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Chlorine 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:

Palladium (Pd) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 1 out of 8 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 Chlorine with other atoms in the Cl 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:Cl205

b:35.4
occ:0.65
 PD A:F6Q205 2.1 23.8 0.7
CL2 A:F6Q205 2.9 28.3 0.7
CAF A:F6Q205 3.2 25.1 0.7
NAL A:F6Q205 3.2 22.9 0.7
O A:HOH414 3.2 55.9 1.0
CAA A:F6Q205 3.5 23.2 0.7
O A:HOH395 4.1 36.4 1.0
O A:HOH375 4.1 53.4 1.0
NAQ A:F6Q205 4.2 25.3 0.7
CAE A:F6Q205 4.4 23.7 0.7
CAG A:F6Q205 4.5 25.4 0.7
CAB A:F6Q205 4.8 24.7 0.7

Chlorine binding site 2 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 2 out of 8 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 Chlorine with other atoms in the Cl 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:Cl205

b:28.3
occ:0.65
 CL2 A:F6Q205 0.0 28.3 0.7
PD A:F6Q205 2.1 23.8 0.7
O A:HOH375 3.0 53.4 1.0
NAQ A:F6Q205 3.2 25.3 0.7
CAI A:F6Q205 3.2 24.6 0.7
O A:HOH414 3.6 55.9 1.0
CD A:ARG5 3.7 26.5 1.0
NAL A:F6Q205 3.9 22.9 0.7
CZ3 A:TRP123 4.1 27.8 1.0
NE A:ARG5 4.3 25.5 1.0
CAH A:F6Q205 4.4 23.5 0.7
CE2 A:PHE38 4.4 22.7 1.0
CB A:ARG5 4.4 26.0 1.0
CAK A:F6Q205 4.5 23.4 0.7
CG A:ARG5 4.6 26.2 1.0
CAG A:F6Q205 4.7 25.4 0.7
O A:HOH395 4.8 36.4 1.0
CE3 A:TRP123 4.8 25.8 1.0
CE A:LYS33 4.9 30.7 0.5
CAA A:F6Q205 4.9 23.2 0.7

Chlorine binding site 3 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 3 out of 8 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 Chlorine with other atoms in the Cl 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:Cl206

b:29.9
occ:0.55
 PD A:F6Q206 1.9 33.2 0.6
NAL A:F6Q206 2.8 26.9 0.6
CL2 A:F6Q206 2.9 37.9 0.6
CAF A:F6Q206 3.1 22.5 0.6
CAA A:F6Q206 3.3 24.1 0.6
O A:HOH344 3.8 38.4 1.0
CAG A:F6Q206 4.1 24.0 0.6
NAQ A:F6Q206 4.1 25.6 0.6
CAE A:F6Q206 4.4 21.1 0.6
CAB A:F6Q206 4.6 24.0 0.6
CAH A:F6Q206 4.7 24.6 0.6
NAM A:F6Q206 5.0 25.8 0.6

Chlorine binding site 4 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 4 out of 8 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 Chlorine with other atoms in the Cl 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:Cl206

b:37.9
occ:0.55
 CL2 A:F6Q206 0.0 37.9 0.6
PD A:F6Q206 2.3 33.2 0.6
NAQ A:F6Q206 3.2 25.6 0.6
CAI A:F6Q206 3.4 23.4 0.6
NAL A:F6Q206 4.1 26.9 0.6
CAH A:F6Q206 4.4 24.6 0.6
CAG A:F6Q206 4.7 24.0 0.6
CAK A:F6Q206 4.8 23.3 0.5

Chlorine binding site 5 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 5 out of 8 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 Chlorine with other atoms in the Cl 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:Cl207

b:21.2
occ:0.60
 CL2 A:F6Q207 0.0 21.2 0.6
PD A:F6Q207 1.9 26.7 0.6
OD1 A:ASP101 2.7 27.0 0.5
OD1 A:ASP101 3.0 42.1 0.5
NAQ A:F6Q207 3.0 22.6 0.6
N A:GLY102 3.3 29.9 1.0
CG A:ASP101 3.4 28.2 0.5
CAI A:F6Q207 3.5 22.9 0.6
NAL A:F6Q207 3.5 27.9 0.6
OD2 A:ASP101 3.8 28.1 0.5
CG A:ASP101 4.0 43.5 0.5
CA A:GLY102 4.0 31.6 1.0
CAH A:F6Q207 4.1 24.0 0.6
CA A:ASP101 4.2 34.1 0.5
CA A:ASP101 4.2 28.9 0.5
C A:ASP101 4.2 30.2 0.5
C A:ASP101 4.2 33.2 0.5
CAG A:F6Q207 4.3 25.0 0.6
CB A:ASP101 4.4 29.1 0.5
CB A:ASP101 4.4 38.6 0.5
CAA A:F6Q207 4.6 26.2 0.6
CAK A:F6Q207 4.9 22.4 0.6
CAF A:F6Q207 5.0 24.8 0.6

Chlorine binding site 6 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 6 out of 8 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 Chlorine with other atoms in the Cl 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:Cl209

b:32.7
occ:0.60
 CL2 A:F6Q209 0.0 32.7 0.6
PD A:F6Q209 2.4 31.7 0.6
ND1 A:HIS15 3.2 40.8 1.0
NAL A:F6Q209 3.3 48.9 0.3
NAL A:F6Q209 3.4 50.1 0.3
CG1 A:VAL92 3.6 21.7 1.0
N A:ASN93 3.6 20.6 1.0
CAF A:F6Q209 3.7 51.8 0.3
CAF A:F6Q209 3.7 53.4 0.3
CB A:ASN93 3.7 26.9 1.0
O A:THR89 3.8 24.2 1.0
CA A:ASN93 3.9 23.4 1.0
NZ A:LYS96 3.9 27.1 1.0
CAA A:F6Q209 3.9 52.3 0.3
CG A:HIS15 3.9 37.1 1.0
CAA A:F6Q209 3.9 53.8 0.3
CB A:HIS15 3.9 35.4 1.0
CB A:VAL92 3.9 21.3 1.0
OD1 A:ASN93 4.0 39.7 1.0
CG2 A:THR89 4.0 23.9 1.0
CE1 A:HIS15 4.1 37.9 1.0
C A:VAL92 4.2 20.5 1.0
O A:HIS15 4.2 40.2 1.0
CG A:ASN93 4.3 32.9 1.0
CA A:THR89 4.5 22.7 1.0
CAG A:F6Q209 4.6 49.1 0.3
C A:THR89 4.6 22.3 1.0
CE A:LYS96 4.6 26.3 1.0
CAG A:F6Q209 4.6 50.5 0.3
NAQ A:F6Q209 4.6 43.2 0.3
CA A:VAL92 4.7 20.1 1.0
CA A:HIS15 4.7 34.5 1.0
CB A:THR89 4.8 25.1 1.0
NAQ A:F6Q209 4.9 44.1 0.3
O A:VAL92 4.9 21.1 1.0
CD A:LYS96 4.9 25.5 1.0
C A:HIS15 5.0 37.2 1.0

Chlorine binding site 7 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 7 out of 8 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 Chlorine with other atoms in the Cl 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:Cl212

b:30.7
occ:0.50
 PD A:PD201 1.9 29.4 0.5
OD2 A:ASP87 2.7 43.4 1.0
CG A:ASP87 3.2 32.8 1.0
OD1 A:ASP87 3.3 30.4 1.0
OG1 A:THR89 3.8 26.6 1.0
O A:HOH323 4.0 33.7 1.0
O A:HOH439 4.2 41.1 1.0
O A:HOH393 4.2 27.9 0.5
CB A:ASP87 4.5 29.9 1.0
O A:HOH447 4.6 56.2 1.0

Chlorine binding site 8 out of 8 in 6gob

Go back to Chlorine Binding Sites List in 6gob
Chlorine binding site 8 out of 8 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl213

b:17.6
occ:0.40
 PD A:PD202 2.6 42.8 0.4
OD1 A:ASN77 2.9 58.1 1.0
O A:HOH441 3.0 66.0 1.0
O A:HOH308 3.0 13.4 0.4
ND2 A:ASN77 3.3 61.7 1.0
CG A:ASN77 3.4 50.9 1.0
O A:HOH407 3.4 54.7 1.0
O A:HOH396 3.8 31.8 1.0
O A:HOH368 4.1 41.7 1.0
ND2 A:ASN74 4.3 24.2 1.0
CB A:ASN77 4.7 41.2 1.0
CA A:ASN77 4.8 30.6 1.0

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: Sun Jul 28 00:03:54 2024

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