Zinc in PDB 7qce: Crystal Structure of An Atypical Phd Finger of VIN3

The structure of Crystal Structure of An Atypical Phd Finger of VIN3, PDB code: 7qce was solved by E.Franco-Echevarria, M.Fiedler, C.Dean, M.Bienz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.84 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.641, 58.641, 225.395, 90, 90, 120
R / Rfree (%)	23 / 26.5

The binding sites of Zinc atom in the Crystal Structure of An Atypical Phd Finger of VIN3 (pdb code 7qce). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of An Atypical Phd Finger of VIN3, PDB code: 7qce:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of An Atypical Phd Finger of VIN3


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 An Atypical Phd Finger of VIN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:59.6 occ:1.00 SG A:CYS136 2.3 68.2 1.0 SG A:CYS152 2.3 61.4 1.0 SG A:CYS155 2.3 56.3 1.0 SG A:CYS141 2.3 62.4 1.0 CB A:CYS152 3.2 76.4 1.0 CB A:CYS155 3.3 63.7 1.0 CB A:CYS141 3.3 77.9 1.0 CB A:CYS136 3.3 73.5 1.0 N A:CYS155 4.0 61.9 1.0 CA A:CYS155 4.2 51.2 1.0 CB A:ASN138 4.3 77.4 1.0 CB A:ALA143 4.5 73.6 1.0 CA A:CYS152 4.6 68.8 1.0 N A:ALA143 4.6 80.0 1.0 ND2 A:ASN138 4.7 69.5 1.0 CA A:CYS141 4.7 84.5 1.0 CA A:CYS136 4.7 89.1 1.0 N A:ARG142 4.7 79.9 1.0 O A:CYS152 4.7 69.7 1.0 C A:CYS152 4.8 81.8 1.0 CB A:ARG154 4.9 75.0 1.0 C A:ARG154 5.0 59.9 1.0 C A:CYS141 5.0 83.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of An Atypical Phd Finger of VIN3


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 An Atypical Phd Finger of VIN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:43.7 occ:1.00 ND1 A:HIS191 2.0 39.5 1.0 SG A:CYS160 2.3 46.4 1.0 SG A:CYS194 2.3 43.3 1.0 SG A:CYS157 2.4 39.8 1.0 CE1 A:HIS191 3.0 41.1 1.0 CG A:HIS191 3.0 37.2 1.0 CB A:CYS157 3.1 35.1 1.0 CB A:CYS160 3.2 43.2 1.0 CB A:CYS194 3.4 51.3 1.0 CB A:HIS191 3.4 43.8 1.0 N A:CYS160 3.8 43.3 1.0 N A:HIS191 4.0 40.4 1.0 CA A:CYS160 4.1 44.3 1.0 NE2 A:HIS191 4.1 37.6 1.0 CD2 A:HIS191 4.2 36.7 1.0 O A:HOH536 4.2 67.3 1.0 CA A:HIS191 4.3 43.4 1.0 CA A:CYS157 4.6 35.8 1.0 CA A:CYS194 4.8 47.4 1.0 CB A:ILE159 4.8 46.5 1.0 C A:CYS160 4.9 44.1 1.0 C A:ILE159 4.9 44.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of An Atypical Phd Finger of VIN3


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 An Atypical Phd Finger of VIN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:42.4 occ:1.00 SG A:CYS186 2.3 44.9 1.0 SG A:CYS221 2.3 45.6 1.0 SG A:CYS175 2.3 41.3 1.0 SG A:CYS218 2.4 40.9 1.0 CB A:CYS175 3.1 39.3 1.0 CB A:CYS218 3.1 39.0 1.0 CB A:CYS186 3.4 57.1 1.0 CB A:CYS221 3.4 44.6 1.0 N A:CYS186 3.6 49.7 1.0 N A:CYS221 3.9 43.1 1.0 CA A:CYS186 4.0 51.3 1.0 CA A:CYS221 4.2 52.6 1.0 CB A:LYS223 4.5 37.2 1.0 CA A:CYS175 4.6 40.3 1.0 CA A:CYS218 4.6 36.4 1.0 C A:SER185 4.6 74.0 1.0 CB A:PHE220 4.7 48.8 1.0 N A:GLY222 4.7 53.6 1.0 C A:CYS221 4.7 48.3 1.0 C A:CYS186 4.8 34.5 1.0 N A:GLY187 4.8 39.2 1.0 N A:LYS223 4.8 44.6 1.0 CA A:SER185 4.8 53.6 1.0 N A:MET188 5.0 47.6 1.0 C A:PHE220 5.0 46.8 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of An Atypical Phd Finger of VIN3


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 An Atypical Phd Finger of VIN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:41.7 occ:1.00 ND1 B:HIS191 2.0 36.3 1.0 SG B:CYS194 2.3 44.1 1.0 SG B:CYS157 2.3 44.2 1.0 SG B:CYS160 2.3 41.8 1.0 CE1 B:HIS191 3.0 49.3 1.0 CG B:HIS191 3.1 37.6 1.0 CB B:CYS157 3.1 48.2 1.0 CB B:CYS160 3.3 39.6 1.0 CB B:CYS194 3.4 49.6 1.0 CB B:HIS191 3.4 35.1 1.0 N B:CYS160 3.8 46.0 1.0 N B:HIS191 4.0 41.7 1.0 CA B:CYS160 4.1 50.1 1.0 NE2 B:HIS191 4.1 38.5 1.0 CD2 B:HIS191 4.2 39.8 1.0 CA B:HIS191 4.3 38.0 1.0 CA B:CYS157 4.5 50.4 1.0 CA B:CYS194 4.7 44.8 1.0 CB B:ILE159 4.8 46.3 1.0 C B:CYS160 4.9 51.5 1.0 C B:ILE159 4.9 47.6 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of An Atypical Phd Finger of VIN3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of An Atypical Phd Finger of VIN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:56.2 occ:1.00 SG B:CYS221 2.3 56.9 1.0 SG B:CYS175 2.3 58.1 1.0 SG B:CYS186 2.3 58.8 1.0 SG B:CYS218 2.4 54.4 1.0 CB B:CYS175 3.1 53.2 1.0 CB B:CYS218 3.1 67.5 1.0 CB B:CYS186 3.4 69.8 1.0 CB B:CYS221 3.4 62.9 1.0 N B:CYS186 3.7 63.1 1.0 N B:CYS221 3.9 54.2 1.0 CA B:CYS186 4.1 58.4 1.0 CA B:CYS221 4.1 64.9 1.0 CA B:CYS175 4.5 58.3 1.0 CB B:LYS223 4.5 67.0 1.0 CA B:CYS218 4.6 54.1 1.0 C B:SER185 4.7 56.9 1.0 N B:GLY222 4.7 51.9 1.0 C B:CYS221 4.7 55.4 1.0 N B:LYS223 4.8 58.5 1.0 CB B:PHE220 4.8 64.5 1.0 C B:CYS186 4.8 60.3 1.0 N B:GLY187 4.8 53.1 1.0 CA B:SER185 4.9 59.4 1.0 N B:MET188 5.0 45.9 1.0

E.Franco-Echevarria, T.J.Rutherford, M.Fiedler, C.Dean, M.Bienz. Plant Vernalization Proteins Contain Unusual Phd Superdomains Without Histone H3 Binding Activity. J.Biol.Chem. V. 298 02540 2022.
ISSN: ESSN 1083-351X
PubMed: 36174674
DOI: 10.1016/J.JBC.2022.102540