
|
2.9
|
27.8
|
1.0
|
CD2
|
C:HIS18
|
3.0
|
28.5
|
1.0
|
C1A
|
C:HEM201
|
3.0
|
29.3
|
1.0
|
C4B
|
C:HEM201
|
3.0
|
29.3
|
1.0
|
C4C
|
C:HEM201
|
3.1
|
26.7
|
1.0
|
C4A
|
C:HEM201
|
3.1
|
30.6
|
1.0
|
C1B
|
C:HEM201
|
3.1
|
30.2
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
27.8
|
1.0
|
CE
|
C:MET80
|
3.3
|
30.4
|
1.0
|
CHD
|
C:HEM201
|
3.4
|
26.3
|
1.0
|
CHA
|
C:HEM201
|
3.4
|
28.7
|
1.0
|
CHC
|
C:HEM201
|
3.4
|
28.6
|
1.0
|
CG
|
C:MET80
|
3.5
|
29.4
|
1.0
|
CHB
|
C:HEM201
|
3.5
|
30.5
|
1.0
|
ND1
|
C:HIS18
|
4.0
|
28.6
|
1.0
|
CG
|
C:HIS18
|
4.1
|
28.2
|
1.0
|
C3D
|
C:HEM201
|
4.1
|
27.2
|
1.0
|
C2D
|
C:HEM201
|
4.1
|
26.5
|
1.0
|
CB
|
C:MET80
|
4.2
|
29.5
|
1.0
|
C2A
|
C:HEM201
|
4.2
|
31.0
|
1.0
|
C3A
|
C:HEM201
|
4.2
|
31.3
|
1.0
|
C2B
|
C:HEM201
|
4.3
|
30.6
|
1.0
|
C3C
|
C:HEM201
|
4.3
|
26.7
|
1.0
|
C2C
|
C:HEM201
|
4.3
|
27.4
|
1.0
|
C3B
|
C:HEM201
|
4.3
|
30.2
|
1.0
|
OH
|
C:TYR67
|
4.7
|
47.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 4rsz
Go back to
Iron Binding Sites List in 4rsz
Iron binding site 4 out
of 6 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:34.7
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
34.7
|
1.0
|
ND
|
D:HEM201
|
1.9
|
34.8
|
1.0
|
NE2
|
D:HIS18
|
1.9
|
33.2
|
1.0
|
NA
|
D:HEM201
|
2.0
|
33.7
|
1.0
|
NB
|
D:HEM201
|
2.1
|
35.8
|
1.0
|
NC
|
D:HEM201
|
2.1
|
35.0
|
1.0
|
SD
|
D:MET80
|
2.3
|
38.9
|
1.0
|
CE1
|
D:HIS18
|
2.9
|
32.7
|
1.0
|
C4D
|
D:HEM201
|
2.9
|
34.6
|
1.0
|
C1D
|
D:HEM201
|
2.9
|
34.7
|
1.0
|
CD2
|
D:HIS18
|
3.0
|
31.6
|
1.0
|
C1A
|
D:HEM201
|
3.0
|
34.3
|
1.0
|
C1B
|
D:HEM201
|
3.0
|
34.9
|
1.0
|
C4A
|
D:HEM201
|
3.0
|
33.6
|
1.0
|
C4B
|
D:HEM201
|
3.0
|
36.5
|
1.0
|
C4C
|
D:HEM201
|
3.1
|
35.2
|
1.0
|
C1C
|
D:HEM201
|
3.1
|
36.3
|
1.0
|
CE
|
D:MET80
|
3.3
|
40.6
|
1.0
|
CHA
|
D:HEM201
|
3.4
|
34.5
|
1.0
|
CHD
|
D:HEM201
|
3.4
|
34.8
|
1.0
|
CHB
|
D:HEM201
|
3.4
|
33.5
|
1.0
|
CG
|
D:MET80
|
3.4
|
39.7
|
1.0
|
CHC
|
D:HEM201
|
3.5
|
35.9
|
1.0
|
ND1
|
D:HIS18
|
4.0
|
31.4
|
1.0
|
CG
|
D:HIS18
|
4.1
|
31.0
|
1.0
|
C3D
|
D:HEM201
|
4.2
|
34.8
|
1.0
|
C2D
|
D:HEM201
|
4.2
|
34.1
|
1.0
|
CB
|
D:MET80
|
4.2
|
41.0
|
1.0
|
C3A
|
D:HEM201
|
4.2
|
33.9
|
1.0
|
C2A
|
D:HEM201
|
4.2
|
34.7
|
1.0
|
C2B
|
D:HEM201
|
4.2
|
35.0
|
1.0
|
C3B
|
D:HEM201
|
4.3
|
34.9
|
1.0
|
C2C
|
D:HEM201
|
4.3
|
36.7
|
1.0
|
C3C
|
D:HEM201
|
4.3
|
35.7
|
1.0
|
OH
|
D:TYR67
|
4.6
|
60.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 4rsz
Go back to
Iron Binding Sites List in 4rsz
Iron binding site 5 out
of 6 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:37.6
occ:1.00
|
FE
|
E:HEM201
|
0.0
|
37.6
|
1.0
|
ND
|
E:HEM201
|
1.9
|
36.5
|
1.0
|
NE2
|
E:HIS18
|
1.9
|
34.6
|
1.0
|
NA
|
E:HEM201
|
2.0
|
38.7
|
1.0
|
NB
|
E:HEM201
|
2.1
|
39.9
|
1.0
|
NC
|
E:HEM201
|
2.1
|
37.6
|
1.0
|
SD
|
E:MET80
|
2.3
|
42.5
|
1.0
|
CE1
|
E:HIS18
|
2.9
|
33.4
|
1.0
|
C1D
|
E:HEM201
|
2.9
|
35.7
|
1.0
|
C4D
|
E:HEM201
|
3.0
|
36.6
|
1.0
|
C4A
|
E:HEM201
|
3.0
|
39.9
|
1.0
|
CD2
|
E:HIS18
|
3.0
|
34.3
|
1.0
|
C1A
|
E:HEM201
|
3.0
|
38.2
|
1.0
|
C1B
|
E:HEM201
|
3.1
|
40.8
|
1.0
|
C4B
|
E:HEM201
|
3.1
|
40.9
|
1.0
|
C1C
|
E:HEM201
|
3.1
|
38.7
|
1.0
|
C4C
|
E:HEM201
|
3.1
|
36.7
|
1.0
|
CE
|
E:MET80
|
3.3
|
44.2
|
1.0
|
CHB
|
E:HEM201
|
3.4
|
40.6
|
1.0
|
CHA
|
E:HEM201
|
3.4
|
37.6
|
1.0
|
CHD
|
E:HEM201
|
3.4
|
35.4
|
1.0
|
CG
|
E:MET80
|
3.4
|
44.4
|
1.0
|
CHC
|
E:HEM201
|
3.5
|
40.3
|
1.0
|
ND1
|
E:HIS18
|
4.0
|
31.8
|
1.0
|
CG
|
E:HIS18
|
4.1
|
33.0
|
1.0
|
C2D
|
E:HEM201
|
4.2
|
35.1
|
1.0
|
C3A
|
E:HEM201
|
4.2
|
39.8
|
1.0
|
C3D
|
E:HEM201
|
4.2
|
35.9
|
1.0
|
C2A
|
E:HEM201
|
4.2
|
38.9
|
1.0
|
CB
|
E:MET80
|
4.2
|
44.7
|
1.0
|
C2B
|
E:HEM201
|
4.3
|
42.4
|
1.0
|
C2C
|
E:HEM201
|
4.3
|
38.4
|
1.0
|
C3C
|
E:HEM201
|
4.3
|
37.0
|
1.0
|
C3B
|
E:HEM201
|
4.4
|
42.4
|
1.0
|
OH
|
E:TYR67
|
4.5
|
48.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 4rsz
Go back to
Iron Binding Sites List in 4rsz
Iron binding site 6 out
of 6 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:32.1
occ:1.00
|
FE
|
F:HEM201
|
0.0
|
32.1
|
1.0
|
ND
|
F:HEM201
|
1.9
|
30.9
|
1.0
|
NE2
|
F:HIS18
|
1.9
|
32.0
|
1.0
|
NA
|
F:HEM201
|
1.9
|
32.5
|
1.0
|
NB
|
F:HEM201
|
2.1
|
33.1
|
1.0
|
NC
|
F:HEM201
|
2.1
|
31.5
|
1.0
|
SD
|
F:MET80
|
2.3
|
33.7
|
1.0
|
CE1
|
F:HIS18
|
2.8
|
31.6
|
1.0
|
C1D
|
F:HEM201
|
2.9
|
30.4
|
1.0
|
C4D
|
F:HEM201
|
2.9
|
30.6
|
1.0
|
C1A
|
F:HEM201
|
2.9
|
31.8
|
1.0
|
C4A
|
F:HEM201
|
3.0
|
33.1
|
1.0
|
CD2
|
F:HIS18
|
3.0
|
32.2
|
1.0
|
C1B
|
F:HEM201
|
3.0
|
33.9
|
1.0
|
C4B
|
F:HEM201
|
3.0
|
33.7
|
1.0
|
C4C
|
F:HEM201
|
3.1
|
31.1
|
1.0
|
C1C
|
F:HEM201
|
3.1
|
32.3
|
1.0
|
CE
|
F:MET80
|
3.3
|
34.8
|
1.0
|
CHB
|
F:HEM201
|
3.4
|
33.8
|
1.0
|
CHA
|
F:HEM201
|
3.4
|
31.1
|
1.0
|
CHD
|
F:HEM201
|
3.4
|
30.7
|
1.0
|
CHC
|
F:HEM201
|
3.4
|
33.3
|
1.0
|
CG
|
F:MET80
|
3.5
|
34.6
|
1.0
|
ND1
|
F:HIS18
|
3.9
|
31.9
|
1.0
|
CG
|
F:HIS18
|
4.1
|
32.5
|
1.0
|
C2A
|
F:HEM201
|
4.1
|
32.7
|
1.0
|
C3A
|
F:HEM201
|
4.1
|
33.2
|
1.0
|
C2D
|
F:HEM201
|
4.2
|
29.8
|
1.0
|
C3D
|
F:HEM201
|
4.2
|
29.8
|
1.0
|
C2B
|
F:HEM201
|
4.2
|
35.0
|
1.0
|
CB
|
F:MET80
|
4.3
|
34.5
|
1.0
|
C3B
|
F:HEM201
|
4.3
|
35.1
|
1.0
|
C2C
|
F:HEM201
|
4.3
|
32.0
|
1.0
|
C3C
|
F:HEM201
|
4.3
|
31.2
|
1.0
|
OH
|
F:TYR67
|
4.6
|
42.8
|
1.0
|
|
Reference:
G.Ferraro,
L.Messori,
A.Merlino.
The X-Ray Structure of the Primary Adducts Formed in the Reaction Between Cisplatin and Cytochrome C Chem.Commun.(Camb.) 2014.
ISSN: ESSN 1364-548X
DOI: 10.1039/C4CC09056J
Page generated: Mon Aug 5 09:28:52 2024
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