Zinc in PDB 3d2s: Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna

The structure of Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna, PDB code: 3d2s was solved by M.Teplova, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.421, 56.899, 58.222, 90.00, 108.81, 90.00
R / Rfree (%)	22.4 / 26

The binding sites of Zinc atom in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna (pdb code 3d2s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna, PDB code: 3d2s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


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 MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:8.2 occ:1.00 NE2 A:HIS204 2.1 3.6 1.0 SG A:CYS200 2.3 8.4 1.0 SG A:CYS193 2.3 15.6 1.0 SG A:CYS185 2.3 7.1 1.0 CE1 A:HIS204 3.0 9.0 1.0 CB A:CYS200 3.1 8.2 1.0 CD2 A:HIS204 3.2 6.2 1.0 CB A:CYS185 3.2 7.7 1.0 CB A:CYS193 3.3 18.2 1.0 N2 E:G5 4.0 9.6 1.0 ND1 A:HIS204 4.1 7.9 1.0 CB A:TYR188 4.3 9.8 1.0 CG A:HIS204 4.3 6.8 1.0 N1 E:G5 4.5 10.8 1.0 CA A:CYS200 4.5 9.3 1.0 O E:HOH125 4.6 21.4 1.0 CA A:CYS193 4.6 19.1 1.0 N A:TYR188 4.6 10.1 1.0 CA A:CYS185 4.7 7.1 1.0 C2 E:G5 4.8 10.9 1.0 O A:GLY196 4.8 14.0 1.0 O A:PHE202 5.0 4.5 1.0 CA A:TYR188 5.0 10.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


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 MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:7.4 occ:1.00 NE2 A:HIS238 2.1 9.3 1.0 SG A:CYS221 2.3 9.2 1.0 SG A:CYS229 2.3 7.4 1.0 SG A:CYS234 2.3 8.2 1.0 CD2 A:HIS238 3.0 6.4 1.0 CE1 A:HIS238 3.1 7.7 1.0 CB A:CYS234 3.2 9.1 1.0 CB A:CYS229 3.2 8.6 1.0 CB A:CYS221 3.3 7.5 1.0 ND1 A:HIS238 4.2 9.2 1.0 CG A:HIS238 4.2 7.4 1.0 O A:HOH309 4.2 12.3 1.0 CB A:TYR224 4.5 7.2 1.0 CA A:CYS234 4.6 9.1 1.0 CA A:CYS221 4.6 7.8 1.0 CA A:CYS229 4.7 9.0 1.0 O A:TYR236 4.8 8.7 1.0 N A:TYR224 4.9 7.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


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 MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:13.9 occ:1.00 NE2 B:HIS204 2.1 14.8 1.0 SG B:CYS200 2.3 12.3 1.0 SG B:CYS185 2.3 11.7 1.0 SG B:CYS193 2.3 18.7 1.0 CE1 B:HIS204 3.0 12.0 1.0 CD2 B:HIS204 3.1 15.6 1.0 CB B:CYS200 3.2 12.4 1.0 CB B:CYS185 3.2 10.7 1.0 CB B:CYS193 3.2 24.9 1.0 ND1 B:HIS204 4.1 13.4 1.0 N2 F:G2 4.2 15.2 1.0 CB B:TYR188 4.2 20.0 1.0 CG B:HIS204 4.2 10.4 1.0 NH1 B:ARG195 4.3 25.0 1.0 N1 F:G2 4.6 14.4 1.0 CA B:CYS200 4.6 13.0 1.0 CA B:CYS185 4.6 10.4 1.0 CA B:CYS193 4.7 25.9 1.0 N B:TYR188 4.7 19.4 1.0 O B:PHE202 4.7 10.8 1.0 C2 F:G2 4.9 15.1 1.0 CA B:TYR188 4.9 19.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


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 MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:8.2 occ:1.00 NE2 B:HIS238 2.1 10.4 1.0 SG B:CYS229 2.3 10.8 1.0 SG B:CYS234 2.3 8.1 1.0 SG B:CYS221 2.3 6.0 1.0 CE1 B:HIS238 3.0 10.8 1.0 CD2 B:HIS238 3.1 9.8 1.0 CB B:CYS234 3.2 8.8 1.0 CB B:CYS229 3.2 14.7 1.0 CB B:CYS221 3.3 6.2 1.0 ND1 B:HIS238 4.2 11.1 1.0 CG B:HIS238 4.2 9.6 1.0 CB A:ALA241 4.6 8.8 1.0 CB B:TYR224 4.6 11.2 1.0 O B:TYR236 4.6 9.7 1.0 CA B:CYS234 4.6 9.5 1.0 CA B:CYS229 4.7 15.7 1.0 CB B:ARG231 4.7 21.8 1.0 O B:HOH306 4.7 12.4 1.0 CA B:CYS221 4.7 5.8 1.0 N B:TYR224 4.9 8.6 1.0 CB B:TYR236 4.9 6.8 1.0 O A:HOH305 4.9 8.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


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 MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:16.4 occ:1.00 NE2 C:HIS204 2.1 12.6 1.0 SG C:CYS200 2.3 14.7 1.0 SG C:CYS193 2.3 23.5 1.0 SG C:CYS185 2.4 14.4 1.0 CE1 C:HIS204 2.9 17.2 1.0 CB C:CYS200 3.1 13.8 1.0 CD2 C:HIS204 3.2 12.2 1.0 CB C:CYS185 3.2 14.1 1.0 CB C:CYS193 3.4 27.2 1.0 N2 G:G5 4.1 16.7 1.0 ND1 C:HIS204 4.1 16.3 1.0 CB C:TYR188 4.2 21.9 1.0 CG C:HIS204 4.2 14.0 1.0 CA C:CYS200 4.5 14.5 1.0 N1 G:G5 4.6 16.9 1.0 CA C:CYS193 4.6 28.1 1.0 N C:TYR188 4.6 22.6 1.0 CA C:CYS185 4.6 13.8 1.0 O G:HOH129 4.7 21.3 1.0 C2 G:G5 4.8 18.2 1.0 O C:GLY196 4.9 22.2 1.0 O C:PHE202 4.9 9.5 1.0 CA C:TYR188 4.9 22.8 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn304 b:14.3 occ:1.00 NE2 C:HIS238 2.1 16.0 1.0 SG C:CYS221 2.3 14.2 1.0 SG C:CYS229 2.3 13.9 1.0 SG C:CYS234 2.3 18.6 1.0 CE1 C:HIS238 3.0 11.6 1.0 CD2 C:HIS238 3.1 11.4 1.0 CB C:CYS234 3.2 20.6 1.0 CB C:CYS229 3.3 14.7 1.0 CB C:CYS221 3.3 11.8 1.0 ND1 C:HIS238 4.2 14.2 1.0 CG C:HIS238 4.2 13.1 1.0 O C:HOH381 4.3 13.7 1.0 CB C:TYR224 4.4 9.9 1.0 CA C:CYS221 4.6 11.6 1.0 CA C:CYS229 4.7 14.5 1.0 CA C:CYS234 4.7 20.6 1.0 N C:TYR224 4.8 11.1 1.0 O C:TYR236 4.8 15.6 1.0 CD C:ARG231 5.0 28.3 1.0 O C:HOH392 5.0 21.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:11.2 occ:1.00 NE2 D:HIS204 2.1 11.2 1.0 SG D:CYS200 2.3 10.6 1.0 SG D:CYS185 2.3 9.9 1.0 SG D:CYS193 2.3 17.0 1.0 CE1 D:HIS204 3.0 9.1 1.0 CD2 D:HIS204 3.1 12.1 1.0 CB D:CYS200 3.2 12.3 1.0 CB D:CYS185 3.2 9.3 1.0 CB D:CYS193 3.3 21.7 1.0 ND1 D:HIS204 4.1 10.2 1.0 N2 H:G2 4.2 15.6 1.0 CG D:HIS204 4.2 8.6 1.0 CB D:TYR188 4.2 16.6 1.0 NH2 D:ARG195 4.4 24.6 1.0 N1 H:G2 4.5 15.3 1.0 CA D:CYS200 4.6 12.4 1.0 CA D:CYS185 4.6 9.2 1.0 CA D:CYS193 4.7 22.4 1.0 N D:TYR188 4.7 15.7 1.0 O D:PHE202 4.7 9.3 1.0 C2 H:G2 4.9 16.2 1.0 CA D:TYR188 5.0 16.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of MBNL1 Tandem Zinc Finger 3 and 4 Domain in Complex with Cgcugu Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn304 b:9.1 occ:1.00 NE2 D:HIS238 2.1 10.5 1.0 SG D:CYS234 2.3 8.2 1.0 SG D:CYS229 2.3 11.3 1.0 SG D:CYS221 2.3 7.8 1.0 CE1 D:HIS238 3.0 8.6 1.0 CD2 D:HIS238 3.1 9.6 1.0 CB D:CYS234 3.2 7.6 1.0 CB D:CYS229 3.2 15.0 1.0 CB D:CYS221 3.3 7.5 1.0 ND1 D:HIS238 4.2 11.1 1.0 CG D:HIS238 4.2 9.3 1.0 CB D:TYR224 4.5 12.8 1.0 O D:TYR236 4.6 8.8 1.0 CB C:ALA241 4.6 9.6 1.0 CA D:CYS234 4.6 8.6 1.0 CA D:CYS229 4.6 16.5 1.0 CA D:CYS221 4.7 8.1 1.0 O D:HOH398 4.7 14.3 1.0 CB D:ARG231 4.8 21.9 1.0 CB D:TYR236 4.9 7.5 1.0 N D:TYR224 4.9 11.5 1.0 O C:HOH371 5.0 6.5 1.0

M.Teplova, D.J.Patel. Structural Insights Into Rna Recognition By the Alternative-Splicing Regulator Muscleblind-Like MBNL1. Nat.Struct.Mol.Biol. V. 15 1343 2008.
ISSN: ISSN 1545-9993
PubMed: 19043415
DOI: 10.1038/NSMB.1519