Zinc in PDB 5od6: Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site.

The structure of Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site., PDB code: 5od6 was solved by Z.Kaczmarska, 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)	27.11 / 2.00
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	105.200, 105.200, 73.240, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.5

The binding sites of Zinc atom in the Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site. (pdb code 5od6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site., PDB code: 5od6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:42.0 occ:1.00 ND1 A:HIS126 2.0 43.0 1.0 SG A:CYS109 2.3 45.5 1.0 SG A:CYS121 2.4 41.1 1.0 SG A:CYS64 2.5 46.1 1.0 CE1 A:HIS126 3.0 43.6 1.0 CG A:HIS126 3.1 41.3 1.0 CB A:CYS121 3.1 38.5 1.0 CB A:CYS64 3.3 42.4 1.0 CB A:CYS109 3.4 43.5 1.0 CB A:HIS126 3.4 37.7 1.0 CA A:CYS64 3.5 41.4 1.0 CA A:CYS109 3.7 46.1 1.0 NE2 A:HIS126 4.2 43.4 1.0 CD2 A:HIS126 4.2 41.9 1.0 N A:GLU110 4.3 49.4 1.0 C A:CYS109 4.4 53.3 1.0 N A:CYS64 4.4 42.8 1.0 N A:PHE111 4.5 47.7 1.0 CA A:CYS121 4.6 37.9 1.0 C A:CYS64 4.7 46.3 1.0 CB A:ASN123 4.7 36.0 1.0 N A:ILE65 4.7 42.8 1.0 O A:HOH328 4.8 56.5 1.0 N A:CYS109 4.9 47.3 1.0 CA A:HIS126 4.9 36.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SMAD3-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:54.3 occ:1.00 ND1 B:HIS126 2.0 50.8 1.0 SG B:CYS109 2.3 57.7 1.0 SG B:CYS121 2.3 48.5 1.0 SG B:CYS64 2.5 58.9 1.0 CE1 B:HIS126 3.0 53.0 1.0 CG B:HIS126 3.0 48.4 1.0 CB B:CYS121 3.1 45.9 1.0 CB B:CYS64 3.3 54.9 1.0 CB B:CYS109 3.3 56.6 1.0 CB B:HIS126 3.4 44.0 1.0 CA B:CYS64 3.5 53.4 1.0 CA B:CYS109 3.7 61.1 1.0 NE2 B:HIS126 4.1 53.6 1.0 CD2 B:HIS126 4.2 51.1 1.0 N B:GLU110 4.3 65.9 1.0 C B:CYS109 4.4 69.0 1.0 N B:CYS64 4.4 56.3 1.0 N B:PHE111 4.5 62.0 1.0 CA B:CYS121 4.6 44.6 1.0 C B:CYS64 4.7 56.3 1.0 N B:ILE65 4.7 51.9 1.0 CB B:ASN123 4.8 41.5 1.0 N B:CYS109 4.9 64.3 1.0 CA B:HIS126 4.9 44.4 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