Zinc in PDB 6kr6: Crystal Structure of Drosophila Piwi

The structure of Crystal Structure of Drosophila Piwi, PDB code: 6kr6 was solved by S.Yamaguchi, A.Oe, K.Yamashita, S.Hirano, N.Mastumoto, R.Ishitani, H.Nishimasu, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.090, 115.640, 119.890, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 25.9

The structure of Crystal Structure of Drosophila Piwi also contains other interesting chemical elements:

Mercury

(Hg)

7 atoms

The binding sites of Zinc atom in the Crystal Structure of Drosophila Piwi (pdb code 6kr6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Drosophila Piwi, PDB code: 6kr6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Drosophila Piwi


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 Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:71.1 occ:0.91 OP1 B:U3 2.0 76.8 1.0 OE1 A:GLN589 2.0 80.3 1.0 O A:LEU843 2.2 76.0 1.0 OP2 B:U1 2.3 77.6 1.0 OP3 B:U1 2.3 85.7 1.0 OXT A:LEU843 2.5 79.8 1.0 C A:LEU843 2.7 79.5 1.0 P B:U1 2.8 76.4 1.0 CD A:GLN589 3.2 81.8 1.0 P B:U3 3.2 75.5 1.0 O3' B:A2 3.7 80.2 1.0 NE2 A:GLN589 3.7 79.7 1.0 O5' B:U1 3.9 71.2 1.0 C5' B:U1 4.0 82.5 1.0 OP1 B:U1 4.0 74.5 1.0 OP2 B:U3 4.0 79.5 1.0 CA A:LEU843 4.3 69.4 1.0 NZ A:LYS593 4.3 73.1 1.0 ND2 A:ASN803 4.3 68.5 1.0 CG A:GLN589 4.4 73.4 1.0 O5' B:U3 4.4 74.6 1.0 OE1 A:GLN567 4.6 78.1 1.0 C5' B:U3 4.7 79.2 1.0 NE2 A:GLN567 4.7 75.1 1.0 CE A:LYS593 4.8 70.4 1.0 CB A:LEU843 4.9 66.8 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Drosophila Piwi


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 Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:0.3 occ:1.00 NE2 A:HIS244 2.0 0.8 1.0 CE1 A:HIS244 2.9 0.4 1.0 CD2 A:HIS244 3.1 0.5 1.0 O A:ASP749 3.3 0.3 1.0 ND1 A:HIS244 4.1 0.8 1.0 CG A:HIS244 4.2 0.3 1.0 C A:ASP749 4.5 0.1 1.0 CG2 A:VAL750 4.7 0.5 1.0 CA A:VAL750 4.7 0.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Drosophila Piwi


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 Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:0.7 occ:1.00 ND1 A:HIS829 2.0 0.3 1.0 CE1 A:HIS829 3.0 96.6 1.0 CG A:HIS829 3.1 97.7 1.0 CB A:HIS829 3.5 91.0 1.0 O A:ASN827 3.6 0.1 1.0 NE2 A:HIS829 4.1 91.9 1.0 CD2 A:HIS829 4.2 90.7 1.0 O A:LEU828 4.3 99.6 1.0 C A:LEU828 4.6 93.9 1.0 C A:ASN827 4.6 97.9 1.0 CA A:HIS829 4.7 92.8 1.0 N A:HIS829 4.8 93.1 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Drosophila Piwi


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 Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn910 b:99.2 occ:0.98 NE2 A:HIS118 2.0 0.3 1.0 NE2 A:HIS116 2.0 95.9 1.0 OE1 A:GLN152 2.1 0.3 1.0 CE1 A:HIS118 2.6 0.2 1.0 CE1 A:HIS116 3.0 99.3 1.0 CD2 A:HIS118 3.0 0.2 1.0 CD2 A:HIS116 3.1 92.7 1.0 CD A:GLN152 3.1 0.6 1.0 NE2 A:GLN152 3.5 0.6 1.0 ND1 A:HIS118 3.6 0.5 1.0 CG A:HIS118 3.9 0.5 1.0 ND1 A:HIS116 4.1 0.6 1.0 CG A:HIS116 4.2 97.2 1.0 CG A:GLN152 4.5 1.0 1.0 CG1 A:VAL183 4.5 0.7 1.0 CG2 A:VAL183 4.6 0.9 1.0 CB A:GLN152 4.8 0.1 1.0 CB A:VAL183 5.0 0.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Drosophila Piwi


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 Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn911 b:0.8 occ:1.00 NE2 A:HIS446 2.1 0.1 1.0 CE1 A:HIS446 3.0 0.8 1.0 CD2 A:HIS446 3.1 0.3 1.0 ND1 A:HIS446 4.1 0.4 1.0 CG A:HIS446 4.2 1.0 1.0 OD1 A:ASN447 4.6 0.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Drosophila Piwi


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 Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn912 b:0.6 occ:0.79 OD1 A:ASP685 2.0 94.6 1.0 OD1 A:ASP614 2.0 0.1 1.0 OD2 A:ASP614 2.0 87.8 1.0 CG A:ASP614 2.3 95.1 1.0 CG A:ASP685 2.7 92.5 1.0 OD2 A:ASP685 3.3 0.3 1.0 CB A:ASP685 3.6 83.8 1.0 CB A:ASP614 3.8 71.9 1.0 CD1 A:ILE615 4.0 0.2 1.0 O A:ILE615 4.1 76.5 1.0 O A:ASP685 4.3 93.1 1.0 N A:ILE615 4.3 80.6 1.0 C A:ASP685 4.5 94.0 1.0 CA A:ASP614 4.6 70.4 1.0 CA A:ASP685 4.6 85.2 1.0 CG1 A:ILE615 4.8 96.1 1.0 CG A:LYS818 5.0 84.0 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn913 b:1.0 occ:0.77 OD2 A:ASP473 2.0 0.9 1.0 OD1 A:ASP473 2.0 0.8 1.0 OD1 A:ASP476 2.0 0.0 1.0 CG A:ASP473 2.0 1.0 1.0 CG A:ASP476 2.4 0.8 1.0 CB A:ASP476 2.7 1.0 1.0 NZ A:LYS537 2.9 0.2 1.0 OD2 A:ASP476 3.3 0.4 1.0 CB A:ASP473 3.3 0.6 1.0 CE A:LYS537 3.8 0.3 1.0 CA A:ASP476 4.2 0.2 1.0 CA A:ASP473 4.3 95.7 1.0 O A:ASP473 4.7 0.9 1.0 C A:ASP473 4.8 98.5 1.0 N A:ASP476 4.8 0.6 1.0 C A:ASP476 4.9 0.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Drosophila Piwi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Drosophila Piwi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn914 b:0.0 occ:1.00 NE2 A:HIS488 2.0 0.7 1.0 CD2 A:HIS488 2.8 0.8 1.0 CE1 A:HIS488 2.9 0.9 1.0 CG A:HIS488 3.9 0.9 1.0 ND1 A:HIS488 3.9 0.1 1.0 OG1 A:THR492 4.6 96.3 1.0

S.Yamaguchi, A.Oe, K.Nishida, K.Yamashita, A.Kajiya, S.Hirano, N.Matsumoto, N.Dohmae, R.Ishitani, K.Saito, H.Siomi, H.Nishimasu, M.Siomi, O.Nureki. Crystal Structure of Drosophila Piwi. Nat Commun V. 11 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-14687-1