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Palladium in PDB 6gob: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 Lysozyme 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 Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain, PDB code: 6gob 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) 56.21 / 1.96
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.487, 79.487, 37.309, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 23.1

Other elements in 6gob:

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

Chlorine (Cl) 8 atoms

Palladium Binding Sites:

The binding sites of Palladium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain (pdb code 6gob). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 7 binding sites of Palladium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain, PDB code: 6gob:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6; 7;

Palladium binding site 1 out of 7 in 6gob

Go back to Palladium Binding Sites List in 6gob
Palladium binding site 1 out of 7 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 Lysozyme 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:29.4
occ:0.50
 CL A:CL212 1.9 30.7 0.5
OD2 A:ASP87 1.9 43.4 1.0
O A:HOH393 2.3 27.9 0.5
CG A:ASP87 2.9 32.8 1.0
OD1 A:ASP87 3.0 30.4 1.0
OG1 A:THR89 3.3 26.6 1.0
CB A:THR89 4.0 25.1 1.0
CB A:ASP87 4.3 29.9 1.0
CG2 A:THR89 4.7 23.9 1.0
O A:HOH439 4.8 41.1 1.0

Palladium binding site 2 out of 7 in 6gob

Go back to Palladium Binding Sites List in 6gob
Palladium binding site 2 out of 7 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 Lysozyme 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:42.8
occ:0.40
 O A:HOH308 2.3 13.4 0.4
OD1 A:ASN77 2.4 58.1 1.0
CL A:CL213 2.6 17.6 0.4
ND2 A:ASN77 2.9 61.7 1.0
CG A:ASN77 3.0 50.9 1.0
O A:HOH365 3.0 38.7 0.3
PD A:F6Q208 3.2 42.9 0.3
NAL A:F6Q208 3.7 36.9 0.3
O A:HOH330 3.9 44.3 0.3
CAA A:F6Q208 4.1 36.3 0.3
CAG A:F6Q208 4.2 36.2 0.3
O A:HOH315 4.3 35.8 1.0
NAQ A:F6Q208 4.4 38.9 0.3
CB A:ASN77 4.4 41.2 1.0
CAH A:F6Q208 4.5 37.6 0.3
CAF A:F6Q208 4.5 37.2 0.3
O A:HOH407 4.6 54.7 1.0
NAM A:F6Q208 4.7 36.9 0.3
CAB A:F6Q208 4.8 36.8 0.3

Palladium binding site 3 out of 7 in 6gob

Go back to Palladium Binding Sites List in 6gob
Palladium binding site 3 out of 7 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 Lysozyme 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:Pd205

b:23.8
occ:0.65
 PD A:F6Q205 0.0 23.8 0.7
NAL A:F6Q205 1.8 22.9 0.7
NAQ A:F6Q205 2.1 25.3 0.7
CL2 A:F6Q205 2.1 28.3 0.7
CAG A:F6Q205 2.8 25.4 0.7
CAA A:F6Q205 2.8 23.2 0.7
CAH A:F6Q205 3.0 23.5 0.7
CAI A:F6Q205 3.1 24.6 0.7
CAF A:F6Q205 3.5 25.1 0.7
O A:HOH395 3.7 36.4 1.0
NAM A:F6Q205 3.9 25.6 0.7
NE A:ARG5 3.9 25.5 1.0
CAB A:F6Q205 3.9 24.7 0.7
O A:HOH414 4.1 55.9 1.0
CD A:ARG5 4.1 26.5 1.0
CAR A:F6Q205 4.3 22.5 0.7
CAK A:F6Q205 4.4 23.4 0.7
O A:HOH375 4.7 53.4 1.0
CAE A:F6Q205 4.9 23.7 0.7
CAJ A:F6Q205 4.9 22.6 0.7
CZ A:ARG5 5.0 25.6 1.0

Palladium binding site 4 out of 7 in 6gob

Go back to Palladium Binding Sites List in 6gob
Palladium binding site 4 out of 7 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 Lysozyme 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:Pd206

b:33.2
occ:0.55
 PD A:F6Q206 0.0 33.2 0.6
NAL A:F6Q206 1.8 26.9 0.6
NAQ A:F6Q206 2.2 25.6 0.6
CL2 A:F6Q206 2.3 37.9 0.6
CAG A:F6Q206 2.6 24.0 0.6
CAH A:F6Q206 2.9 24.6 0.6
CAA A:F6Q206 2.9 24.1 0.6
CAI A:F6Q206 3.3 23.4 0.6
CAF A:F6Q206 3.6 22.5 0.6
NAM A:F6Q206 3.8 25.8 0.6
CAB A:F6Q206 3.9 24.0 0.6
CAR A:F6Q206 4.2 24.5 0.5
CAK A:F6Q206 4.6 23.3 0.5
CAE A:F6Q206 4.9 21.1 0.6
CAJ A:F6Q206 5.0 23.3 0.5

Palladium binding site 5 out of 7 in 6gob

Go back to Palladium Binding Sites List in 6gob
Palladium binding site 5 out of 7 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 5 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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:Pd207

b:26.7
occ:0.60
 PD A:F6Q207 0.0 26.7 0.6
NAL A:F6Q207 1.7 27.9 0.6
CL2 A:F6Q207 1.9 21.2 0.6
OD1 A:ASP101 1.9 27.0 0.5
NAQ A:F6Q207 2.7 22.6 0.6
CAA A:F6Q207 2.7 26.2 0.6
OD1 A:ASP101 2.7 42.1 0.5
CAG A:F6Q207 2.8 25.0 0.6
CG A:ASP101 2.9 28.2 0.5
OD2 A:ASP101 3.1 28.1 0.5
CAF A:F6Q207 3.2 24.8 0.6
CAH A:F6Q207 3.2 24.0 0.6
CG A:ASP101 3.8 43.5 0.5
CAB A:F6Q207 3.8 25.8 0.6
CAI A:F6Q207 3.8 22.9 0.6
NAM A:F6Q207 3.8 30.5 0.6
CB A:ASP101 4.2 29.1 0.5
CB A:ASP101 4.2 38.6 0.5
N A:GLY102 4.4 29.9 1.0
CAE A:F6Q207 4.5 24.1 0.6
CA A:ASP101 4.6 34.1 0.5
CA A:ASP101 4.6 28.9 0.5
CAR A:F6Q207 4.6 22.8 0.6
OD2 A:ASP101 4.8 44.9 0.5
CAC A:F6Q207 5.0 26.0 0.6

Palladium binding site 6 out of 7 in 6gob

Go back to Palladium Binding Sites List in 6gob
Palladium binding site 6 out of 7 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 6 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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:Pd208

b:42.9
occ:0.30
 PD A:F6Q208 0.0 42.9 0.3
NAL A:F6Q208 1.8 36.9 0.3
NAQ A:F6Q208 1.8 38.9 0.3
O A:HOH330 2.1 44.3 0.3
O A:HOH365 2.3 38.7 0.3
CAG A:F6Q208 2.4 36.2 0.3
CAH A:F6Q208 2.4 37.6 0.3
CAI A:F6Q208 3.0 38.5 0.3
CAA A:F6Q208 3.0 36.3 0.3
PD A:PD202 3.2 42.8 0.4
O A:HOH373 3.6 35.2 0.5
NAM A:F6Q208 3.6 36.9 0.3
CAF A:F6Q208 3.7 37.2 0.3
CAR A:F6Q208 3.8 37.1 0.3
O A:HOH315 3.8 35.8 1.0
CAB A:F6Q208 3.9 36.8 0.3
OD1 A:ASN77 4.0 58.1 1.0
CAK A:F6Q208 4.1 38.2 0.3
CG A:ASN77 4.2 50.9 1.0
ND2 A:ASN77 4.3 61.7 1.0
CAJ A:F6Q208 4.4 37.9 0.3
O A:HOH308 4.5 13.4 0.4
CAN A:F6Q208 4.9 37.1 0.3

Palladium binding site 7 out of 7 in 6gob

Go back to Palladium Binding Sites List in 6gob
Palladium binding site 7 out of 7 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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 7 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme 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:Pd209

b:31.7
occ:0.60
 PD A:F6Q209 0.0 31.7 0.6
NAL A:F6Q209 2.0 48.9 0.3
NAL A:F6Q209 2.0 50.1 0.3
NAQ A:F6Q209 2.3 43.2 0.3
ND1 A:HIS15 2.3 40.8 1.0
CL2 A:F6Q209 2.4 32.7 0.6
NAQ A:F6Q209 2.5 44.1 0.3
CAG A:F6Q209 2.7 49.1 0.3
CAG A:F6Q209 2.7 50.5 0.3
CAH A:F6Q209 2.8 47.1 0.3
CAH A:F6Q209 3.0 48.2 0.3
CAA A:F6Q209 3.2 52.3 0.3
CAA A:F6Q209 3.2 53.8 0.3
CG A:HIS15 3.2 37.1 1.0
CE1 A:HIS15 3.3 37.9 1.0
CAI A:F6Q209 3.4 46.8 0.3
CB A:HIS15 3.4 35.4 1.0
CA A:HIS15 3.6 34.5 1.0
CAI A:F6Q209 3.7 48.2 0.3
O A:HIS15 3.8 40.2 1.0
CAF A:F6Q209 3.9 51.8 0.3
CAF A:F6Q209 3.9 53.4 0.3
NAM A:F6Q209 3.9 51.1 0.3
NAM A:F6Q209 4.0 53.0 0.3
CAB A:F6Q209 4.2 52.0 0.3
CAB A:F6Q209 4.2 53.5 0.3
C A:HIS15 4.2 37.2 1.0
CAR A:F6Q209 4.2 48.1 0.3
O A:HOH421 4.3 31.9 1.0
CAR A:F6Q209 4.4 49.1 0.3
CD2 A:HIS15 4.4 37.2 1.0
NE2 A:HIS15 4.4 32.8 1.0
NZ A:LYS96 4.4 27.1 1.0
CG2 A:THR89 4.6 23.9 1.0
CAK A:F6Q209 4.6 48.9 0.3
N A:HIS15 4.9 34.6 1.0
CAK A:F6Q209 4.9 49.9 0.3
CAJ A:F6Q209 5.0 49.3 0.3

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: Mon Jan 25 16:01:23 2021

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