Zinc in PDB 4m9v: ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna

The structure of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna, PDB code: 4m9v was solved by Y.Liu, Y.O.Olanrewaju, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.46 / 0.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.388, 96.093, 36.408, 90.00, 113.14, 90.00
R / Rfree (%)	13 / 14.3

The structure of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna (pdb code 4m9v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna, PDB code: 4m9v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:7.7 occ:1.00 NE2 C:HIS186 2.0 7.4 1.0 NE2 C:HIS190 2.0 7.7 1.0 SG C:CYS173 2.3 9.3 1.0 SG C:CYS170 2.3 8.0 1.0 CD2 C:HIS186 3.0 7.0 1.0 CE1 C:HIS190 3.0 8.1 1.0 CD2 C:HIS190 3.0 7.5 1.0 CE1 C:HIS186 3.0 7.2 1.0 HB3 C:CYS170 3.1 10.3 1.0 H C:CYS173 3.1 12.7 0.5 CB C:CYS170 3.1 8.6 1.0 HD2 C:HIS186 3.2 8.4 1.0 HE1 C:HIS190 3.2 9.7 1.0 HB3 C:CYS173 3.2 12.3 1.0 HB2 C:CYS170 3.2 10.3 1.0 HD2 C:HIS190 3.2 9.0 1.0 HE1 C:HIS186 3.3 8.7 1.0 HB3 C:GLU172 3.3 13.3 0.5 CB C:CYS173 3.3 10.3 1.0 HB3 C:GLU172 3.4 13.9 0.5 N C:CYS173 3.7 10.6 1.0 CA C:CYS173 4.1 10.9 1.0 ND1 C:HIS190 4.1 8.1 1.0 HG22 C:VAL189 4.1 10.3 0.5 HB2 C:CYS173 4.1 12.3 1.0 ND1 C:HIS186 4.1 7.2 1.0 CG C:HIS186 4.2 6.8 1.0 CG C:HIS190 4.2 7.3 1.0 HB3 C:LYS175 4.2 12.8 1.0 HG21 C:VAL189 4.2 10.3 0.5 CB C:GLU172 4.2 11.1 0.5 H C:LYS175 4.2 12.1 1.0 CB C:GLU172 4.4 11.6 0.5 H C:GLU172 4.4 12.3 0.5 HG3 C:GLU172 4.4 13.8 0.5 HG23 C:VAL189 4.4 10.3 0.5 H C:GLU172 4.4 12.1 0.5 CG2 C:VAL189 4.5 8.6 0.5 O B:HOH236 4.5 28.7 1.0 HD23 C:LEU187 4.5 10.3 1.0 H C:GLY174 4.5 12.4 1.0 HA C:LEU187 4.5 8.3 1.0 HG2 C:GLU172 4.5 13.8 0.5 CA C:CYS170 4.6 8.9 1.0 OE2 C:GLU172 4.6 14.0 0.5 HB C:VAL189 4.6 9.7 0.6 C C:GLU172 4.6 11.0 0.5 CG C:GLU172 4.6 11.5 0.5 HB2 C:GLU172 4.7 13.9 0.5 C C:GLU172 4.7 10.7 0.5 HB2 C:LYS175 4.8 12.8 1.0 C C:CYS173 4.8 11.1 1.0 HB2 C:GLU172 4.8 13.3 0.5 N C:GLY174 4.9 10.3 1.0 CA C:GLU172 4.9 10.5 0.5 CA C:GLU172 4.9 10.8 0.5 HA C:CYS173 4.9 13.1 1.0 HD1 C:HIS190 4.9 9.7 1.0 N C:GLU172 4.9 10.2 0.5 CB C:LYS175 4.9 10.6 1.0 HA C:CYS170 4.9 10.7 1.0 HD1 C:HIS186 4.9 8.6 1.0 N C:GLU172 4.9 10.1 0.5 HE1 C:PHE177 5.0 11.0 1.0 C C:CYS170 5.0 9.0 1.0

Zinc binding site 2 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:8.8 occ:1.00 NE2 C:HIS158 2.0 8.7 1.0 NE2 C:HIS162 2.0 8.9 1.0 SG C:CYS145 2.3 8.2 1.0 SG C:CYS142 2.3 10.2 1.0 HB2 C:PHE144 2.8 12.1 0.5 CD2 C:HIS162 3.0 8.2 1.0 CE1 C:HIS158 3.0 8.5 1.0 CD2 C:HIS158 3.0 8.6 1.0 HD2 C:HIS162 3.1 9.9 1.0 HB3 C:CYS142 3.1 10.5 1.0 CE1 C:HIS162 3.1 8.2 1.0 CB C:CYS142 3.1 8.8 1.0 HE1 C:HIS158 3.2 10.2 1.0 HB3 C:CYS145 3.2 9.7 1.0 HD2 C:HIS158 3.2 10.3 1.0 HB2 C:CYS142 3.2 10.5 1.0 H C:CYS145 3.3 10.3 0.5 HE1 C:HIS162 3.3 9.8 1.0 CB C:CYS145 3.3 8.1 1.0 CB C:PHE144 3.7 10.1 0.5 HB2 C:LYS147 3.7 12.4 1.0 N C:CYS145 3.8 8.6 1.0 HB3 C:PHE144 3.8 12.1 0.5 H C:LYS147 4.0 9.8 1.0 O F:HOH324 4.0 11.5 1.0 CA C:CYS145 4.0 7.8 1.0 ND1 C:HIS158 4.1 8.5 1.0 HB2 C:CYS145 4.1 9.7 1.0 HB2 C:PHE144 4.1 11.6 0.5 CG C:HIS162 4.1 7.5 1.0 CG C:HIS158 4.1 8.3 1.0 HD1 C:PHE144 4.1 11.4 0.5 ND1 C:HIS162 4.2 7.5 1.0 H C:PHE144 4.2 14.3 0.5 HD3 C:LYS147 4.3 18.2 1.0 H C:PHE144 4.4 14.4 0.5 H C:GLY146 4.4 9.6 1.0 CG C:PHE144 4.5 9.7 0.5 CD1 C:PHE144 4.5 9.5 0.5 C C:CYS145 4.6 7.4 1.0 C C:PHE144 4.6 10.1 0.5 CA C:CYS142 4.6 8.1 1.0 CA C:PHE144 4.6 11.1 0.5 C C:PHE144 4.6 9.7 0.5 CB C:LYS147 4.7 10.4 1.0 N C:GLY146 4.7 8.0 1.0 O C:HOH369 4.7 17.8 0.8 N C:LYS147 4.8 8.2 1.0 H51 B:MPD101 4.8 10.3 1.0 HD1 C:HIS158 4.9 10.2 1.0 N C:PHE144 4.9 12.0 0.5 N C:PHE144 4.9 11.9 0.5 HA C:CYS145 4.9 9.4 1.0 HA C:CYS142 5.0 9.7 1.0 HD1 C:HIS162 5.0 9.0 1.0 CB C:PHE144 5.0 9.7 0.5

Zinc binding site 3 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:7.6 occ:1.00 NE2 F:HIS190 2.0 7.5 1.0 NE2 F:HIS186 2.1 7.3 1.0 SG F:CYS173 2.3 9.1 1.0 SG F:CYS170 2.3 8.0 1.0 CE1 F:HIS190 3.0 8.2 1.0 CD2 F:HIS186 3.0 6.9 1.0 H F:CYS173 3.0 12.9 0.5 CD2 F:HIS190 3.0 7.2 1.0 HB3 F:CYS170 3.1 10.1 1.0 CE1 F:HIS186 3.1 7.0 1.0 CB F:CYS170 3.1 8.4 1.0 HB3 F:CYS173 3.2 12.3 1.0 HE1 F:HIS190 3.2 9.8 1.0 HD2 F:HIS186 3.2 8.3 1.0 HB2 F:CYS170 3.2 10.1 1.0 HD2 F:HIS190 3.2 8.7 1.0 HE1 F:HIS186 3.3 8.4 1.0 HB3 F:GLU172 3.3 12.6 0.5 CB F:CYS173 3.3 10.3 1.0 HB3 F:GLU172 3.4 12.9 0.5 N F:CYS173 3.7 10.7 1.0 CA F:CYS173 4.0 10.7 1.0 HB2 F:CYS173 4.1 12.3 1.0 ND1 F:HIS190 4.1 7.7 1.0 HB3 F:LYS175 4.1 12.5 0.5 HB3 F:LYS175 4.2 12.5 0.5 HG22 F:VAL189 4.2 10.2 0.4 ND1 F:HIS186 4.2 7.0 1.0 CG F:HIS190 4.2 7.3 1.0 CG F:HIS186 4.2 6.6 1.0 HG21 F:VAL189 4.2 10.2 0.4 CB F:GLU172 4.2 10.5 0.5 H F:LYS175 4.2 11.8 0.5 H F:LYS175 4.2 11.9 0.5 CB F:GLU172 4.4 10.7 0.5 H F:GLU172 4.4 12.0 0.5 HG3 F:GLU172 4.4 13.4 0.5 HG23 F:VAL189 4.4 10.2 0.4 H F:GLU172 4.5 11.8 0.5 CG2 F:VAL189 4.5 8.5 0.4 HD23 F:LEU187 4.5 10.4 1.0 H F:GLY174 4.5 12.5 1.0 O E:HOH238 4.5 25.8 1.0 HA F:LEU187 4.5 7.9 1.0 HG2 F:GLU172 4.5 13.4 0.5 CA F:CYS170 4.6 8.9 1.0 C F:GLU172 4.6 11.0 0.5 OE2 F:GLU172 4.6 13.9 0.5 HB F:VAL189 4.6 9.7 0.6 CG F:GLU172 4.6 11.2 0.5 HB2 F:GLU172 4.7 12.9 0.5 C F:GLU172 4.7 10.8 0.5 C F:CYS173 4.8 10.7 1.0 HB2 F:LYS175 4.8 12.5 0.5 HB2 F:LYS175 4.8 12.5 0.5 HB2 F:GLU172 4.8 12.6 0.5 N F:GLY174 4.8 10.4 1.0 HA F:CYS173 4.9 12.8 1.0 CA F:GLU172 4.9 10.2 0.5 CA F:GLU172 4.9 10.4 0.5 CB F:LYS175 4.9 10.4 0.5 HA F:CYS170 4.9 10.6 1.0 HD1 F:HIS190 4.9 9.2 1.0 N F:GLU172 4.9 10.0 0.5 CB F:LYS175 4.9 10.4 0.5 N F:GLU172 4.9 9.8 0.5 HD1 F:HIS186 5.0 8.3 1.0 C F:CYS170 5.0 9.0 1.0 HE1 F:PHE177 5.0 10.3 1.0

Zinc binding site 4 out of 4 in the ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ZFP57 Mutant (E182Q) in Complex with 5-Carboxylcytosine Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn202 b:8.7 occ:1.00 NE2 F:HIS162 2.0 8.5 1.0 NE2 F:HIS158 2.1 8.8 1.0 SG F:CYS145 2.3 8.0 1.0 SG F:CYS142 2.3 10.1 1.0 HB2 F:PHE144 2.8 12.1 0.5 CD2 F:HIS162 2.9 8.4 1.0 CE1 F:HIS158 3.0 8.5 1.0 CD2 F:HIS158 3.0 8.6 1.0 HD2 F:HIS162 3.0 10.0 1.0 CE1 F:HIS162 3.1 8.0 1.0 HB3 F:CYS142 3.1 10.2 1.0 CB F:CYS142 3.2 8.5 1.0 HB3 F:CYS145 3.2 9.7 1.0 HD2 F:HIS158 3.2 10.3 1.0 HE1 F:HIS158 3.2 10.2 1.0 HB2 F:CYS142 3.2 10.2 1.0 H F:CYS145 3.3 10.1 0.5 HE1 F:HIS162 3.3 9.6 1.0 CB F:CYS145 3.3 8.1 1.0 CB F:PHE144 3.7 10.1 0.5 HB2 F:LYS147 3.7 12.1 1.0 N F:CYS145 3.7 8.4 1.0 HB3 F:PHE144 3.8 12.1 0.5 H F:LYS147 4.0 9.7 1.0 CA F:CYS145 4.0 7.7 1.0 O C:HOH321 4.1 11.7 1.0 CG F:HIS162 4.1 7.8 1.0 HB2 F:PHE144 4.1 11.6 0.6 ND1 F:HIS158 4.1 8.4 1.0 HB2 F:CYS145 4.1 9.7 1.0 ND1 F:HIS162 4.1 7.7 1.0 HD1 F:PHE144 4.2 10.9 0.5 CG F:HIS158 4.2 8.3 1.0 H F:PHE144 4.2 13.9 0.6 HD3 F:LYS147 4.3 17.9 1.0 H F:PHE144 4.4 14.1 0.5 H F:GLY146 4.4 9.3 1.0 CG F:PHE144 4.4 9.4 0.5 CD1 F:PHE144 4.5 9.1 0.5 C F:CYS145 4.6 7.6 1.0 C F:PHE144 4.6 9.7 0.5 CA F:CYS142 4.6 8.0 1.0 CA F:PHE144 4.6 10.9 0.5 C F:PHE144 4.6 9.4 0.6 CB F:LYS147 4.7 10.0 1.0 N F:GLY146 4.7 7.7 1.0 O F:HOH365 4.7 13.9 0.7 HO4 E:MPD101 4.8 51.8 1.0 N F:LYS147 4.8 8.1 1.0 N F:PHE144 4.9 11.7 0.5 N F:PHE144 4.9 11.6 0.6 HD1 F:HIS158 4.9 10.1 1.0 HA F:CYS145 4.9 9.2 1.0 HD1 F:HIS162 4.9 9.2 1.0 HA F:CYS142 5.0 9.6 1.0 CB F:PHE144 5.0 9.6 0.6

Y.Liu, Y.O.Olanrewaju, X.Zhang, X.Cheng. Dna Recognition of 5-Carboxylcytosine By A ZFP57 Mutant at An Atomic Resolution of 0.97 Angstrom. Biochemistry V. 52 9310 2013.
ISSN: ISSN 0006-2960
PubMed: 24236546
DOI: 10.1021/BI401360N