Atomistry » Platinum » PDB 5djm-5v6i » 5old
Atomistry »
  Platinum »
    PDB 5djm-5v6i »
      5old »

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: Wed Dec 16 02:05:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy