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Palladium in PDB 6gok: X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain:
3.1.27.5;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain, PDB code: 6gok was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.66 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.282, 32.805, 72.661, 90.00, 90.61, 90.00
R / Rfree (%) 18.7 / 25.5

Other elements in 6gok:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Palladium Binding Sites:

The binding sites of Palladium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain (pdb code 6gok). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 4 binding sites of Palladium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain, PDB code: 6gok:
Jump to Palladium binding site number: 1; 2; 3; 4;

Palladium binding site 1 out of 4 in 6gok

Go back to Palladium Binding Sites List in 6gok
Palladium binding site 1 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd201

b:55.0
occ:0.50
 NE2 A:HIS105 2.0 49.0 1.0
O A:HOH311 2.4 39.8 0.5
O A:HOH319 2.7 43.7 0.5
CE1 A:HIS105 2.8 50.0 1.0
CD2 A:HIS105 3.2 52.0 1.0
ND1 A:HIS105 4.0 49.0 1.0
CG A:HIS105 4.2 49.2 1.0
CG2 A:THR78 4.9 38.4 1.0
O A:TYR76 5.0 41.6 1.0

Palladium binding site 2 out of 4 in 6gok

Go back to Palladium Binding Sites List in 6gok
Palladium binding site 2 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd202

b:33.6
occ:0.70
 PD A:F6Q202 0.0 33.6 0.7
NAL A:F6Q202 2.0 36.4 0.7
NAQ A:F6Q202 2.0 38.9 0.7
ND1 A:HIS119 2.1 48.6 1.0
O A:HOH307 2.4 33.0 0.7
CAG A:F6Q202 2.8 38.6 0.7
CAH A:F6Q202 2.8 38.0 0.7
CAI A:F6Q202 3.0 41.4 0.7
CE1 A:HIS119 3.1 56.5 1.0
CAA A:F6Q202 3.2 37.9 0.7
CG A:HIS119 3.2 48.2 1.0
CB A:HIS119 3.5 43.6 1.0
CAF A:F6Q202 3.8 37.5 0.7
CA A:HIS119 3.9 41.0 1.0
NAM A:F6Q202 4.0 40.0 0.7
O A:VAL118 4.1 44.0 1.0
O A:HOH326 4.1 49.5 1.0
CAR A:F6Q202 4.2 38.5 0.7
CAB A:F6Q202 4.2 40.2 0.7
NE2 A:HIS119 4.2 52.6 1.0
CD2 A:HIS119 4.3 50.2 1.0
CAK A:F6Q202 4.3 39.5 0.7
N A:PHE120 4.7 40.4 1.0
CAJ A:F6Q202 4.8 37.9 0.7
C A:HIS119 4.8 42.0 1.0
N A:HIS119 4.9 40.4 1.0
C A:VAL118 4.9 42.7 1.0
O A:HOH321 4.9 24.0 1.0

Palladium binding site 3 out of 4 in 6gok

Go back to Palladium Binding Sites List in 6gok
Palladium binding site 3 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pd201

b:52.5
occ:0.20
 NE2 B:HIS105 2.6 42.2 1.0
CE1 B:HIS105 3.5 43.0 1.0
CD2 B:HIS105 3.6 42.2 1.0
CG2 B:THR78 4.4 40.6 1.0
ND1 B:HIS105 4.7 38.6 1.0
CG B:HIS105 4.7 39.4 1.0

Palladium binding site 4 out of 4 in 6gok

Go back to Palladium Binding Sites List in 6gok
Palladium binding site 4 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 4 of X-Ray Structure of the Adduct Formed Upon Reaction of Bovine Pancreatic Ribonuclease with A Pd(II) Complex Bearing N,N- Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pd202

b:44.0
occ:0.50
 PD B:F6Q202 0.0 44.0 0.5
NAL B:F6Q202 1.8 44.2 0.5
NAQ B:F6Q202 1.9 49.4 0.5
ND1 B:HIS119 2.0 53.2 1.0
CAG B:F6Q202 2.4 47.6 0.5
CAH B:F6Q202 2.5 48.9 0.5
CE1 B:HIS119 2.6 57.1 1.0
CL2 B:F6Q202 2.7 36.9 0.5
CAA B:F6Q202 3.0 46.6 0.5
CAI B:F6Q202 3.0 49.4 0.5
CG B:HIS119 3.2 51.0 1.0
NAM B:F6Q202 3.7 48.0 0.5
CAF B:F6Q202 3.7 45.8 0.5
CB B:HIS119 3.8 45.5 1.0
CAR B:F6Q202 3.9 48.4 0.5
NE2 B:HIS119 3.9 53.7 1.0
CAB B:F6Q202 3.9 47.9 0.5
O B:HOH328 4.0 44.0 1.0
O B:VAL118 4.1 39.9 1.0
CD2 B:HIS119 4.2 55.0 1.0
CA B:HIS119 4.2 42.6 1.0
CAK B:F6Q202 4.2 49.8 0.5
CAJ B:F6Q202 4.5 48.3 0.5
O B:HOH321 4.5 43.3 1.0
CAN B:F6Q202 4.8 49.4 0.5

Reference:

G.Ferraro, A.M.Mansour, A.Merlino. Exploring the Interactions Between Model Proteins and Pd(II) or Pt(II) Compounds Bearing Charged N,N-Pyridylbenzimidazole Bidentate Ligands By X-Ray Crystallography. Dalton Trans V. 47 10130 2018.
ISSN: ESSN 1477-9234
PubMed: 30004541
DOI: 10.1039/C8DT01663A
Page generated: Thu Oct 10 10:22:49 2024

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