Zinc in PDB 5x6g: Crystal Structure of SMAD5-MH1/Palindromic Sbe Dna Complex

The structure of Crystal Structure of SMAD5-MH1/Palindromic Sbe Dna Complex, PDB code: 5x6g was solved by N.Chai, J.Wang, Z.X.Wang, J.W.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.04 / 3.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.535, 74.502, 83.740, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.6

The binding sites of Zinc atom in the Crystal Structure of SMAD5-MH1/Palindromic Sbe Dna Complex (pdb code 5x6g). 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 SMAD5-MH1/Palindromic Sbe Dna Complex, PDB code: 5x6g:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of SMAD5-MH1/Palindromic Sbe Dna Complex


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 SMAD5-MH1/Palindromic Sbe Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:70.2 occ:1.00 ND1 A:HIS127 2.0 71.6 1.0 SG A:CYS122 2.2 71.5 1.0 SG A:CYS65 2.2 77.9 1.0 SG A:CYS110 2.6 79.2 1.0 CG A:HIS127 2.9 70.2 1.0 CE1 A:HIS127 3.0 72.6 1.0 CB A:CYS110 3.1 87.8 1.0 CB A:CYS122 3.2 64.8 1.0 CB A:HIS127 3.2 67.2 1.0 CB A:CYS65 3.3 73.6 1.0 CA A:CYS110 3.4 89.0 1.0 CA A:CYS65 3.6 75.5 1.0 CD2 A:HIS127 4.0 70.2 1.0 NE2 A:HIS127 4.1 71.3 1.0 N A:GLU111 4.2 90.5 1.0 C A:CYS110 4.3 94.7 1.0 N A:CYS65 4.3 75.5 1.0 CB A:ASN124 4.3 69.7 1.0 N A:CYS110 4.5 87.8 1.0 CA A:CYS122 4.7 69.7 1.0 N A:PHE112 4.7 94.8 1.0 CA A:HIS127 4.8 62.4 1.0 C A:CYS65 4.8 73.8 1.0 N A:VAL66 4.9 60.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SMAD5-MH1/Palindromic Sbe Dna Complex


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 SMAD5-MH1/Palindromic Sbe Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:69.5 occ:1.00 ND1 B:HIS127 2.0 69.6 1.0 SG B:CYS65 2.3 74.4 1.0 SG B:CYS122 2.4 83.1 1.0 SG B:CYS110 2.5 75.2 1.0 CE1 B:HIS127 2.9 76.5 1.0 CB B:CYS122 2.9 84.5 1.0 CG B:HIS127 3.0 71.7 1.0 CB B:CYS110 3.1 79.2 1.0 CB B:CYS65 3.2 74.9 1.0 CB B:HIS127 3.4 69.5 1.0 CA B:CYS110 3.5 81.5 1.0 CA B:CYS65 3.6 72.1 1.0 NE2 B:HIS127 4.1 75.6 1.0 CD2 B:HIS127 4.1 76.2 1.0 N B:GLU111 4.3 74.0 1.0 C B:CYS110 4.4 80.9 1.0 N B:CYS65 4.4 79.9 1.0 CA B:CYS122 4.4 83.7 1.0 N B:PHE112 4.6 83.8 1.0 N B:CYS110 4.6 84.9 1.0 CB B:ASN124 4.6 83.8 1.0 C B:CYS65 4.8 75.1 1.0 N B:VAL66 4.8 87.0 1.0 CA B:HIS127 4.9 65.9 1.0

N.Chai, W.X.Li, J.Wang, Z.X.Wang, S.M.Yang, J.W.Wu. Structural Basis For the SMAD5 MH1 Domain to Recognize Different Dna Sequences. Nucleic Acids Res. V. 43 9051 2015.
ISSN: ESSN 1362-4962
PubMed: 26304548
DOI: 10.1093/NAR/GKV848