Chlorine in PDB 5i4z: Structure of Apo Omomyc

The structure of Structure of Apo Omomyc, PDB code: 5i4z was solved by W.Koelmel, L.A.Jung, J.Kuper, M.Eilers, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.35 / 1.95
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	65.700, 65.700, 149.500, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.4

The structure of Structure of Apo Omomyc also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Chlorine atom in the Structure of Apo Omomyc (pdb code 5i4z). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of Apo Omomyc, PDB code: 5i4z:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of Apo Omomyc


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Apo Omomyc within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl103 b:71.5 occ:1.00 H A:LYS45 2.4 49.6 1.0 HG3 A:LYS45 3.0 53.2 1.0 HA A:PRO44 3.2 45.6 1.0 N A:LYS45 3.2 41.3 1.0 HB2 A:LYS45 3.3 50.2 1.0 CL A:CL104 3.4 63.9 1.0 HB3 A:PRO44 3.4 55.6 1.0 HD2 A:LYS45 3.6 83.3 1.0 CG A:LYS45 3.7 44.4 1.0 HE3 A:LYS45 3.7 0.1 1.0 CB A:LYS45 3.8 41.8 1.0 CA A:PRO44 3.9 38.0 1.0 CD A:LYS45 4.0 69.4 1.0 C A:PRO44 4.0 31.7 1.0 CB A:PRO44 4.1 46.3 1.0 O2 A:GOL101 4.1 62.6 1.0 CA A:LYS45 4.1 41.7 1.0 CE A:LYS45 4.3 85.9 1.0 HG2 A:LYS45 4.5 53.2 1.0 H A:VAL46 4.5 36.0 1.0 HB2 A:PRO44 4.6 55.6 1.0 HO2 A:GOL101 4.7 75.1 1.0 HB3 A:LYS45 4.7 50.2 1.0 HA A:LYS45 4.7 50.0 1.0 H2 A:GOL101 4.9 95.3 1.0 HE2 A:LYS45 4.9 0.1 1.0 HD3 A:LYS45 4.9 83.3 1.0

Chlorine binding site 2 out of 3 in the Structure of Apo Omomyc


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Apo Omomyc within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl104 b:63.9 occ:1.00 H A:VAL46 2.2 36.0 1.0 HG23 A:VAL46 2.6 61.3 1.0 HB2 A:LYS45 3.0 50.2 1.0 HB A:VAL46 3.0 47.3 1.0 N A:VAL46 3.0 30.0 1.0 H A:LYS45 3.1 49.6 1.0 HB3 A:PRO44 3.2 55.6 1.0 CG2 A:VAL46 3.4 51.1 1.0 CL A:CL103 3.4 71.5 1.0 N A:LYS45 3.4 41.3 1.0 CB A:VAL46 3.5 39.4 1.0 HB2 A:PRO44 3.5 55.6 1.0 HG21 A:VAL46 3.6 61.3 1.0 CB A:PRO44 3.8 46.3 1.0 CB A:LYS45 3.8 41.8 1.0 CA A:VAL46 3.8 36.1 1.0 CA A:LYS45 3.9 41.7 1.0 C A:LYS45 3.9 35.9 1.0 C A:PRO44 4.0 31.7 1.0 HD13 B:LEU23 4.1 65.3 1.0 HG22 A:VAL46 4.2 61.3 1.0 H A:VAL47 4.2 40.2 1.0 CA A:PRO44 4.3 38.0 1.0 HB3 A:LYS45 4.3 50.2 1.0 HA A:PRO44 4.4 45.6 1.0 HA A:VAL46 4.5 43.3 1.0 HD2 A:LYS45 4.6 83.3 1.0 HG3 A:LYS45 4.7 53.2 1.0 O A:PRO44 4.8 34.9 1.0 N A:VAL47 4.8 33.5 1.0 CG A:LYS45 4.8 44.4 1.0 HA A:LYS45 4.8 50.0 1.0 C A:VAL46 4.9 40.2 1.0 CG1 A:VAL46 4.9 37.7 1.0 CD1 B:LEU23 5.0 54.4 1.0 HD12 B:LEU23 5.0 65.3 1.0

Chlorine binding site 3 out of 3 in the Structure of Apo Omomyc


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Apo Omomyc within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl102 b:66.4 occ:1.00 H B:LYS45 2.2 36.8 1.0 HG3 B:LYS45 2.7 35.0 1.0 N B:LYS45 3.1 30.7 1.0 HA B:PRO44 3.2 43.7 1.0 HB2 B:LYS45 3.3 34.6 1.0 HB2 B:PRO44 3.3 45.0 1.0 O B:HOH228 3.4 29.1 1.0 CG B:LYS45 3.5 29.1 1.0 HB3 B:PRO44 3.5 45.0 1.0 HD2 B:LYS45 3.7 51.8 1.0 CB B:PRO44 3.7 37.5 1.0 CA B:PRO44 3.7 36.4 1.0 CB B:LYS45 3.7 28.8 1.0 C B:PRO44 3.9 31.3 1.0 HE3 B:LYS45 4.0 92.4 1.0 CA B:LYS45 4.0 29.9 1.0 CD B:LYS45 4.1 43.2 1.0 O B:HOH235 4.1 52.4 1.0 HG2 B:LYS45 4.3 35.0 1.0 H B:VAL46 4.5 29.8 1.0 CE B:LYS45 4.6 77.0 1.0 HA B:LYS45 4.6 35.8 1.0 HB3 B:LYS45 4.7 34.6 1.0 HH11 A:ARG20 4.7 88.8 1.0 HD3 B:LYS45 4.9 51.8 1.0

L.A.Jung, A.Gebhardt, W.Koelmel, C.P.Ade, S.Walz, J.Kuper, B.Von Eyss, S.Letschert, C.Redel, L.D'artista, A.Biankin, L.Zender, M.Sauer, E.Wolf, G.Evan, C.Kisker, M.Eilers. Omomyc Blunts Promoter Invasion By Oncogenic Myc to Inhibit Gene Expression Characteristic of Myc-Dependent Tumors. Oncogene V. 36 1911 2017.
ISSN: ESSN 1476-5594
PubMed: 27748763
DOI: 10.1038/ONC.2016.354