Zinc in PDB 4bpx: Crystal Structure of Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha

All present enzymatic activity of Crystal Structure of Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha:
2.7.7.7;

The structure of Crystal Structure of Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha, PDB code: 4bpx was solved by M.L.Kilkenny, R.L.Perera, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.325 / 3.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	120.680, 70.701, 127.160, 90.00, 105.83, 90.00
R / Rfree (%)	23.44 / 26.69

The binding sites of Zinc atom in the Crystal Structure of Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha (pdb code 4bpx). 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 Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha, PDB code: 4bpx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha


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 Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn430 b:1.0 occ:1.00 SG A:CYS121 2.3 0.2 1.0 SG A:CYS122 2.3 0.4 1.0 SG A:CYS128 2.3 0.0 1.0 SG A:CYS131 2.4 0.0 1.0 HB2 A:CYS121 2.6 0.8 1.0 HB3 A:CYS131 2.9 0.7 1.0 CB A:CYS121 3.0 0.0 1.0 H A:CYS128 3.1 0.6 1.0 H A:CYS131 3.2 0.6 1.0 CB A:CYS131 3.2 0.9 1.0 HB3 A:CYS128 3.2 0.2 1.0 CB A:CYS128 3.3 0.6 1.0 HB2 A:CYS122 3.4 0.1 1.0 N A:CYS128 3.5 0.3 1.0 H A:CYS122 3.5 0.3 1.0 CB A:CYS122 3.5 0.7 1.0 HB3 A:CYS121 3.6 0.8 1.0 N A:CYS131 3.7 0.7 1.0 N A:CYS122 3.7 0.7 1.0 HH11 A:ARG119 3.8 0.5 1.0 HB2 A:LYS130 3.8 0.6 1.0 CA A:CYS128 3.9 0.2 1.0 HA A:ILE127 3.9 0.3 1.0 HB2 A:CYS131 3.9 0.7 1.0 CA A:CYS131 4.0 0.3 1.0 C A:CYS121 4.1 0.5 1.0 CA A:CYS121 4.1 0.0 1.0 HD2 A:ARG119 4.1 0.1 1.0 HB2 A:CYS128 4.1 0.2 1.0 C A:ILE127 4.2 0.1 1.0 CA A:CYS122 4.3 0.9 1.0 HB3 A:CYS122 4.3 0.1 1.0 HE22 A:GLN231 4.3 0.1 1.0 O A:CYS128 4.3 0.9 1.0 C A:CYS128 4.3 0.1 1.0 H A:LYS130 4.3 0.4 1.0 H A:CYS121 4.4 0.4 1.0 NH1 A:ARG119 4.5 0.1 1.0 CA A:ILE127 4.6 0.9 1.0 C A:LYS130 4.6 0.0 1.0 HA A:CYS131 4.6 0.9 1.0 HE3 A:LYS130 4.6 0.7 1.0 HH12 A:ARG119 4.7 0.5 1.0 CB A:LYS130 4.7 1.0 1.0 N A:CYS121 4.8 0.3 1.0 HA A:CYS128 4.8 0.8 1.0 HA A:CYS122 4.8 0.7 1.0 N A:LYS130 4.8 0.1 1.0 HA A:CYS121 4.8 0.8 1.0 O A:CYS121 4.9 0.8 1.0 HB2 A:ARG119 4.9 0.1 1.0 CA A:LYS130 5.0 0.6 1.0 CD A:ARG119 5.0 0.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha


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 Human Primase in Complex with the Primase-Binding Motif of Dna Polymerase Alpha within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn430 b:0.6 occ:1.00 SG C:CYS128 2.3 0.8 1.0 SG C:CYS121 2.3 0.3 1.0 SG C:CYS131 2.3 0.9 1.0 SG C:CYS122 2.3 0.5 1.0 HB2 C:CYS121 2.5 0.1 1.0 H C:CYS128 2.7 0.5 1.0 HB3 C:CYS131 2.8 0.2 1.0 CB C:CYS121 3.0 0.8 1.0 HB3 C:CYS128 3.1 1.0 1.0 CB C:CYS131 3.1 0.5 1.0 N C:CYS128 3.2 0.5 1.0 H C:CYS131 3.2 0.7 1.0 CB C:CYS128 3.2 0.8 1.0 HB2 C:CYS122 3.5 0.6 1.0 HB3 C:CYS121 3.6 0.1 1.0 CB C:CYS122 3.6 0.5 1.0 H C:CYS122 3.6 0.0 1.0 CA C:CYS128 3.6 0.1 1.0 N C:CYS131 3.7 0.6 1.0 HA C:ILE127 3.7 0.6 1.0 N C:CYS122 3.8 0.9 1.0 HB2 C:LYS130 3.9 0.2 1.0 HB2 C:CYS131 3.9 0.2 1.0 HE22 C:GLN231 3.9 0.1 1.0 O C:CYS128 3.9 0.8 1.0 C C:ILE127 4.1 0.0 1.0 CA C:CYS131 4.1 0.8 1.0 C C:CYS128 4.1 0.4 1.0 C C:CYS121 4.1 0.6 1.0 HB2 C:CYS128 4.1 1.0 1.0 CA C:CYS121 4.1 0.6 1.0 HH11 C:ARG119 4.1 0.3 1.0 H C:LYS130 4.3 0.7 1.0 CA C:CYS122 4.3 0.8 1.0 HB3 C:CYS122 4.4 0.6 1.0 HD2 C:ARG119 4.4 0.4 1.0 CA C:ILE127 4.4 0.5 1.0 H C:CYS121 4.5 0.8 1.0 HA C:CYS128 4.5 0.6 1.0 HA C:CYS131 4.6 1.0 1.0 NE2 C:GLN231 4.6 0.5 1.0 C C:LYS130 4.6 0.2 1.0 HE21 C:GLN231 4.7 0.1 1.0 N C:LYS130 4.7 0.6 1.0 HE3 C:LYS130 4.7 0.6 1.0 CB C:LYS130 4.8 0.4 1.0 N C:CYS121 4.8 0.9 1.0 HA C:CYS121 4.8 0.1 1.0 HA C:CYS122 4.8 0.1 1.0 O C:CYS121 4.8 0.5 1.0 NH1 C:ARG119 4.9 0.9 1.0 O C:ILE127 4.9 0.6 1.0 CA C:LYS130 5.0 0.8 1.0 HB2 C:ARG119 5.0 0.9 1.0

M.L.Kilkenny, M.Longo, R.L.Perera, L.Pellegrini. Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering Proc.Natl.Acad.Sci.Usa V. 110 15961 2013.
ISSN: ISSN 0027-8424
PubMed: 24043831
DOI: 10.1073/PNAS.1311185110