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Platinum in PDB 4s18: The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin:
3.1.27.5;

Protein crystallography data

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin, PDB code: 4s18 was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.27
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.722, 32.736, 73.233, 90.00, 90.36, 90.00
R / Rfree (%) 22.5 / 30.1

Platinum Binding Sites:

The binding sites of Platinum atom in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin (pdb code 4s18). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin, PDB code: 4s18:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 4s18

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Platinum binding site 1 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:55.4
occ:0.80
 PT A:1PT201 0.0 55.4 0.8
N2 A:1PT201 2.1 51.7 0.8
N1 A:1PT201 2.1 56.0 0.8
ND1 A:HIS119 2.1 51.8 1.0
O A:HOH301 2.3 48.9 0.8
C1 A:1PT201 2.8 55.4 0.8
C2 A:1PT201 2.9 55.0 0.8
CE1 A:HIS119 3.0 44.5 1.0
CG A:HIS119 3.0 42.7 1.0
CB A:HIS119 3.4 41.1 1.0
O A:HOH316 3.4 41.7 1.0
CA A:HIS119 3.8 36.9 1.0
NE2 A:HIS119 4.0 44.7 1.0
O A:HOH311 4.1 49.5 1.0
CD2 A:HIS119 4.1 47.2 1.0
O A:VAL118 4.2 31.4 1.0
C3 A:1PT201 4.2 53.5 0.8
O A:HOH310 4.2 63.5 1.0
C6 A:1PT201 4.3 56.7 0.8
N A:PHE120 4.6 34.5 1.0
C A:HIS119 4.7 36.0 1.0
O A:HOH321 4.7 42.1 1.0
N A:HIS119 4.9 35.6 1.0
C A:VAL118 5.0 33.0 1.0

Platinum binding site 2 out of 6 in 4s18

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Platinum binding site 2 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:63.9
occ:0.40
 PT A:1PT202 0.0 63.9 0.4
N1 A:1PT202 2.0 54.6 0.4
N2 A:1PT202 2.0 57.6 0.4
SD A:MET29 2.1 41.6 1.0
OD2 A:ASP14 2.3 74.2 1.0
C2 A:1PT202 2.8 56.3 0.4
C1 A:1PT202 2.8 58.2 0.4
CG A:ASP14 3.1 73.2 1.0
CE A:MET29 3.1 47.4 1.0
OD1 A:ASP14 3.2 66.9 1.0
CG A:MET29 3.6 53.0 1.0
CE1 A:TYR25 3.6 91.2 1.0
OH A:TYR25 4.1 84.3 1.0
CZ A:TYR25 4.2 86.6 1.0
CD1 A:TYR25 4.5 87.5 1.0
CB A:ASP14 4.5 76.0 1.0
CB A:MET29 4.8 57.6 1.0

Platinum binding site 3 out of 6 in 4s18

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Platinum binding site 3 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:55.6
occ:0.20
 NE2 A:HIS105 2.2 45.6 1.0
CE1 A:HIS105 2.6 44.2 1.0
CD2 A:HIS105 3.5 43.4 1.0
ND1 A:HIS105 3.9 47.5 1.0
CG2 A:THR78 4.0 53.5 1.0
CG A:HIS105 4.4 46.6 1.0
O A:TYR76 4.6 34.4 1.0
N A:THR78 4.8 51.3 1.0

Platinum binding site 4 out of 6 in 4s18

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Platinum binding site 4 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:53.0
occ:0.60
 PT B:1PT201 0.0 53.0 0.6
N1 B:1PT201 2.0 47.9 0.6
N2 B:1PT201 2.1 51.3 0.6
ND1 B:HIS119 2.2 45.6 1.0
O B:HOH301 2.3 44.5 0.6
C2 B:1PT201 2.6 51.2 0.6
C1 B:1PT201 2.8 49.9 0.6
CG B:HIS119 3.1 39.5 1.0
CE1 B:HIS119 3.1 41.1 1.0
CB B:HIS119 3.4 30.3 1.0
CA B:HIS119 3.8 27.1 1.0
C6 B:1PT201 4.0 52.0 0.6
C3 B:1PT201 4.1 52.0 0.6
NE2 B:HIS119 4.2 39.9 1.0
CD2 B:HIS119 4.3 43.0 1.0
O B:VAL118 4.4 29.2 1.0
N B:PHE120 4.4 26.2 1.0
O B:HOH341 4.5 53.2 1.0
O B:HOH340 4.6 33.0 1.0
C B:HIS119 4.6 26.0 1.0
O B:HOH333 4.8 43.4 1.0
O B:PHE120 4.9 33.1 1.0
C4 B:1PT201 4.9 51.2 0.6
N B:HIS119 5.0 25.2 1.0

Platinum binding site 5 out of 6 in 4s18

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Platinum binding site 5 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:51.6
occ:0.80
 PT B:1PT202 0.0 51.6 0.8
N1 B:1PT202 2.0 41.5 0.8
N2 B:1PT202 2.1 44.8 0.8
SD B:MET29 2.2 37.0 1.0
OD2 B:ASP14 2.2 35.5 1.0
C1 B:1PT202 2.8 46.6 0.8
C2 B:1PT202 2.9 47.5 0.8
CG B:ASP14 2.9 36.4 1.0
OD1 B:ASP14 3.0 33.9 1.0
CG B:MET29 3.1 39.2 1.0
CE B:MET29 3.2 41.0 1.0
CE1 B:TYR25 3.2 65.3 1.0
OH B:TYR25 3.7 57.3 1.0
CZ B:TYR25 3.8 65.6 1.0
C3 B:1PT202 4.1 49.2 0.8
CD1 B:TYR25 4.1 62.3 1.0
C6 B:1PT202 4.2 47.7 0.8
CB B:ASP14 4.3 34.4 1.0
CB B:MET29 4.5 38.4 1.0
O B:HOH329 4.7 55.1 1.0
CE2 B:TYR25 4.9 67.7 1.0
O B:HOH330 4.9 35.1 1.0

Platinum binding site 6 out of 6 in 4s18

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Platinum binding site 6 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt203

b:60.9
occ:0.20
 NE2 B:HIS105 2.2 44.0 1.0
CD2 B:HIS105 3.1 39.8 1.0
CE1 B:HIS105 3.2 43.1 1.0
CG2 B:THR78 3.9 30.6 1.0
O B:HOH322 4.0 36.9 1.0
CG B:HIS105 4.3 37.9 1.0
ND1 B:HIS105 4.3 41.4 1.0

Reference:

L.Messori, T.Marzo, A.Merlino. Interactions of Carboplatin and Oxaliplatin with Proteins: Insights From X-Ray Structures and Mass Spectrometry Studies of Their Ribonuclease A Adducts. J.Inorg.Biochem. V. 153 136 2015.
ISSN: ISSN 0162-0134
PubMed: 26239545
DOI: 10.1016/J.JINORGBIO.2015.07.011
Page generated: Thu Oct 10 11:31:04 2024

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