Zinc in PDB 1p47: Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna

The structure of Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna, PDB code: 1p47 was solved by E.Peisach, C.O.Pabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.86 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	70.629, 70.629, 99.608, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 26.7

The binding sites of Zinc atom in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna (pdb code 1p47). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna, PDB code: 1p47:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna


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 Tandem ZIF268 Molecules Complexed to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:83.7 occ:1.00 NE2 A:HIS129 2.0 70.9 1.0 NE2 A:HIS125 2.2 72.8 1.0 SG A:CYS107 2.3 78.1 1.0 SG A:CYS112 2.3 87.2 1.0 CD2 A:HIS129 2.6 75.4 1.0 CD2 A:HIS125 3.1 69.8 1.0 CE1 A:HIS125 3.2 74.9 1.0 CB A:CYS112 3.2 94.4 1.0 CE1 A:HIS129 3.3 76.9 1.0 CB A:CYS107 3.3 78.8 1.0 CG A:HIS129 3.9 77.8 1.0 ND1 A:HIS129 4.1 76.7 1.0 CG A:HIS125 4.3 67.8 1.0 ND1 A:HIS125 4.3 78.5 1.0 CB A:VAL109 4.3 86.3 1.0 CG2 A:VAL109 4.5 86.7 1.0 CA A:CYS112 4.7 96.0 1.0 CA A:CYS107 4.8 78.4 1.0 O A:HIS125 4.9 68.5 1.0 CG1 A:VAL109 5.0 84.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna


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 Tandem ZIF268 Molecules Complexed to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:51.6 occ:1.00 NE2 A:HIS157 2.0 52.4 1.0 NE2 A:HIS153 2.1 62.2 1.0 SG A:CYS137 2.2 48.4 1.0 SG A:CYS140 2.3 60.2 1.0 CD2 A:HIS153 2.9 47.9 1.0 CB A:CYS137 3.0 44.4 1.0 CE1 A:HIS157 3.0 58.1 1.0 CD2 A:HIS157 3.0 58.3 1.0 CB A:CYS140 3.2 53.4 1.0 CE1 A:HIS153 3.2 64.0 1.0 N A:CYS140 3.7 57.2 1.0 CA A:CYS140 4.1 57.3 1.0 ND1 A:HIS157 4.1 58.1 1.0 CG A:HIS153 4.1 51.7 1.0 CG A:HIS157 4.1 52.5 1.0 ND1 A:HIS153 4.3 54.0 1.0 CA A:CYS137 4.5 47.2 1.0 CB A:ILE139 4.5 60.5 1.0 C A:ILE139 4.7 59.8 1.0 CG2 A:ILE139 4.8 59.4 1.0 C A:CYS140 4.9 55.5 1.0 C A:CYS137 5.0 49.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna


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 Tandem ZIF268 Molecules Complexed to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:55.2 occ:1.00 SG A:CYS168 2.1 50.5 1.0 NE2 A:HIS185 2.1 61.6 1.0 SG A:CYS165 2.2 54.0 1.0 NE2 A:HIS181 2.3 62.6 1.0 CD2 A:HIS181 3.0 49.1 1.0 CE1 A:HIS185 3.1 64.7 1.0 CB A:CYS165 3.1 58.6 1.0 CD2 A:HIS185 3.1 66.7 1.0 CB A:CYS168 3.2 56.6 1.0 CE1 A:HIS181 3.3 61.3 1.0 N A:CYS168 3.6 59.5 1.0 CA A:CYS168 3.9 55.8 1.0 CG A:HIS181 4.2 57.3 1.0 ND1 A:HIS185 4.2 56.9 1.0 CG A:HIS185 4.3 63.5 1.0 ND1 A:HIS181 4.4 63.1 1.0 CA A:CYS165 4.5 57.6 1.0 CB A:ILE167 4.6 61.4 1.0 C A:ILE167 4.6 61.5 1.0 C A:CYS168 4.6 55.7 1.0 N A:GLY169 4.9 58.6 1.0 CA A:ILE167 5.0 62.3 1.0 N A:ARG170 5.0 61.5 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna


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 Tandem ZIF268 Molecules Complexed to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:78.6 occ:1.00 NE2 B:HIS125 2.0 71.8 1.0 NE2 B:HIS129 2.2 90.3 1.0 SG B:CYS107 2.3 70.0 1.0 SG B:CYS112 2.4 85.5 1.0 CE1 B:HIS125 3.0 72.6 1.0 CD2 B:HIS125 3.1 69.8 1.0 CE1 B:HIS129 3.1 95.0 1.0 CD2 B:HIS129 3.1 93.3 1.0 CB B:CYS107 3.3 74.8 1.0 CB B:CYS112 3.3 93.1 1.0 ND1 B:HIS125 4.1 73.6 1.0 CG B:HIS125 4.2 66.4 1.0 ND1 B:HIS129 4.2 92.8 1.0 CG B:HIS129 4.2 92.7 1.0 CB B:VAL109 4.6 97.5 1.0 CA B:CYS107 4.6 76.7 1.0 CB B:ARG114 4.8 86.4 1.0 CA B:CYS112 4.8 92.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna


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 Tandem ZIF268 Molecules Complexed to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:82.5 occ:1.00 NE2 B:HIS157 2.1 79.5 1.0 NE2 B:HIS153 2.2 74.8 1.0 SG B:CYS140 2.3 71.2 1.0 SG B:CYS137 2.4 94.8 1.0 CE1 B:HIS157 2.9 79.0 1.0 CB B:CYS140 3.1 85.7 1.0 CE1 B:HIS153 3.1 74.7 1.0 CD2 B:HIS153 3.2 71.4 1.0 CD2 B:HIS157 3.2 79.5 1.0 CB B:CYS137 3.3 97.0 1.0 N B:CYS140 3.6 89.5 1.0 CA B:CYS140 3.9 86.4 1.0 ND1 B:HIS157 4.1 82.7 1.0 CG B:HIS157 4.2 77.2 1.0 ND1 B:HIS153 4.3 72.2 1.0 CG B:HIS153 4.3 64.6 1.0 C B:ILE139 4.6 92.4 1.0 CB B:ILE139 4.6 95.5 1.0 CA B:CYS137 4.7 98.5 1.0 CG2 B:ILE139 4.9 97.2 1.0 C B:CYS140 4.9 86.7 1.0 CZ B:PHE144 5.0 93.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Tandem ZIF268 Molecules Complexed to Dna


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 Tandem ZIF268 Molecules Complexed to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn206 b:71.5 occ:1.00 NE2 B:HIS185 2.1 51.3 1.0 CE1 B:HIS185 2.2 63.1 1.0 SG B:CYS165 2.3 56.0 1.0 SG B:CYS168 2.4 82.1 1.0 NE2 B:HIS181 2.4 80.2 1.0 CE1 B:HIS181 3.2 79.2 1.0 CB B:CYS165 3.2 60.9 1.0 CB B:CYS168 3.3 85.0 1.0 CD2 B:HIS181 3.4 74.6 1.0 CD2 B:HIS185 3.4 70.5 1.0 N B:CYS168 3.5 85.7 1.0 ND1 B:HIS185 3.6 69.9 1.0 CA B:CYS168 3.9 84.2 1.0 CG B:HIS185 4.2 81.3 1.0 ND1 B:HIS181 4.3 81.6 1.0 CG B:HIS181 4.5 75.5 1.0 C B:ILE167 4.5 85.9 1.0 CA B:CYS165 4.5 64.7 1.0 C B:CYS168 4.6 84.1 1.0 CB B:ILE167 4.6 86.2 1.0 N B:GLY169 4.7 82.8 1.0 CA B:ILE167 4.8 85.3 1.0 N B:ARG170 4.9 84.5 1.0 C B:CYS165 5.0 70.2 1.0 N B:ILE167 5.0 83.4 1.0 CB B:ARG170 5.0 83.2 1.0

E.Peisach, C.O.Pabo. Constraints For Zinc Finger Linker Design As Inferred From X-Ray Crystal Structure of Tandem ZIF268-Dna Complexes J.Mol.Biol. V. 330 1 2003.
ISSN: ISSN 0022-2836
PubMed: 12818197
DOI: 10.1016/S0022-2836(03)00572-2