Chlorine in PDB 5l4r: X-Ray Structure of the Adduct Between Thaumatin and Cisplatin

The structure of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin, PDB code: 5l4r was solved by I.Russo Krauss, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.97 / 1.45
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.837, 57.837, 150.159, 90.00, 90.00, 90.00
R / Rfree (%)	11.2 / 15.4

The structure of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin also contains other interesting chemical elements:

Platinum

(Pt)

15 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin (pdb code 5l4r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin, PDB code: 5l4r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:21.4 occ:0.88 CL1 A:73M503 0.0 21.4 0.9 PT1 A:73M503 2.3 15.2 0.9 N1 A:73M503 2.9 19.5 0.9 O2 A:73M503 3.1 19.2 0.9 O A:HOH924 3.4 59.6 1.0 O A:HOH861 3.6 46.3 1.0 CG A:PRO43 4.1 17.4 1.0 O A:HOH685 4.2 22.6 1.0 CL1 A:CPT510 4.3 21.6 0.2 N A:ALA1 4.4 15.0 1.0 CD A:PRO43 4.5 15.7 1.0 O A:HOH614 4.6 31.0 1.0 O A:HOH654 4.7 29.8 0.8 O A:HOH700 4.7 19.2 1.0

Chlorine binding site 2 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:20.0 occ:0.25 CL1 A:CPT504 0.0 20.0 0.2 CL1 A:CPT504 0.9 39.0 0.2 PT1 A:CPT504 1.5 49.2 0.2 PT1 A:CPT504 2.2 16.5 0.2 N1 A:CPT504 2.3 41.8 0.2 O A:HOH603 2.9 36.2 0.8 NZ A:LYS106 3.0 25.5 1.0 N1 A:CPT504 3.1 6.9 0.2 O A:HOH601 3.3 76.5 0.8 N2 A:CPT504 3.5 33.1 0.2 O A:HOH907 3.9 55.2 1.0 CD A:PRO83 4.0 15.2 1.0 O A:HOH867 4.0 46.9 0.6 CE A:LYS106 4.0 27.9 1.0 CG A:PRO83 4.0 17.9 1.0 O A:HOH688 4.1 33.3 0.8 CD A:LYS106 4.2 22.7 1.0 N2 A:CPT504 4.3 14.8 0.2 O A:HOH704 4.6 8.8 0.3 O A:HOH836 4.8 17.8 0.3 PT1 A:CPT504 4.9 71.8 0.2 O A:HOH1004 4.9 21.4 0.2

Chlorine binding site 3 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:39.0 occ:0.20 CL1 A:CPT504 0.0 39.0 0.2 CL1 A:CPT504 0.9 20.0 0.2 PT1 A:CPT504 1.8 16.5 0.2 N1 A:CPT504 2.3 6.9 0.2 PT1 A:CPT504 2.3 49.2 0.2 NZ A:LYS106 3.1 25.5 1.0 O A:HOH688 3.2 33.3 0.8 N1 A:CPT504 3.2 41.8 0.2 CD A:PRO83 3.6 15.2 1.0 CG A:PRO83 3.6 17.9 1.0 O A:HOH603 3.6 36.2 0.8 N2 A:CPT504 3.7 14.8 0.2 O A:HOH907 3.9 55.2 1.0 O A:HOH704 4.1 8.8 0.3 O A:HOH1004 4.1 21.4 0.2 O A:HOH601 4.2 76.5 0.8 CD A:LYS106 4.2 22.7 1.0 CE A:LYS106 4.3 27.9 1.0 O A:HOH836 4.3 17.8 0.3 N2 A:CPT504 4.4 33.1 0.2 O A:HOH867 4.7 46.9 0.6 OG1 A:THR150 4.9 14.2 1.0 CB A:PRO83 5.0 14.9 1.0

Chlorine binding site 4 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:38.2 occ:0.20 CL2 A:CPT506 0.0 38.2 0.2 PT1 A:CPT506 1.9 44.4 0.2 PT1 A:CPT506 2.3 29.3 0.2 CL1 A:CPT506 2.5 41.8 0.2 N1 A:CPT506 2.9 21.2 0.2 CL2 A:CPT506 3.0 12.5 0.2 O1 A:GOL514 3.1 31.0 0.6 NZ A:LYS49 3.2 18.4 1.0 CL1 A:CPT506 3.3 54.6 0.2 O A:HOH963 3.3 31.5 0.4 OE2 A:GLU89 3.5 14.4 1.0 O A:HOH677 3.8 10.2 0.5 CD A:GLU89 4.1 12.3 1.0 C1 A:GOL514 4.1 27.2 0.6 O A:HOH634 4.2 13.9 0.5 OE1 A:GLU89 4.2 13.3 1.0 O A:HOH900 4.2 34.1 1.0 O2 A:GOL514 4.3 43.7 0.6 N1 A:CPT506 4.4 26.1 0.2 CE A:LYS49 4.4 18.4 1.0 O A:HOH707 4.5 20.1 1.0 O A:HOH904 4.5 58.3 1.0 C2 A:GOL514 4.6 30.1 0.6 C3 A:GOL514 4.6 40.4 0.6 O A:HOH604 4.7 71.4 0.4 O A:HOH720 4.8 32.2 1.0 O A:HOH946 5.0 27.1 0.5

Chlorine binding site 5 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:12.5 occ:0.20 CL2 A:CPT506 0.0 12.5 0.2 PT1 A:CPT506 0.7 29.3 0.2 N1 A:CPT506 1.4 26.1 0.2 O A:HOH946 2.2 27.1 0.5 O A:HOH850 2.3 30.0 0.5 PT1 A:CPT506 2.3 44.4 0.2 CL1 A:CPT506 2.3 54.6 0.2 O A:HOH900 2.8 34.1 1.0 NZ A:LYS49 2.8 18.4 1.0 CE A:LYS49 2.9 18.4 1.0 CL2 A:CPT506 3.0 38.2 0.2 CL1 A:CPT506 3.1 41.8 0.2 N1 A:CPT504 4.1 57.2 0.2 O A:HOH634 4.1 13.9 0.5 OE2 A:GLU89 4.2 14.4 1.0 N1 A:CPT506 4.4 21.2 0.2 CD A:LYS49 4.4 16.8 1.0 O A:HOH677 4.4 10.2 0.5 O A:HOH720 4.5 32.2 1.0 O A:HOH851 4.5 36.9 1.0 O A:HOH876 4.7 34.4 1.0 N2 A:CPT504 4.8 33.1 0.2 CE2 A:PHE80 4.8 19.4 1.0 O A:HOH867 4.8 46.9 0.6 O A:HOH904 5.0 58.3 1.0

Chlorine binding site 6 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:54.6 occ:0.20 CL1 A:CPT506 0.0 54.6 0.2 CL1 A:CPT506 2.0 41.8 0.2 PT1 A:CPT506 2.3 29.3 0.2 CL2 A:CPT506 2.3 12.5 0.2 N1 A:CPT504 2.8 57.2 0.2 N1 A:CPT506 3.0 26.1 0.2 O A:HOH850 3.1 30.0 0.5 PT1 A:CPT506 3.2 44.4 0.2 O A:HOH900 3.3 34.1 1.0 CL2 A:CPT506 3.3 38.2 0.2 O A:HOH904 3.3 58.3 1.0 O A:HOH876 3.5 34.4 1.0 O A:HOH946 3.7 27.1 0.5 O A:HOH978 4.3 55.5 1.0 O A:HOH963 4.6 31.5 0.4 NZ A:LYS49 4.8 18.4 1.0 O A:HOH867 4.8 46.9 0.6 N1 A:CPT506 4.9 21.2 0.2 O A:HOH677 5.0 10.2 0.5

Chlorine binding site 7 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:41.8 occ:0.20 CL1 A:CPT506 0.0 41.8 0.2 CL1 A:CPT506 2.0 54.6 0.2 PT1 A:CPT506 2.3 44.4 0.2 CL2 A:CPT506 2.5 38.2 0.2 PT1 A:CPT506 2.6 29.3 0.2 CL2 A:CPT506 3.1 12.5 0.2 N1 A:CPT506 3.3 21.2 0.2 N1 A:CPT506 4.0 26.1 0.2 O A:HOH904 4.1 58.3 1.0 O A:HOH850 4.3 30.0 0.5 NZ A:LYS49 4.6 18.4 1.0 O A:HOH720 4.6 32.2 1.0 O A:HOH963 4.6 31.5 0.4 N1 A:CPT504 4.6 57.2 0.2 O A:HOH900 4.7 34.1 1.0

Chlorine binding site 8 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


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 Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:39.5 occ:0.30 CL1 A:CPT507 0.0 39.5 0.3 O A:HOH874 1.0 38.7 0.7 PT1 A:CPT507 2.3 39.6 0.3 NZ A:LYS97 2.8 44.0 1.0 O A:HOH972 3.0 43.9 0.7 N1 A:CPT507 3.1 32.5 0.3 N A:PRO194 3.3 15.6 1.0 O A:HOH694 3.3 46.6 1.0 C A:CYS193 3.3 15.5 1.0 CD A:LYS97 3.4 30.6 1.0 CE A:LYS97 3.5 42.2 1.0 CA A:PRO194 3.6 17.3 1.0 O A:CYS193 3.6 16.4 1.0 CD A:PRO194 3.7 18.1 1.0 CG A:PRO194 3.9 19.7 1.0 CA A:CYS193 4.0 15.7 1.0 O A:HOH669 4.0 53.9 1.0 O A:THR192 4.1 16.0 1.0 CG2 A:THR192 4.1 20.2 1.0 C A:THR192 4.3 16.0 1.0 N A:CYS193 4.3 14.1 1.0 N2 A:CPT507 4.3 29.6 0.3 CB A:PRO194 4.4 20.0 1.0 O41 A:TLA501 4.6 17.7 0.5 O A:GLY120 4.6 20.9 1.0 CG A:LYS97 4.8 25.8 1.0 O A:HOH984 4.8 47.4 0.7 PT1 A:CPT507 4.9 83.6 0.1 C A:PRO194 4.9 16.3 1.0 CB A:THR192 4.9 16.4 1.0

Chlorine binding site 9 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl508 b:60.0 occ:0.22 CL1 A:CPT508 0.0 60.0 0.2 PT1 A:CPT508 2.4 50.3 0.2 N1 A:CPT508 3.2 27.2 0.2 NZ A:LYS137 3.3 45.7 1.0 CE A:LYS137 3.7 39.0 1.0 O A:HOH886 4.1 44.9 1.0 N2 A:CPT508 4.5 45.1 0.2 CD A:LYS137 4.9 23.7 1.0

Chlorine binding site 10 out of 11 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl509 b:23.2 occ:0.18 CL1 A:73M509 0.0 23.2 0.2 O A:HOH973 1.9 38.0 0.8 PT1 A:73M509 2.1 33.2 0.2 O A:HOH821 2.8 33.4 1.0 O A:HOH703 2.9 22.8 0.8 O2 A:73M509 3.0 39.1 0.2 N1 A:73M509 3.1 32.4 0.2 N2 A:73M509 4.1 25.9 0.2 O A:HOH814 4.2 17.6 0.5 ND2 A:ASN146 4.3 18.9 1.0 O A:HOH1016 4.4 50.9 1.0 CG2 A:THR150 4.4 17.6 1.0 O A:HOH605 4.4 41.3 1.0 NH2 A:ARG82 4.6 25.9 1.0 OD1 A:ASN146 4.7 19.2 1.0 O A:HOH845 4.8 36.5 1.0 CG A:ASN146 4.8 16.6 1.0

I.Russo Krauss, G.Ferraro, A.Merlino. Cisplatin-Protein Interactions: Unexpected Drug Binding to N-Terminal Amine and Lysine Side Chains. Inorg.Chem. V. 55 7814 2016.
ISSN: ISSN 0020-1669
PubMed: 27482735
DOI: 10.1021/ACS.INORGCHEM.6B01234