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 / R_free (%)*	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

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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

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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

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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

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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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