Zinc in PDB 5nm9: Crystal Structure of the Placozoa Trichoplax Adhaerens SMAD4-MH1 Bound to the Ggcgc Site.

The structure of Crystal Structure of the Placozoa Trichoplax Adhaerens SMAD4-MH1 Bound to the Ggcgc Site., PDB code: 5nm9 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)	29.46 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.150, 76.980, 145.040, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.1

The binding sites of Zinc atom in the Crystal Structure of the Placozoa Trichoplax Adhaerens SMAD4-MH1 Bound to the Ggcgc Site. (pdb code 5nm9). 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 the Placozoa Trichoplax Adhaerens SMAD4-MH1 Bound to the Ggcgc Site., PDB code: 5nm9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Placozoa Trichoplax Adhaerens SMAD4-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 the Placozoa Trichoplax Adhaerens SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:60.8 occ:1.00 SG A:CYS65 2.1 60.9 1.0 ND1 A:HIS126 2.2 67.1 1.0 SG A:CYS109 2.3 62.9 1.0 SG A:CYS121 2.5 58.0 1.0 CB A:CYS121 3.1 54.5 1.0 CG A:HIS126 3.1 64.3 1.0 CE1 A:HIS126 3.1 67.8 1.0 CB A:CYS65 3.2 55.0 1.0 CB A:HIS126 3.4 59.6 1.0 CB A:CYS109 3.4 64.7 1.0 CA A:CYS65 3.6 54.6 1.0 CA A:CYS109 3.7 68.4 1.0 NE2 A:HIS126 4.2 67.8 1.0 CD2 A:HIS126 4.2 66.4 1.0 N A:CYS65 4.4 59.1 1.0 C A:CYS109 4.4 75.5 1.0 N A:LYS110 4.4 72.0 1.0 CA A:CYS121 4.6 51.4 1.0 CB A:ASN123 4.7 52.9 1.0 N A:PHE111 4.7 65.8 1.0 C A:CYS65 4.8 53.4 1.0 N A:VAL66 4.8 50.7 1.0 CA A:HIS126 4.9 60.2 1.0 N A:CYS109 4.9 73.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Placozoa Trichoplax Adhaerens SMAD4-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 the Placozoa Trichoplax Adhaerens SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:56.1 occ:1.00 SG B:CYS65 2.2 53.0 1.0 ND1 B:HIS126 2.2 59.8 1.0 SG B:CYS109 2.2 60.9 1.0 SG B:CYS121 2.3 61.1 1.0 CB B:CYS121 3.0 56.0 1.0 CG B:HIS126 3.2 58.8 1.0 CE1 B:HIS126 3.2 60.0 1.0 CB B:CYS65 3.3 49.7 1.0 CB B:CYS109 3.4 61.1 1.0 CB B:HIS126 3.4 55.7 1.0 CA B:CYS109 3.7 63.5 1.0 CA B:CYS65 3.7 51.4 1.0 CD2 B:HIS126 4.3 61.0 1.0 C B:CYS109 4.3 67.8 1.0 NE2 B:HIS126 4.3 61.3 1.0 N B:LYS110 4.4 64.5 1.0 N B:CYS65 4.5 54.8 1.0 CA B:CYS121 4.5 53.2 1.0 N B:PHE111 4.6 59.1 1.0 CB B:ASN123 4.7 56.2 1.0 C B:CYS65 4.9 57.1 1.0 N B:VAL66 4.9 51.2 1.0 CA B:HIS126 4.9 57.4 1.0 N B:CYS109 4.9 67.6 1.0 N B:ALA112 4.9 55.6 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