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

The structure of Crystal Structure of SMAD4-MH1 Bound to the Ggct Site., PDB code: 5mez 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)	29.05 / 2.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.790, 79.060, 114.160, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.2

The structure of Crystal Structure of SMAD4-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 SMAD4-MH1 Bound to the Ggct Site. (pdb code 5mez). 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 Ggct Site., PDB code: 5mez:
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 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 SMAD4-MH1 Bound to the Ggct Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:64.9 occ:1.00 ND1 A:HIS132 2.0 64.5 1.0 SG A:CYS115 2.1 70.3 1.0 SG A:CYS127 2.4 59.1 1.0 SG A:CYS71 2.4 69.1 1.0 CE1 A:HIS132 3.0 63.9 1.0 CB A:CYS127 3.0 55.0 1.0 CG A:HIS132 3.1 63.2 1.0 CB A:CYS115 3.3 66.8 1.0 CB A:CYS71 3.3 64.9 1.0 CB A:HIS132 3.4 59.9 1.0 CA A:CYS71 3.6 63.5 1.0 CA A:CYS115 3.8 67.6 1.0 NE2 A:HIS132 4.1 64.3 1.0 CD2 A:HIS132 4.2 64.6 1.0 N A:GLN116 4.4 69.2 1.0 N A:CYS71 4.4 63.9 1.0 C A:CYS115 4.4 72.7 1.0 CA A:CYS127 4.5 55.0 1.0 N A:TYR117 4.6 69.7 1.0 C A:CYS71 4.8 62.2 1.0 CB A:ASN129 4.8 54.4 1.0 N A:VAL72 4.8 55.1 1.0 CA A:HIS132 4.9 58.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SMAD4-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 SMAD4-MH1 Bound to the Ggct Site. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:68.7 occ:1.00 ND1 B:HIS132 1.9 67.4 1.0 SG B:CYS115 2.2 68.6 1.0 SG B:CYS127 2.2 62.1 1.0 SG B:CYS71 2.4 72.0 1.0 CE1 B:HIS132 2.9 66.8 1.0 CG B:HIS132 3.0 65.9 1.0 CB B:CYS127 3.0 58.9 1.0 CB B:CYS115 3.2 66.0 1.0 CB B:HIS132 3.4 63.1 1.0 CB B:CYS71 3.4 68.0 1.0 CA B:CYS71 3.6 67.8 1.0 CA B:CYS115 3.7 67.4 1.0 NE2 B:HIS132 4.0 67.1 1.0 CD2 B:HIS132 4.1 67.2 1.0 N B:GLN116 4.3 68.8 1.0 C B:CYS115 4.4 72.9 1.0 N B:CYS71 4.4 69.1 1.0 CA B:CYS127 4.5 59.6 1.0 N B:TYR117 4.6 72.2 1.0 CB B:ASN129 4.8 58.6 1.0 C B:CYS71 4.8 69.9 1.0 CA B:HIS132 4.8 63.1 1.0 N B:VAL72 4.9 63.9 1.0 N B:CYS115 5.0 69.5 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