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Magnesium 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:

Platinum (Pt) 7 atoms
Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin, PDB code: 5n26:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5n26

Go back to Magnesium Binding Sites List in 5n26
Magnesium binding site 1 out of 5 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg211

b:17.4
occ:0.33
 O A:HOH333 2.1 15.8 1.0
O A:HOH475 2.1 15.4 1.0
OE2 A:GLU134 3.8 14.1 1.0
O A:HOH513 4.2 16.0 1.0
OE1 A:GLU134 4.2 21.9 1.0
O A:HOH365 4.2 23.3 1.0
CD A:GLU134 4.5 16.9 1.0

Magnesium binding site 2 out of 5 in 5n26

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Magnesium binding site 2 out of 5 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg212

b:18.9
occ:0.50
 O A:HOH523 2.1 18.4 0.5
O A:HOH482 2.2 17.3 1.0
O A:HOH328 4.1 17.2 1.0
NZ A:LYS86 4.6 30.8 1.0
O A:HOH522 4.6 25.5 1.0
O A:HOH500 4.6 33.0 1.0
CE A:LYS87 4.7 29.9 1.0
CD A:LYS86 4.7 21.3 1.0

Magnesium binding site 3 out of 5 in 5n26

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Magnesium binding site 3 out of 5 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg213

b:18.9
occ:0.60
 O A:HOH423 1.8 17.4 0.6
O A:HOH514 2.0 21.6 0.6
O A:HOH415 2.5 14.1 0.6
OD2 A:ASP131 3.9 18.7 1.0
CG2 A:THR135 4.4 23.9 1.0
OG1 A:THR135 4.6 20.4 1.0
OD1 A:ASP131 4.7 21.7 1.0
CG A:ASP131 4.7 18.8 1.0
O A:HOH465 4.7 34.5 1.0

Magnesium binding site 4 out of 5 in 5n26

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Magnesium binding site 4 out of 5 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Cisplatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg214

b:30.2
occ:0.60
 O A:HOH305 1.9 11.5 0.6
O A:HOH334 2.1 23.2 0.6
OE1 A:GLN58 2.1 36.2 1.0
OE1 A:GLU61 2.2 45.0 1.0
O A:HOH313 2.6 20.4 0.6
OE2 A:GLU140 2.9 20.2 0.4
O A:HOH386 3.0 42.9 1.0
CD A:GLN58 3.3 27.6 1.0
CD A:GLU61 3.4 38.2 1.0
O A:HOH425 3.7 49.7 1.0
NE2 A:GLN58 3.9 35.7 1.0
O A:HOH301 4.0 34.8 1.0
CD A:GLU140 4.1 20.0 0.4
OE2 A:GLU61 4.2 51.5 1.0
CB A:GLU61 4.3 22.5 1.0
OE1 A:GLU62 4.4 32.7 1.0
OE2 A:GLU107 4.4 37.8 1.0
CB A:ALA144 4.5 13.7 1.0
CG A:GLU61 4.5 31.5 1.0
CG A:GLN58 4.5 23.0 1.0
OE1 A:GLU140 4.6 21.0 0.4
CB A:GLN58 4.7 20.7 1.0
CA A:GLN58 4.8 17.5 1.0
CE1 A:HIS65 4.9 31.5 1.0

Magnesium binding site 5 out of 5 in 5n26

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg215

b:16.6
occ:0.80
 OE2 A:GLU62 2.0 25.2 1.0
OE2 A:GLU27 2.0 17.1 1.0
O A:HOH315 2.1 40.2 0.8
O A:HOH350 2.1 11.3 0.8
O A:HOH349 2.1 16.4 0.8
ND1 A:HIS65 2.2 26.6 1.0
CE1 A:HIS65 3.0 31.5 1.0
CD A:GLU27 3.0 16.9 1.0
CD A:GLU62 3.0 24.7 1.0
CG A:HIS65 3.3 24.9 1.0
OE1 A:GLU27 3.3 17.2 1.0
OE1 A:GLU62 3.4 32.7 1.0
CB A:HIS65 3.7 18.5 1.0
O A:HOH377 3.9 26.9 1.0
O A:HOH345 4.1 47.5 1.0
OE1 A:GLN141 4.1 24.3 1.0
NE2 A:HIS65 4.2 28.8 1.0
CG1 A:VAL110 4.2 17.2 1.0
CG A:GLU27 4.3 15.4 1.0
CD2 A:HIS65 4.4 27.2 1.0
CG A:GLU62 4.4 20.9 1.0
CA A:GLU62 4.6 16.5 1.0
CB A:GLU27 4.7 14.0 1.0
CB A:GLU62 4.7 18.1 1.0
CA A:GLU27 4.9 13.3 1.0
CD A:GLN141 4.9 20.8 1.0
O A:HOH403 5.0 32.5 1.0
OE1 A:GLU107 5.0 36.9 1.0

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: Mon Dec 14 20:54:45 2020

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