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Platinum in PDB 5n26: X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin

Enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin

All present enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin:
1.16.3.1;

Protein crystallography data

The structure of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin, PDB code: 5n26 was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.69 / 2.05
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.069, 183.069, 183.069, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.6

Other elements in 5n26:

The structure of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 8 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin (pdb code 5n26). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 7 binding sites of Platinum where determined in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin, PDB code: 5n26:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7;

Platinum binding site 1 out of 7 in 5n26

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Platinum binding site 1 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:45.9
occ:0.50
 PT1 A:CPT201 0.0 45.9 0.5
N1 A:CPT201 2.0 38.5 0.5
NZ A:LYS68 2.1 34.3 1.0
ND1 A:HIS136 2.1 31.1 1.0
N2 A:CPT201 2.1 39.8 0.5
CE1 A:HIS136 3.1 26.7 1.0
CG A:HIS136 3.1 22.9 1.0
CB A:HIS136 3.4 20.9 1.0
CA A:HIS136 3.5 17.8 1.0
CE A:LYS68 3.6 34.4 1.0
O A:THR135 4.1 23.9 1.0
NE2 A:HIS136 4.2 25.5 1.0
CD2 A:HIS136 4.2 23.9 1.0
O A:HIS136 4.4 16.3 1.0
N A:HIS136 4.5 19.1 1.0
C A:HIS136 4.5 16.8 1.0
CD A:LYS68 4.6 29.8 1.0
C A:THR135 4.7 22.3 1.0

Platinum binding site 2 out of 7 in 5n26

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Platinum binding site 2 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:45.0
occ:0.50
 PT1 A:73M202 0.0 45.0 0.5
ND1 A:HIS105 1.9 27.8 0.5
N1 A:73M202 2.0 23.9 0.5
N2 A:73M202 2.1 24.6 0.5
CD2 A:HIS105 2.1 35.2 0.5
O2 A:73M202 2.2 31.8 0.5
CG A:HIS105 2.8 23.3 0.5
CE1 A:HIS105 2.8 25.5 0.5
CG A:HIS105 3.1 31.0 0.5
CB A:HIS105 3.2 19.2 0.5
NE2 A:HIS105 3.2 36.6 0.5
O A:HOH464 3.2 12.7 0.5
O A:HOH344 3.4 19.6 0.5
CA A:HIS105 3.6 18.4 0.5
CB A:HIS105 3.6 23.9 0.5
CA A:HIS105 3.6 20.6 0.5
NE2 A:HIS105 3.8 26.2 0.5
CD2 A:HIS105 3.8 24.9 0.5
ND1 A:HIS105 4.2 38.3 0.5
O A:HIS105 4.2 18.2 0.5
CE1 A:HIS105 4.3 37.3 0.5
O A:HIS105 4.3 17.1 0.5
C A:HIS105 4.3 18.8 0.5
C A:HIS105 4.4 17.6 0.5
N A:HIS105 4.8 17.5 0.5
N A:HIS105 4.8 16.4 0.5
O A:HOH469 4.8 44.0 1.0
OD1 A:ASN109 4.9 38.7 1.0
O A:HOH322 5.0 26.1 1.0

Platinum binding site 3 out of 7 in 5n26

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Platinum binding site 3 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:55.9
occ:0.40
 ND1 A:HIS105 2.1 38.3 0.5
PT1 A:CPT203 2.8 50.9 0.2
CE1 A:HIS105 3.0 37.3 0.5
CG A:HIS105 3.0 31.0 0.5
CL1 A:CPT203 3.2 38.1 0.4
SG A:CYS102 3.3 37.7 1.0
CB A:HIS105 3.4 23.9 0.5
CD2 A:HIS105 3.4 24.9 0.5
PT1 A:CPT203 3.5 47.7 0.4
CB A:CYS102 3.5 24.7 1.0
CG A:HIS105 3.5 23.3 0.5
CA A:CYS102 3.5 20.3 1.0
CB A:HIS105 3.6 19.2 0.5
O A:CYS102 3.9 15.3 1.0
NE2 A:HIS105 4.0 36.6 0.5
CD2 A:HIS105 4.1 35.2 0.5
NE2 A:HIS105 4.2 26.2 0.5
C A:CYS102 4.2 18.2 1.0
ND1 A:HIS105 4.3 27.8 0.5
CE1 A:HIS105 4.7 25.5 0.5
N A:CYS102 4.7 17.9 1.0
CA A:HIS105 4.8 20.6 0.5
O A:HOH468 4.9 35.8 1.0
CA A:HIS105 5.0 18.4 0.5
O A:GLU101 5.0 18.1 1.0

Platinum binding site 4 out of 7 in 5n26

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Platinum binding site 4 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:50.9
occ:0.20
 PT1 A:CPT203 0.0 50.9 0.2
SG A:CYS102 2.3 37.7 1.0
PT1 A:73M202 2.8 55.9 0.4
PT1 A:CPT203 3.5 47.7 0.4
CB A:CYS102 3.5 24.7 1.0
CA A:CYS102 3.6 20.3 1.0
N A:CYS102 3.9 17.9 1.0
OD1 A:ASN98 4.4 26.5 1.0
ND1 A:HIS105 4.4 38.3 0.5
C A:GLU101 4.4 17.6 1.0
O A:GLU101 4.6 18.1 1.0
O A:ASN98 4.6 13.1 1.0
CB A:GLU101 4.8 19.9 1.0
CB A:HIS105 4.8 23.9 0.5
CL1 A:CPT203 4.9 38.1 0.4
CG A:HIS105 4.9 31.0 0.5
C A:CYS102 5.0 18.2 1.0

Platinum binding site 5 out of 7 in 5n26

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Platinum binding site 5 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:47.7
occ:0.40
 PT1 A:CPT203 0.0 47.7 0.4
CL1 A:CPT203 2.3 38.1 0.4
SG A:CYS102 2.4 37.7 1.0
CL1 A:CPT204 2.8 33.1 0.2
PT1 A:CPT204 3.2 56.2 0.2
CZ3 A:TRP93 3.4 31.4 1.0
CB A:CYS102 3.4 24.7 1.0
PT1 A:73M202 3.5 55.9 0.4
PT1 A:CPT203 3.5 50.9 0.2
CE3 A:TRP93 4.1 26.8 1.0
CH2 A:TRP93 4.3 32.5 1.0
SG A:CYS90 4.4 20.8 0.5
CA A:CYS102 4.7 20.3 1.0
CB A:CYS90 4.8 29.1 0.5
CB A:CYS90 4.8 34.1 0.5
ND2 A:ASN98 4.9 20.0 1.0

Platinum binding site 6 out of 7 in 5n26

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Platinum binding site 6 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:56.2
occ:0.25
 PT1 A:CPT204 0.0 56.2 0.2
SG A:CYS90 2.0 20.8 0.5
CL1 A:CPT204 2.3 33.1 0.2
SG A:CYS90 2.4 42.5 0.5
CB A:CYS90 2.7 34.1 0.5
PT1 A:CPT203 3.2 47.7 0.4
CB A:CYS90 3.4 29.1 0.5
CA A:CYS90 3.8 40.1 0.5
N A:CYS90 3.9 41.2 0.5
CA A:CYS90 4.1 32.9 0.5
N A:CYS90 4.2 35.8 0.5
CB A:ASP89 4.3 48.7 1.0
CL1 A:CPT203 4.4 38.1 0.4
C A:ASP89 4.5 41.6 1.0
PT1 A:CPT204 4.7 51.5 0.4
O A:ASP89 4.9 50.8 1.0
CZ3 A:TRP93 5.0 31.4 1.0

Platinum binding site 7 out of 7 in 5n26

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Platinum binding site 7 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:51.5
occ:0.40
 PT1 A:CPT204 0.0 51.5 0.4
SG A:CYS90 2.4 42.5 0.5
CB A:CYS90 3.4 34.1 0.5
SG A:CYS90 3.5 20.8 0.5
O A:ASP92 3.7 33.5 1.0
CA A:CYS90 4.0 40.1 0.5
N A:ASP92 4.1 33.4 1.0
CB A:ASP92 4.1 35.3 1.0
N A:ASP91 4.3 36.2 1.0
CB A:CYS90 4.4 29.1 0.5
CA A:CYS90 4.5 32.9 0.5
C A:ASP92 4.5 32.5 1.0
CA A:ASP92 4.5 33.5 1.0
C A:CYS90 4.6 38.3 0.5
PT1 A:CPT204 4.7 56.2 0.2
C A:CYS90 4.9 32.8 0.5

Reference:

G.Ferraro, S.Ciambellotti, L.Messori, A.Merlino. Cisplatin Binding Sites in Human H-Chain Ferritin. Inorg Chem V. 56 9064 2017.
ISSN: ISSN 1520-510X
PubMed: 28737381
DOI: 10.1021/ACS.INORGCHEM.7B01072
Page generated: Thu Oct 10 11:38:59 2024

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