Zinc in PDB 5x6m: Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence

The structure of Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence, PDB code: 5x6m 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)	29.94 / 3.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	119.464, 119.464, 93.067, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 25.3

The binding sites of Zinc atom in the Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence (pdb code 5x6m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence, PDB code: 5x6m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence


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 in Complex with A Composite Dna Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:0.1 occ:1.00 ND1 B:HIS127 2.1 0.9 1.0 SG B:CYS110 2.1 0.1 1.0 SG B:CYS122 2.7 1.0 1.0 CE1 B:HIS127 2.8 0.2 1.0 SG B:CYS65 3.1 0.9 1.0 CG B:HIS127 3.1 0.4 1.0 CB B:CYS110 3.2 0.0 1.0 CB B:HIS127 3.6 0.9 1.0 CA B:CYS110 3.7 0.6 1.0 ND2 B:ASN124 3.8 0.2 1.0 NE2 B:HIS127 3.9 0.9 1.0 CD2 B:HIS127 4.0 0.7 1.0 CB B:CYS122 4.1 0.6 1.0 N B:GLU111 4.1 0.0 1.0 CB B:CYS65 4.2 0.0 1.0 CB B:ASN124 4.2 0.9 1.0 CA B:CYS65 4.3 0.0 1.0 CG B:ASN124 4.3 0.0 1.0 O B:PHE112 4.3 0.4 1.0 C B:CYS110 4.3 0.2 1.0 N B:PHE112 4.4 0.3 1.0 N B:CYS65 4.8 0.7 1.0 C B:PHE112 4.9 0.8 1.0 N B:CYS110 5.0 1.0 1.0 CA B:HIS127 5.0 0.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence


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 in Complex with A Composite Dna Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:0.9 occ:1.00 ND1 A:HIS127 1.9 0.4 1.0 SG A:CYS110 2.3 0.7 1.0 SG A:CYS122 2.8 0.4 1.0 SG A:CYS65 2.8 0.5 1.0 CE1 A:HIS127 2.8 0.7 1.0 CG A:HIS127 2.9 0.1 1.0 CB A:CYS110 3.1 0.0 1.0 CB A:CYS122 3.3 0.8 1.0 CB A:HIS127 3.3 0.5 1.0 CA A:CYS110 3.4 0.1 1.0 CB A:CYS65 3.9 0.8 1.0 NE2 A:HIS127 3.9 0.4 1.0 CD2 A:HIS127 4.0 0.5 1.0 CA A:CYS65 4.1 0.1 1.0 C A:CYS110 4.2 0.2 1.0 N A:GLU111 4.3 0.0 1.0 O A:PHE112 4.5 0.8 1.0 N A:CYS110 4.5 0.4 1.0 N A:CYS65 4.6 0.4 1.0 N A:PHE112 4.7 1.0 1.0 CA A:CYS122 4.8 0.4 1.0 CA A:HIS127 4.9 0.3 1.0 CB A:ASN124 4.9 0.2 1.0 C A:PHE112 5.0 0.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:95.7 occ:1.00 ND1 E:HIS127 1.8 91.3 1.0 SG E:CYS122 2.2 94.6 1.0 SG E:CYS110 2.3 95.5 1.0 CE1 E:HIS127 2.3 94.2 1.0 SG E:CYS65 2.4 0.4 1.0 CG E:HIS127 3.0 90.2 1.0 CB E:CYS122 3.1 96.8 1.0 CB E:CYS65 3.2 98.4 1.0 CB E:CYS110 3.4 0.9 1.0 CA E:CYS65 3.4 0.4 1.0 CA E:CYS110 3.6 0.8 1.0 NE2 E:HIS127 3.6 95.2 1.0 CB E:HIS127 3.7 87.2 1.0 N E:GLU111 3.9 0.2 1.0 CD2 E:HIS127 3.9 92.5 1.0 C E:CYS110 4.1 0.5 1.0 N E:CYS65 4.2 0.1 1.0 N E:PHE112 4.5 0.2 1.0 CA E:CYS122 4.5 96.9 1.0 C E:CYS65 4.6 0.6 1.0 N E:VAL66 4.7 0.5 1.0 N E:CYS110 4.8 0.6 1.0 CB E:ASN124 4.9 96.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of SMAD5-MH1 in Complex with A Composite Dna Sequence within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:95.4 occ:1.00 ND1 F:HIS127 2.0 93.5 1.0 SG F:CYS122 2.1 0.7 1.0 CE1 F:HIS127 2.4 97.8 1.0 SG F:CYS65 2.5 0.3 1.0 SG F:CYS110 2.5 90.7 1.0 CG F:HIS127 2.9 90.9 1.0 CB F:CYS122 3.0 95.1 1.0 CB F:CYS65 3.2 0.4 1.0 NE2 F:HIS127 3.4 98.7 1.0 CA F:CYS65 3.4 0.6 1.0 CB F:CYS110 3.6 93.8 1.0 CB F:HIS127 3.6 89.0 1.0 CD2 F:HIS127 3.6 95.4 1.0 CA F:CYS110 3.7 95.7 1.0 N F:GLU111 4.1 0.3 1.0 N F:CYS65 4.2 0.5 1.0 C F:CYS110 4.3 97.8 1.0 CA F:CYS122 4.5 94.1 1.0 N F:PHE112 4.6 0.9 1.0 C F:CYS65 4.6 0.0 1.0 N F:VAL66 4.6 0.6 1.0 CB F:ASN124 4.7 83.6 1.0 N F:CYS110 5.0 98.2 1.0 C F:CYS122 5.0 90.3 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