Zinc in PDB 1nui: Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein

The structure of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein, PDB code: 1nui was solved by M.Kato, T.Ito, G.Wagner, C.C.Richardson, T.Ellenberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.459, 136.460, 85.445, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 27.7

The structure of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein (pdb code 1nui). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein, PDB code: 1nui:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein


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 Primase Fragment of Bacteriophage T7 Primase- Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:84.9 occ:1.00 SG A:CYS20 2.2 31.7 1.0 SG A:CYS36 2.3 19.8 1.0 SG A:CYS39 2.4 22.8 1.0 SG A:CYS17 2.5 29.2 1.0 CB A:CYS20 2.5 27.4 1.0 N A:CYS20 2.9 27.1 1.0 CA A:CYS20 3.2 27.1 1.0 CB A:CYS17 3.3 28.4 1.0 CB A:CYS36 3.3 20.9 1.0 CB A:CYS39 3.3 19.8 1.0 N A:CYS39 3.9 19.9 1.0 N A:GLY21 4.0 25.5 1.0 O A:HOH803 4.0 43.1 1.0 C A:CYS20 4.1 26.5 1.0 C A:ASN19 4.1 27.6 1.0 CB A:ASN19 4.2 28.1 1.0 CA A:CYS39 4.2 19.5 1.0 CB A:VAL38 4.5 19.7 1.0 OD1 A:ASN19 4.5 28.0 1.0 CA A:ASN19 4.6 28.1 1.0 CA A:CYS17 4.7 28.4 1.0 N A:ASN19 4.7 28.7 1.0 CA A:CYS36 4.7 20.9 1.0 CG A:ASN19 4.8 27.9 1.0 OG A:SER22 4.8 18.7 1.0 N A:SER22 4.8 22.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein


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 Primase Fragment of Bacteriophage T7 Primase- Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:83.8 occ:1.00 SG B:CYS36 2.2 21.0 1.0 SG B:CYS20 2.4 27.9 1.0 SG B:CYS39 2.6 25.9 1.0 SG B:CYS17 2.6 8.7 1.0 CB B:CYS39 3.1 22.6 1.0 CB B:CYS20 3.1 26.8 1.0 N B:CYS39 3.2 22.4 1.0 CB B:CYS36 3.3 17.3 1.0 CB B:CYS17 3.4 15.8 1.0 CA B:CYS39 3.7 22.5 1.0 CB B:VAL38 3.7 21.8 1.0 OD1 B:ASN19 4.2 21.8 1.0 C B:VAL38 4.2 22.2 1.0 CA B:CYS20 4.3 26.4 1.0 NZ B:LYS41 4.3 16.4 1.0 CG1 B:VAL38 4.4 19.8 1.0 CA B:VAL38 4.4 21.4 1.0 N B:GLY21 4.5 27.9 1.0 OG B:SER22 4.5 27.2 1.0 N B:CYS20 4.5 25.4 1.0 O B:CYS36 4.5 14.9 1.0 CA B:CYS36 4.6 17.3 1.0 CG2 B:VAL38 4.6 22.0 1.0 C B:CYS39 4.7 21.9 1.0 C B:CYS36 4.7 16.8 1.0 N B:VAL38 4.7 20.9 1.0 C B:CYS20 4.7 27.0 1.0 CA B:CYS17 4.8 16.1 1.0

M.Kato, T.Ito, G.Wagner, C.C.Richardson, T.Ellenberger. Modular Architecture of the Bacteriophage T7 Primase Couples Rna Primer Synthesis to Dna Synthesis Mol.Cell V. 11 1349 2003.
ISSN: ISSN 1097-2765
PubMed: 12769857
DOI: 10.1016/S1097-2765(03)00195-3