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

The structure of Crystal Structure of SMAD3-MH1 Bound to the Ggct Site., PDB code: 5odg 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)	29.83 / 2.12
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	104.990, 104.990, 72.490, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.2

The structure of Crystal Structure of SMAD3-MH1 Bound to the Ggct Site. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of SMAD3-MH1 Bound to the Ggct Site. (pdb code 5odg). 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 Ggct Site., PDB code: 5odg:
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 Ggct 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 Ggct Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:47.6 occ:1.00 ND1 A:HIS126 2.1 50.5 1.0 SG A:CYS109 2.2 48.5 1.0 SG A:CYS121 2.4 49.3 1.0 SG A:CYS64 2.4 55.7 1.0 CE1 A:HIS126 3.0 49.0 1.0 CG A:HIS126 3.1 48.2 1.0 CB A:CYS121 3.1 45.2 1.0 CB A:CYS109 3.3 46.6 1.0 CB A:HIS126 3.4 45.3 1.0 CB A:CYS64 3.4 51.9 1.0 CA A:CYS64 3.6 50.2 1.0 CA A:CYS109 3.7 50.0 1.0 NE2 A:HIS126 4.2 48.5 1.0 CD2 A:HIS126 4.2 47.5 1.0 C A:CYS109 4.4 58.2 1.0 N A:GLU110 4.4 53.4 1.0 N A:PHE111 4.5 51.6 1.0 N A:CYS64 4.5 51.0 1.0 CA A:CYS121 4.6 43.9 1.0 C A:CYS64 4.8 53.3 1.0 N A:ILE65 4.8 49.8 1.0 CB A:ASN123 4.8 42.9 1.0 CA A:HIS126 4.9 44.3 1.0 N A:ALA112 4.9 46.1 1.0 N A:CYS109 5.0 52.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SMAD3-MH1 Bound to the Ggct 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 Ggct Site. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:58.8 occ:1.00 ND1 B:HIS126 2.0 55.8 1.0 SG B:CYS109 2.3 65.9 1.0 SG B:CYS121 2.3 52.9 1.0 SG B:CYS64 2.4 68.5 1.0 CE1 B:HIS126 3.0 57.3 1.0 CG B:HIS126 3.0 53.0 1.0 CB B:CYS121 3.1 51.1 1.0 CB B:CYS109 3.3 64.6 1.0 CB B:HIS126 3.4 48.5 1.0 CB B:CYS64 3.4 65.1 1.0 CA B:CYS64 3.6 63.3 1.0 CA B:CYS109 3.8 68.7 1.0 NE2 B:HIS126 4.1 57.0 1.0 CD2 B:HIS126 4.1 54.4 1.0 N B:GLU110 4.4 72.9 1.0 C B:CYS109 4.4 74.6 1.0 N B:PHE111 4.5 68.3 1.0 N B:CYS64 4.5 65.8 1.0 CA B:CYS121 4.6 50.9 1.0 C B:CYS64 4.8 67.0 1.0 N B:ILE65 4.8 59.5 1.0 CB B:ASN123 4.8 43.7 1.0 CA B:HIS126 4.9 48.6 1.0 N B:CYS109 5.0 71.3 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