Atomistry » Platinum » PDB 4nsj-5bna » 4qh3
Atomistry »
  Platinum »
    PDB 4nsj-5bna »
      4qh3 »

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

Go back to Platinum Binding Sites List in 4qh3
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

Go back to Platinum Binding Sites List in 4qh3
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

Go back to Platinum Binding Sites List in 4qh3
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

Go back to Platinum Binding Sites List in 4qh3
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

Go back to Platinum Binding Sites List in 4qh3
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

Go back to Platinum Binding Sites List in 4qh3
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

Go back to Platinum Binding Sites List in 4qh3
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

Go back to Platinum Binding Sites List in 4qh3
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: Wed Dec 16 02:05:00 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy