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Platinum in PDB 4qh3: X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)

Enzymatic activity of X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)

All present enzymatic activity of X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II):
3.1.27.5;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II), PDB code: 4qh3 was solved by I.Russo Krauss, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.09 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.824, 32.537, 67.237, 90.00, 93.75, 90.00
R / Rfree (%) 21.4 / 27.5

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) (pdb code 4qh3). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 8 binding sites of Platinum where determined in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II), PDB code: 4qh3:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Platinum binding site 1 out of 8 in 4qh3

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Platinum binding site 1 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


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 Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:64.4
occ:0.40
 PT A:I83201 0.0 64.4 0.4
N18 A:I83201 1.9 64.8 0.4
N21 A:I83201 2.0 47.4 0.4
NE2 A:HIS119 2.0 53.5 0.5
CE1 A:HIS119 2.2 54.7 0.5
NE2 A:HIS119 2.2 58.0 0.5
CE1 A:HIS119 2.5 46.4 0.5
C17 A:I83201 2.8 64.3 0.4
C22 A:I83201 2.8 45.0 0.4
C19 A:I83201 2.8 44.8 0.4
CD2 A:HIS119 3.3 53.7 0.5
ND1 A:HIS119 3.5 54.4 0.5
CD2 A:HIS119 3.5 56.8 0.5
ND1 A:HIS119 3.8 48.9 0.5
CG A:HIS119 4.1 53.7 0.5
CG A:HIS119 4.2 50.0 0.5
O A:PHE120 4.3 30.6 1.0
O A:HOH310 4.8 29.8 0.5
C19 A:I83203 4.9 56.3 0.3
PT A:I83203 5.0 66.9 0.3

Platinum binding site 2 out of 8 in 4qh3

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Platinum binding site 2 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


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 Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:60.4
occ:1.00
 PT A:I83202 0.0 60.4 1.0
N21 A:I83202 1.9 43.3 1.0
N18 A:I83202 1.9 45.7 1.0
NE2 A:HIS105 2.3 43.0 1.0
O A:HOH303 2.6 54.8 1.0
C17 A:I83202 2.7 54.1 1.0
C22 A:I83202 2.7 49.2 1.0
C19 A:I83202 2.8 55.0 1.0
CD2 A:HIS105 3.2 38.1 1.0
CE1 A:HIS105 3.4 43.8 1.0
CG A:HIS105 4.3 39.5 1.0
ND1 A:HIS105 4.4 42.5 1.0

Platinum binding site 3 out of 8 in 4qh3

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Platinum binding site 3 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


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 Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:66.9
occ:0.30
 PT A:I83203 0.0 66.9 0.3
ND1 A:HIS119 1.9 48.9 0.5
N18 A:I83203 1.9 61.1 0.3
N21 A:I83203 1.9 54.2 0.3
ND1 A:HIS119 2.0 54.4 0.5
CE1 A:HIS119 2.6 46.4 0.5
CG A:HIS119 2.7 50.0 0.5
C19 A:I83203 2.8 56.3 0.3
C22 A:I83203 2.8 56.8 0.3
C17 A:I83203 2.8 63.3 0.3
O A:HOH306 2.8 66.3 1.0
CG A:HIS119 2.9 53.7 0.5
CE1 A:HIS119 3.0 54.7 0.5
CB A:HIS119 3.2 42.3 0.5
CB A:HIS119 3.2 40.6 0.5
NE2 A:HIS119 3.6 53.5 0.5
CD2 A:HIS119 3.6 53.7 0.5
O A:VAL118 4.0 35.8 1.0
CD2 A:HIS119 4.0 56.8 0.5
NE2 A:HIS119 4.0 58.0 0.5
CA A:HIS119 4.3 37.4 0.5
CA A:HIS119 4.3 36.7 0.5
C A:VAL118 4.9 35.7 1.0
O A:HOH323 5.0 39.3 1.0
PT A:I83201 5.0 64.4 0.4
N A:HIS119 5.0 35.0 1.0

Platinum binding site 4 out of 8 in 4qh3

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Platinum binding site 4 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


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 Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:68.2
occ:0.30
 PT A:I83204 0.0 68.2 0.3
N21 A:I83204 1.9 48.7 0.3
N18 A:I83204 2.0 60.5 0.3
ND1 A:HIS48 2.3 82.3 1.0
C22 A:I83204 2.8 45.9 0.3
C19 A:I83204 2.8 49.4 0.3
C17 A:I83204 2.8 60.6 0.3
O A:HOH305 2.9 47.7 1.0
CG A:HIS48 3.1 73.1 1.0
CB A:HIS48 3.2 64.8 1.0
CE1 A:HIS48 3.4 82.8 1.0
CD2 A:HIS48 4.3 77.1 1.0
NE2 A:HIS48 4.4 82.4 1.0
CA A:HIS48 4.6 66.0 1.0
OG A:SER80 4.7 51.0 1.0
O A:HIS48 5.0 57.7 1.0

Platinum binding site 5 out of 8 in 4qh3

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Platinum binding site 5 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


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 the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:50.8
occ:1.00
 PT B:I83201 0.0 50.8 1.0
N18 B:I83201 1.9 32.2 1.0
N21 B:I83201 1.9 40.5 1.0
NE2 B:HIS105 2.4 33.6 1.0
C17 B:I83201 2.6 47.3 1.0
C22 B:I83201 2.7 46.6 1.0
C19 B:I83201 2.7 51.9 1.0
O B:HOH307 2.8 52.8 1.0
CD2 B:HIS105 3.0 34.4 1.0
CE1 B:HIS105 3.5 34.0 1.0
CG B:HIS105 4.3 34.0 1.0
O B:HOH304 4.4 37.0 1.0
ND1 B:HIS105 4.5 38.4 1.0

Platinum binding site 6 out of 8 in 4qh3

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Platinum binding site 6 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


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 the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:44.1
occ:0.50
 PT B:I83202 0.0 44.1 0.5
N21 B:I83202 1.9 40.5 0.5
N18 B:I83202 1.9 42.0 0.5
NE2 B:HIS119 2.1 25.4 0.5
C22 B:I83202 2.7 40.4 0.5
C19 B:I83202 2.8 43.9 0.5
CD2 B:HIS119 2.8 25.8 0.5
C17 B:I83202 2.8 40.1 0.5
CE1 B:HIS119 3.3 27.2 0.5
O B:HOH308 3.5 55.0 1.0
CG B:HIS119 4.0 26.8 0.5
ND1 B:HIS119 4.2 26.8 0.5

Platinum binding site 7 out of 8 in 4qh3

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Platinum binding site 7 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


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 the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt203

b:66.3
occ:0.50
 PT B:I83203 0.0 66.3 0.5
N18 B:I83203 1.9 63.1 0.5
N21 B:I83203 2.0 50.5 0.5
NE2 B:HIS119 2.1 36.3 0.5
O B:HOH309 2.7 57.2 1.0
C17 B:I83203 2.7 65.9 0.5
C22 B:I83203 2.8 42.1 0.5
C19 B:I83203 2.8 48.6 0.5
CD2 B:HIS119 2.9 34.0 0.5
CE1 B:HIS119 3.1 33.0 0.5
CG B:HIS119 4.1 33.9 0.5
ND1 B:HIS119 4.2 33.7 0.5
O B:HOH341 4.2 38.6 1.0
ND1 B:HIS119 4.5 26.8 0.5
O B:PHE120 4.5 29.1 1.0
CE1 B:HIS119 4.8 27.2 0.5

Platinum binding site 8 out of 8 in 4qh3

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Platinum binding site 8 out of 8 in the X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of X-Ray Structure of the Adduct Formed Between Bovine Pancreatic Ribonuclease and Trans-Dimethylamine Methylamine Dichlorido Platinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt204

b:69.2
occ:0.50
 PT B:I83204 0.0 69.2 0.5
N18 B:I83204 1.9 24.4 0.5
N21 B:I83204 1.9 70.6 0.5
ND1 B:HIS48 2.2 59.5 1.0
C17 B:I83204 2.7 21.6 0.5
C22 B:I83204 2.8 71.1 0.5
C19 B:I83204 2.8 71.0 0.5
O B:HOH320 3.0 54.1 1.0
CG B:HIS48 3.1 48.6 1.0
CB B:HIS48 3.3 42.7 1.0
CE1 B:HIS48 3.3 55.5 1.0
CD2 B:HIS48 4.3 60.2 1.0
NE2 B:HIS48 4.4 54.0 1.0
OG B:SER80 4.5 40.8 1.0
CA B:HIS48 4.7 39.2 1.0

Reference:

L.Messori, T.Marzo, E.Michelucci, I.Russo Krauss, C.Navarro-Ranninger, A.G.Quiroga, A.Merlino. Interactions Between Anticancer Trans-Platinum Compounds and Proteins: Crystal Structures and Esi-Ms Spectra of Two Protein Adducts of Trans-(Dimethylamino)(Methylamino)Dichloridoplatinum(II). Inorg.Chem. V. 53 7806 2014.
ISSN: ISSN 0020-1669
PubMed: 25025479
DOI: 10.1021/IC5012583
Page generated: Thu Oct 10 11:09:00 2024

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