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Platinum in PDB 5old: X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound:
3.1.27.5;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound, PDB code: 5old 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) 72.50 / 1.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.951, 32.584, 72.502, 90.00, 89.35, 90.00
R / Rfree (%) 19.6 / 25

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound (pdb code 5old). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound, PDB code: 5old:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 5old

Go back to Platinum Binding Sites List in 5old
Platinum binding site 1 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound


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 the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:28.0
occ:0.60
 NE2 A:HIS119 2.2 21.1 0.6
O A:HOH402 2.3 20.9 0.6
S A:DMS204 2.6 7.5 0.6
S A:DMS203 2.6 9.0 0.6
CD2 A:HIS119 2.9 22.3 0.6
CE1 A:HIS119 3.4 19.3 0.6
O A:HOH396 3.5 57.7 1.0
CG A:HIS119 4.2 22.2 0.6
OE2 A:GLU111 4.3 29.7 1.0
ND1 A:HIS119 4.3 22.1 0.6
CG1 A:VAL118 4.9 15.8 0.5

Platinum binding site 2 out of 4 in 5old

Go back to Platinum Binding Sites List in 5old
Platinum binding site 2 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound


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 the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:48.0
occ:0.60
 NE2 A:HIS105 2.1 31.6 1.0
O A:HOH423 2.4 31.4 0.6
O A:HOH395 2.6 24.3 0.6
S A:DMS205 2.8 19.2 0.6
CE1 A:HIS105 3.1 28.4 1.0
CD2 A:HIS105 3.1 30.9 1.0
ND1 A:HIS105 4.2 27.8 1.0
CG A:HIS105 4.2 28.7 1.0
O A:HOH346 4.4 48.8 1.0
CG2 A:THR78 4.6 30.1 1.0
O A:HOH347 4.9 45.3 1.0
O A:HOH326 5.0 29.8 1.0

Platinum binding site 3 out of 4 in 5old

Go back to Platinum Binding Sites List in 5old
Platinum binding site 3 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound


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 the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:55.1
occ:0.50
 NE2 B:HIS105 2.1 35.2 1.0
S B:DMS203 2.4 22.6 0.5
O B:HOH382 2.6 41.7 0.5
O B:HOH359 2.6 24.5 0.5
CE1 B:HIS105 2.8 33.7 1.0
CD2 B:HIS105 3.3 33.2 1.0
O B:HOH367 3.6 19.2 0.5
ND1 B:HIS105 4.0 32.3 1.0
CG B:HIS105 4.3 31.2 1.0
CG2 B:THR78 4.4 37.7 1.0
O B:TYR76 4.8 29.8 1.0

Platinum binding site 4 out of 4 in 5old

Go back to Platinum Binding Sites List in 5old
Platinum binding site 4 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound


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 the Adduct Formed Upon Reaction of Ribonuclease A with A Tetranuclear Pt-Thiosemicarbazone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:51.0
occ:0.45
 ND1 B:HIS119 2.0 43.3 0.5
O B:HOH372 2.2 28.0 0.5
O B:HOH302 2.4 22.7 0.5
S B:DMS204 2.7 25.8 0.5
CG B:HIS119 2.8 40.1 0.5
ND1 B:HIS119 2.9 45.0 0.6
CE1 B:HIS119 3.0 46.7 0.5
CB B:HIS119 3.1 32.3 0.5
CB B:HIS119 3.1 30.4 0.6
CG B:HIS119 3.3 36.6 0.6
O B:HOH370 3.9 33.6 0.6
CD2 B:HIS119 3.9 47.0 0.5
NE2 B:HIS119 4.0 46.2 0.5
CE1 B:HIS119 4.0 43.8 0.6
O B:VAL118 4.1 30.4 1.0
CA B:HIS119 4.2 30.9 0.5
CA B:HIS119 4.3 30.1 0.6
CD2 B:HIS119 4.4 35.2 0.6
O B:HOH358 4.5 34.2 1.0
NE2 B:HIS119 4.7 39.6 0.6
C B:VAL118 4.8 29.0 1.0
N B:HIS119 4.9 26.0 0.5
N B:HIS119 5.0 24.9 0.6

Reference:

T.Marzo, F.Navas, D.Cirri, A.Merlino, G.Ferraro, L.Messori, A.G.Quiroga. Reactions of A Tetranuclear Pt-Thiosemicarbazone Complex with Model Proteins. J. Inorg. Biochem. V. 181 11 2018.
ISSN: ISSN 1873-3344
PubMed: 29353085
DOI: 10.1016/J.JINORGBIO.2018.01.002
Page generated: Thu Oct 10 11:40:08 2024

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