Zinc in PDB 1zme: Crystal Structure of PUT3/Dna Complex

The structure of Crystal Structure of PUT3/Dna Complex, PDB code: 1zme was solved by K.Swaminathan, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.50
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	121.650, 121.650, 39.100, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 29.2

The structure of Crystal Structure of PUT3/Dna Complex also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PUT3/Dna Complex (pdb code 1zme). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of PUT3/Dna Complex, PDB code: 1zme:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of PUT3/Dna Complex


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 PUT3/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1 b:17.2 occ:1.00 SG C:CYS37 2.3 16.7 1.0 SG C:CYS44 2.3 16.6 1.0 SG C:CYS50 2.3 20.6 1.0 SG C:CYS34 2.4 20.3 1.0 ZN C:ZN2 3.0 23.8 1.0 CB C:CYS37 3.2 16.6 1.0 CB C:CYS44 3.3 17.6 1.0 CB C:CYS50 3.4 27.0 1.0 CB C:CYS34 3.8 17.8 1.0 CA C:CYS44 3.9 17.8 1.0 N C:CYS34 4.0 18.6 1.0 N C:CYS37 4.2 14.2 1.0 CD C:PRO45 4.3 21.3 1.0 CA C:CYS37 4.3 15.4 1.0 CA C:CYS34 4.5 19.0 1.0 O C:HOH102 4.5 20.0 1.0 SG C:CYS53 4.6 19.6 1.0 O C:CYS34 4.6 21.4 1.0 OH C:TYR62 4.6 21.8 1.0 C C:CYS44 4.7 21.6 1.0 CB C:LYS52 4.8 16.1 1.0 N C:PRO45 4.8 22.3 1.0 CA C:CYS50 4.8 27.7 1.0 SG C:CYS60 4.8 21.5 1.0 C C:CYS34 4.9 19.0 1.0 CG C:PRO45 5.0 20.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of PUT3/Dna Complex


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 PUT3/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2 b:23.8 occ:1.00 SG C:CYS53 2.3 19.6 1.0 SG C:CYS50 2.3 20.6 1.0 SG C:CYS34 2.3 20.3 1.0 SG C:CYS60 2.4 21.5 1.0 ZN C:ZN1 3.0 17.2 1.0 CB C:CYS60 3.3 23.8 1.0 CB C:CYS53 3.4 21.2 1.0 CB C:CYS34 3.4 17.8 1.0 CB C:CYS50 3.6 27.0 1.0 CA C:CYS60 3.7 24.3 1.0 N C:CYS50 3.8 28.6 1.0 O C:HOH104 3.9 38.5 1.0 CA C:CYS50 4.3 27.7 1.0 N C:CYS53 4.3 18.8 1.0 O C:HOH102 4.3 20.0 1.0 O C:CYS50 4.4 26.7 1.0 CA C:CYS53 4.4 20.0 1.0 SG C:CYS37 4.5 16.7 1.0 C C:CYS60 4.6 21.5 1.0 CB C:SER36 4.7 15.6 1.0 C C:CYS50 4.7 26.8 1.0 N C:GLU61 4.7 21.6 1.0 N C:CYS60 4.8 24.1 1.0 SG C:CYS44 4.8 16.6 1.0 CA C:CYS34 4.8 19.0 1.0 C C:PRO49 4.9 31.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of PUT3/Dna Complex


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 PUT3/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:22.4 occ:1.00 SG D:CYS37 2.2 17.6 1.0 SG D:CYS50 2.3 20.6 1.0 SG D:CYS44 2.3 20.2 1.0 SG D:CYS34 2.4 21.1 1.0 ZN D:ZN2 3.0 21.2 1.0 CB D:CYS37 3.3 21.7 1.0 CB D:CYS50 3.4 21.9 1.0 CB D:CYS44 3.5 24.5 1.0 CB D:CYS34 3.7 20.3 1.0 CD D:PRO45 4.0 18.4 1.0 CA D:CYS44 4.0 20.8 1.0 N D:CYS34 4.0 18.3 1.0 N D:CYS37 4.4 23.9 1.0 CA D:CYS34 4.4 23.2 1.0 CA D:CYS37 4.4 21.9 1.0 CG D:PRO45 4.5 17.3 1.0 CB D:LYS52 4.6 27.7 1.0 SG D:CYS53 4.6 19.6 1.0 N D:PRO45 4.6 20.5 1.0 CG D:LYS52 4.7 21.3 1.0 C D:CYS44 4.7 20.8 1.0 O D:HOH106 4.8 24.9 1.0 SG D:CYS60 4.8 21.1 1.0 OH D:TYR62 4.8 27.6 1.0 CA D:CYS50 4.8 26.9 1.0 O D:CYS34 5.0 25.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of PUT3/Dna Complex


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 PUT3/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2 b:21.2 occ:1.00 SG D:CYS60 2.3 21.1 1.0 SG D:CYS53 2.3 19.6 1.0 SG D:CYS34 2.4 21.1 1.0 SG D:CYS50 2.4 20.6 1.0 ZN D:ZN1 3.0 22.4 1.0 CB D:CYS60 3.2 30.0 1.0 CB D:CYS53 3.4 25.3 1.0 CB D:CYS34 3.4 20.3 1.0 CB D:CYS50 3.5 21.9 1.0 CA D:CYS60 3.8 33.3 1.0 N D:CYS50 3.9 26.9 1.0 CA D:CYS50 4.2 26.9 1.0 N D:CYS53 4.3 29.0 1.0 CA D:CYS53 4.4 28.9 1.0 O D:CYS50 4.5 34.5 1.0 SG D:CYS37 4.5 17.6 1.0 C D:CYS50 4.6 31.2 1.0 OH D:TYR62 4.6 27.6 1.0 O D:HOH106 4.7 24.9 1.0 N D:CYS60 4.8 35.5 1.0 C D:CYS60 4.8 35.9 1.0 SG D:CYS44 4.8 20.2 1.0 CA D:CYS34 4.8 23.2 1.0 CB D:SER36 4.9 24.8 1.0 O D:HOH113 4.9 23.9 1.0 C D:PRO49 5.0 25.9 1.0

K.Swaminathan, P.Flynn, R.J.Reece, R.Marmorstein. Crystal Structure of A PUT3-Dna Complex Reveals A Novel Mechanism For Dna Recognition By A Protein Containing A ZN2CYS6 Binuclear Cluster. Nat.Struct.Biol. V. 4 751 1997.
ISSN: ISSN 1072-8368
PubMed: 9303004
DOI: 10.1038/NSB0997-751