Zinc in PDB 3vyq: Crystal Structure of the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1

The structure of Crystal Structure of the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1, PDB code: 3vyq was solved by J.Otani, K.Arita, T.Kato, M.Kinoshita, M.Ariyoshi, M.Shirakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.97 / 2.52
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.604, 34.093, 61.165, 75.28, 77.76, 87.31
R / Rfree (%)	19.3 / 23.6

The binding sites of Zinc atom in the Crystal Structure of the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1 (pdb code 3vyq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1, PDB code: 3vyq:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1


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 Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:40.4 occ:1.00 O A:HOH311 2.1 24.0 1.0 SG A:CYS75 2.4 35.5 1.0 CB A:CYS75 3.2 32.1 1.0 CA A:CYS75 3.8 30.3 1.0 N A:CYS75 4.4 30.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1


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 Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:43.2 occ:1.00 SG D:CYS75 2.5 35.5 1.0 CB D:CYS75 3.4 31.9 1.0 CA D:CYS75 3.9 30.8 1.0 N D:CYS75 4.4 31.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1


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 the Methyl Cpg Binding Domain of MBD4 in Complex with the 5MCG/Tg Sequence in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:91.7 occ:1.00 ND1 D:HIS70 2.2 93.7 1.0 CE1 D:HIS70 2.8 94.3 1.0 CG D:HIS70 3.1 91.4 1.0 CB D:HIS70 3.8 88.5 1.0 NE2 D:HIS70 3.8 93.1 1.0 CD2 D:HIS70 4.0 91.5 1.0

J.Otani, K.Arita, T.Kato, M.Kinoshita, H.Kimura, I.Suetake, S.Tajima, M.Ariyoshi, M.Shirakawa. Structural Basis of the Versatile Dna Recognition Ability of the Methyl-Cpg Binding Domain of Methyl-Cpg Binding Domain Protein 4 J.Biol.Chem. V. 288 6351 2013.
ISSN: ISSN 0021-9258
PubMed: 23316048
DOI: 10.1074/JBC.M112.431098