Chlorine in PDB 5mey: Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.

The structure of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site., PDB code: 5mey was solved by Z.Kaczmarska, R.Freier, J.A.Marquez, M.J.Macias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 2.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.170, 79.000, 90.100, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 23.8

The structure of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Calcium	(Ca)	5 atoms

The binding sites of Chlorine atom in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. (pdb code 5mey). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site., PDB code: 5mey:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:36.9 occ:1.00 NH1 A:ARG27 3.2 33.2 1.0 N A:GLY29 3.3 36.0 1.0 O A:HOH307 3.3 34.9 1.0 O A:HOH351 3.5 39.6 1.0 N A:GLU31 3.5 31.5 1.0 N A:GLY30 3.5 33.1 1.0 CA A:GLY29 3.6 34.2 1.0 CB A:ARG27 3.7 32.5 1.0 CD A:ARG27 3.7 34.3 1.0 C A:GLY29 3.8 37.9 1.0 CG A:ARG27 3.8 36.0 1.0 CD1 A:LEU98 3.8 38.8 1.0 O A:GLU31 3.9 30.2 1.0 CB A:ALA36 4.1 30.5 1.0 N A:GLN28 4.2 35.8 1.0 CA A:GLU31 4.2 31.1 1.0 CZ A:ARG27 4.2 45.9 1.0 CB A:GLU31 4.3 32.6 1.0 C A:GLU31 4.3 32.6 1.0 C A:GLN28 4.4 40.2 1.0 CA A:GLY30 4.4 32.8 1.0 NE A:ARG27 4.4 38.8 1.0 C A:GLY30 4.5 36.1 1.0 O A:LEU98 4.5 35.5 1.0 C A:ARG27 4.6 39.3 1.0 CA A:ARG27 4.6 34.6 1.0 CA A:LEU98 4.7 32.4 1.0 O A:GLY29 4.7 38.6 1.0 CA A:GLN28 4.8 35.0 1.0 O A:SER32 4.9 34.4 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:53.1 occ:1.00 N A:GLN75 3.1 33.6 1.0 O A:HOH315 3.5 37.8 1.0 CA A:ILE74 3.6 30.8 1.0 CD A:LYS46 3.8 35.5 1.0 CB A:ILE74 3.8 32.8 1.0 C A:ILE74 3.8 34.8 1.0 CG A:LYS46 3.8 34.9 1.0 CB A:LYS46 3.9 37.8 1.0 CB A:GLN75 4.0 35.3 1.0 CG A:GLN75 4.0 58.2 1.0 CA A:GLN75 4.1 33.6 1.0 CG2 A:ILE74 4.3 33.5 1.0 CE A:LYS46 4.5 32.1 1.0 CA A:LYS46 4.9 38.4 1.0 O A:LYS46 4.9 46.0 1.0 N A:ILE74 4.9 32.7 1.0 O A:HOH362 4.9 66.6 1.0 O A:GLN75 5.0 37.1 1.0 O A:THR73 5.0 37.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:80.2 occ:1.00 N A:ASP120 3.1 43.9 1.0 CE2 A:TYR133 3.4 38.2 1.0 CB A:ASP120 3.4 49.0 1.0 CG A:ASP120 3.4 68.8 1.0 N A:PHE119 3.6 40.8 1.0 OD1 A:ASP120 3.6 70.5 1.0 ND1 A:HIS111 3.7 54.4 1.0 CA A:ASP120 3.8 45.7 1.0 CB A:ALA118 3.9 43.8 1.0 CB A:PHE119 3.9 40.4 1.0 OD2 A:ASP120 4.0 77.2 1.0 CA A:PHE119 4.0 39.7 1.0 C A:PHE119 4.0 43.5 1.0 C A:ALA118 4.1 46.1 1.0 CB A:HIS111 4.2 49.3 1.0 CD2 A:TYR133 4.2 38.3 1.0 OH A:TYR133 4.3 42.4 1.0 CZ A:TYR133 4.3 42.2 1.0 CG A:HIS111 4.4 52.7 1.0 CA A:ALA118 4.5 43.0 1.0 NE2 A:HIS92 4.5 29.4 1.0 CD2 A:HIS92 4.5 29.8 1.0 N A:HIS111 4.7 48.7 1.0 CE1 A:HIS111 4.7 53.9 1.0 O A:ALA118 4.9 44.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:77.6 occ:1.00 N A:SER32 3.0 29.6 1.0 NH2 A:ARG87 3.0 42.8 1.0 OE2 A:GLU31 3.1 62.1 1.0 CB A:SER32 3.5 33.7 1.0 OG A:SER32 3.5 38.8 1.0 NH1 A:ARG87 3.6 47.7 1.0 CZ A:ARG87 3.7 60.1 1.0 CA A:GLU31 3.8 31.1 1.0 C A:GLU31 3.8 32.6 1.0 CA A:SER32 3.8 30.0 1.0 CB A:GLU31 3.9 32.6 1.0 CD A:GLU31 4.1 75.2 1.0 O A:HOH304 4.3 44.0 1.0 CG A:GLU31 4.5 40.6 1.0 CB A:PHE35 4.5 28.6 1.0 O A:GLU31 4.9 30.2 1.0 C A:SER32 5.0 35.3 1.0

P.Martin-Malpartida, M.Batet, Z.Kaczmarska, R.Freier, T.Gomes, E.Aragon, Y.Zou, Q.Wang, Q.Xi, L.Ruiz, A.Vea, J.A.Marquez, J.Massague, M.J.Macias. Structural Basis For Genome Wide Recognition of 5-Bp Gc Motifs By Smad Transcription Factors. Nat Commun V. 8 2070 2017.
ISSN: ESSN 2041-1723
PubMed: 29234012
DOI: 10.1038/S41467-017-02054-6