Chlorine in PDB 5j5y: Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog

The structure of Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog, PDB code: 5j5y was solved by M.Warminski, E.Nowak, A.M.Rydzik, J.Kowalska, J.Jemielity, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.00 / 1.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.040, 38.060, 146.740, 88.36, 95.63, 103.54
R / Rfree (%)	23.7 / 28.6

The binding sites of Chlorine atom in the Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog (pdb code 5j5y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog, PDB code: 5j5y:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl300 b:55.0 occ:1.00 CL1 A:6G6300 0.0 55.0 1.0 C1 A:6G6300 1.8 47.1 1.0 P2 A:6G6300 2.9 44.7 0.8 P3 A:6G6300 3.0 39.4 1.0 CL2 A:6G6300 3.0 54.6 1.0 O4 A:6G6300 3.0 44.0 1.0 O11 A:6G6300 3.0 24.8 1.0 O8 A:6G6300 3.2 46.2 1.0 NE A:ARG157 3.4 22.1 1.0 O6 A:6G6300 3.5 46.5 0.7 O A:HOH461 3.5 34.7 1.0 O9 A:6G6300 3.6 36.6 1.0 P4 A:6G6300 3.8 29.6 1.0 C2 A:6G6300 3.9 30.1 1.0 CZ A:ARG157 4.1 19.7 1.0 NH2 A:ARG157 4.1 17.2 1.0 O5 A:6G6300 4.2 41.8 1.0 CD A:ARG157 4.2 19.6 1.0 O7 A:6G6300 4.3 39.4 1.0 O12 A:6G6300 4.4 27.4 1.0 O A:HOH498 4.7 40.4 1.0 ND2 A:ASN50 4.8 54.6 1.0

Chlorine binding site 2 out of 4 in the Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl300 b:54.6 occ:1.00 CL2 A:6G6300 0.0 54.6 1.0 C1 A:6G6300 1.8 47.1 1.0 O A:HOH478 2.9 39.0 1.0 P2 A:6G6300 2.9 44.7 0.8 P3 A:6G6300 2.9 39.4 1.0 CL1 A:6G6300 3.0 55.0 1.0 O5 A:6G6300 3.0 41.8 1.0 O7 A:6G6300 3.3 39.4 1.0 O9 A:6G6300 3.4 36.6 1.0 O4 A:6G6300 3.6 44.0 1.0 C2 A:6G6300 3.8 30.1 1.0 O6 A:6G6300 4.2 46.5 0.7 O8 A:6G6300 4.3 46.2 1.0 P4 A:6G6300 4.4 29.6 1.0 O A:HOH493 4.4 40.5 1.0 O12 A:6G6300 4.5 27.4 1.0 O11 A:6G6300 4.7 24.8 1.0 C3 A:6G6300 4.9 31.8 1.0

Chlorine binding site 3 out of 4 in the Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:58.7 occ:1.00 CL1 B:6G6301 0.0 58.7 1.0 C1 B:6G6301 1.8 52.0 1.0 CL2 B:6G6301 2.9 55.7 1.0 O2 B:6G6301 2.9 60.4 1.0 P3 B:6G6301 2.9 55.1 1.0 P2 B:6G6301 3.0 47.6 1.0 O8 B:6G6301 3.2 61.4 1.0 O4 B:6G6301 3.3 55.4 1.0 O6 B:6G6301 3.5 41.9 1.0 O9 B:6G6301 3.5 39.7 1.0 NE B:ARG157 3.5 19.9 1.0 P1 B:6G6301 3.5 60.5 0.5 O11 B:6G6301 3.6 23.1 1.0 O B:HOH471 3.7 22.5 1.0 C2 B:6G6301 4.0 20.6 1.0 O B:HOH453 4.0 34.3 1.0 O1 B:6G6301 4.0 61.2 0.6 P4 B:6G6301 4.0 31.0 1.0 CD B:ARG157 4.2 27.5 1.0 O7 B:6G6301 4.2 63.3 1.0 O5 B:6G6301 4.3 46.8 1.0 CZ B:ARG157 4.4 18.4 1.0 NH2 B:ARG157 4.5 18.3 1.0 O12 B:6G6301 4.6 28.8 1.0 O3 B:6G6301 5.0 65.6 1.0

Chlorine binding site 4 out of 4 in the Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Translation Initiation Factor 4E in Complex with M2(7,2'O)GPPCCL2PPG Mrna 5' Cap Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:55.7 occ:1.00 CL2 B:6G6301 0.0 55.7 1.0 C1 B:6G6301 1.8 52.0 1.0 P2 B:6G6301 2.9 47.6 1.0 P3 B:6G6301 2.9 55.1 1.0 CL1 B:6G6301 2.9 58.7 1.0 O9 B:6G6301 3.1 39.7 1.0 O5 B:6G6301 3.2 46.8 1.0 O4 B:6G6301 3.3 55.4 1.0 O7 B:6G6301 3.4 63.3 1.0 C2 B:6G6301 3.5 20.6 1.0 O8 B:6G6301 4.2 61.4 1.0 O6 B:6G6301 4.3 41.9 1.0 P4 B:6G6301 4.3 31.0 1.0 O12 B:6G6301 4.4 28.8 1.0 P1 B:6G6301 4.6 60.5 0.5 C3 B:6G6301 4.6 24.7 1.0 O2 B:6G6301 4.8 60.4 1.0 O11 B:6G6301 4.8 23.1 1.0 O14 B:6G6301 4.9 34.6 1.0 O1 B:6G6301 4.9 61.2 0.6

A.M.Rydzik, M.Warminski, P.J.Sikorski, M.R.Baranowski, S.Walczak, J.Kowalska, J.Zuberek, M.Lukaszewicz, E.Nowak, T.D.W Claridge, E.Darzynkiewicz, M.Nowotny, J.Jemielity. Mrna Cap Analogues Substituted in the Tetraphosphate Chain with CX2: Identification of O-to-CCL2 As the First Bridging Modification That Confers Resistance to Decapping Without Impairing Translation. Nucleic Acids Res. V. 45 8661 2017.
ISSN: ESSN 1362-4962
PubMed: 28666355
DOI: 10.1093/NAR/GKX569