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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:

Platinum (Pt) 5 atoms
Chlorine (Cl) 3 atoms

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

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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: Sun Dec 13 15:46:19 2020

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