Zinc in PDB 5mf0: Crystal Structure of SMAD4-MH1 Bound to the Ggccg Site.

The structure of Crystal Structure of SMAD4-MH1 Bound to the Ggccg Site., PDB code: 5mf0 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)	28.25 / 3.03
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	101.520, 101.520, 45.780, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27

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

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of SMAD4-MH1 Bound to the Ggccg Site. (pdb code 5mf0). 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 SMAD4-MH1 Bound to the Ggccg Site., PDB code: 5mf0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of SMAD4-MH1 Bound to the Ggccg 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 SMAD4-MH1 Bound to the Ggccg Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:52.3 occ:1.00 ND1 A:HIS132 2.0 53.4 1.0 SG A:CYS127 2.3 50.2 1.0 SG A:CYS115 2.4 61.9 1.0 SG A:CYS71 2.5 52.8 1.0 CE1 A:HIS132 2.9 52.7 1.0 CG A:HIS132 3.0 51.8 1.0 CB A:CYS127 3.1 46.4 1.0 CB A:CYS115 3.4 58.0 1.0 CB A:HIS132 3.4 48.6 1.0 CB A:CYS71 3.4 48.8 1.0 CA A:CYS71 3.6 48.2 1.0 CA A:CYS115 3.7 58.0 1.0 NE2 A:HIS132 4.1 53.1 1.0 CD2 A:HIS132 4.1 53.3 1.0 N A:GLN116 4.3 54.6 1.0 C A:CYS115 4.4 60.1 1.0 N A:CYS71 4.5 48.1 1.0 CA A:CYS127 4.5 46.2 1.0 N A:TYR117 4.6 54.0 1.0 C A:CYS71 4.7 51.8 1.0 N A:VAL72 4.7 48.5 1.0 CB A:ASN129 4.8 40.9 1.0 CA A:HIS132 4.9 48.0 1.0 N A:CYS115 4.9 59.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SMAD4-MH1 Bound to the Ggccg 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 SMAD4-MH1 Bound to the Ggccg Site. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:51.4 occ:1.00 ND1 B:HIS132 2.2 56.5 1.0 SG B:CYS127 2.2 51.9 1.0 SG B:CYS115 2.4 61.0 1.0 SG B:CYS71 2.4 50.7 1.0 CB B:CYS127 3.0 48.0 1.0 CE1 B:HIS132 3.1 55.7 1.0 CG B:HIS132 3.2 54.8 1.0 CB B:CYS71 3.3 47.0 1.0 CB B:CYS115 3.4 57.1 1.0 CB B:HIS132 3.5 51.5 1.0 CA B:CYS71 3.6 46.8 1.0 CA B:CYS115 3.8 56.9 1.0 N B:GLN116 4.2 53.5 1.0 NE2 B:HIS132 4.2 56.0 1.0 CD2 B:HIS132 4.3 56.3 1.0 C B:CYS115 4.3 59.2 1.0 N B:TYR117 4.4 51.7 1.0 CA B:CYS127 4.5 47.6 1.0 N B:CYS71 4.5 47.1 1.0 N B:VAL72 4.7 47.2 1.0 C B:CYS71 4.7 50.6 1.0 CB B:ASN129 4.9 40.0 1.0 N B:ALA118 4.9 53.6 1.0 N B:CYS115 5.0 58.2 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