Zinc in PDB 3alr: Crystal Structure of Nanos

The structure of Crystal Structure of Nanos, PDB code: 3alr was solved by H.Hashimoto, K.Hara, A.Hishiki, S.Kawaguchi, N.Shichijo, K.Nakamura, S.Unzai, Y.Tamaru, T.Shimizu, M.Sato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	100.961, 100.961, 71.577, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.8

The binding sites of Zinc atom in the Crystal Structure of Nanos (pdb code 3alr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Nanos, PDB code: 3alr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:33.0 occ:1.00 NE2 A:HIS108 2.1 45.2 1.0 SG A:CYS95 2.3 50.1 1.0 SG A:CYS119 2.3 49.7 1.0 SG A:CYS92 2.3 52.4 1.0 CD2 A:HIS108 3.1 42.2 1.0 CE1 A:HIS108 3.1 44.1 1.0 CB A:CYS92 3.2 51.8 1.0 CB A:CYS119 3.3 49.2 1.0 CB A:CYS95 3.3 53.8 1.0 N A:CYS95 3.9 50.7 1.0 CA A:CYS119 4.1 50.9 1.0 CA A:CYS95 4.1 54.3 1.0 ND1 A:HIS108 4.2 43.0 1.0 CG A:HIS108 4.2 43.3 1.0 CD1 A:PHE94 4.5 51.5 1.0 CD A:PRO120 4.5 53.1 1.0 CD1 A:TYR121 4.7 55.2 1.0 CA A:CYS92 4.7 51.7 1.0 CB A:PHE94 4.7 53.3 1.0 C A:CYS119 4.8 51.0 1.0 C A:PHE94 4.9 60.9 1.0 N A:PRO120 4.9 52.4 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:36.8 occ:1.00 NE2 A:HIS138 2.1 59.7 1.0 SG A:CYS143 2.3 61.3 1.0 SG A:CYS127 2.3 62.9 1.0 SG A:CYS130 2.3 64.0 1.0 CD2 A:HIS138 3.1 56.1 1.0 CB A:CYS127 3.1 64.3 1.0 CE1 A:HIS138 3.1 61.7 1.0 CB A:CYS143 3.2 58.4 1.0 CB A:CYS130 3.4 76.7 1.0 CA A:CYS143 3.8 57.6 1.0 N A:CYS130 3.8 79.2 1.0 CA A:CYS130 4.2 74.6 1.0 CG A:HIS138 4.2 59.1 1.0 ND1 A:HIS138 4.2 58.4 1.0 CD A:PRO144 4.3 68.0 1.0 CB A:LEU129 4.5 75.4 1.0 CA A:CYS127 4.6 62.5 1.0 C A:LEU129 4.7 86.2 1.0 CB A:ALA132 4.7 68.6 1.0 C A:CYS143 4.7 56.3 1.0 C A:CYS130 4.8 76.3 1.0 N A:PRO144 4.8 65.2 1.0 N A:CYS143 4.9 56.8 1.0 CA A:LEU129 4.9 80.8 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:44.6 occ:1.00 ND1 A:HIS97 2.0 69.4 1.0 CE1 A:HIS97 2.9 71.8 1.0 CG A:HIS97 3.0 64.6 1.0 CB A:HIS97 3.5 61.1 1.0 CA A:HIS97 3.8 64.8 1.0 NE2 A:HIS97 4.0 72.2 1.0 CD2 A:HIS97 4.1 67.4 1.0 N A:HIS97 4.8 54.7 1.0 O A:HIS97 4.8 68.7 1.0 C A:HIS97 4.9 67.7 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:38.7 occ:1.00 NE2 B:HIS108 2.1 47.1 1.0 SG B:CYS95 2.3 48.7 1.0 SG B:CYS92 2.3 44.0 1.0 SG B:CYS119 2.3 43.6 1.0 CD2 B:HIS108 3.1 45.8 1.0 CE1 B:HIS108 3.1 45.5 1.0 CB B:CYS119 3.2 43.2 1.0 CB B:CYS92 3.2 46.0 1.0 CB B:CYS95 3.3 48.7 1.0 N B:CYS95 3.8 46.5 1.0 CA B:CYS119 4.0 44.3 1.0 CA B:CYS95 4.1 45.2 1.0 ND1 B:HIS108 4.2 45.0 1.0 CG B:HIS108 4.2 40.3 1.0 CD B:PRO120 4.5 42.4 1.0 CB B:PHE94 4.5 44.2 1.0 CA B:CYS92 4.7 47.9 1.0 CD1 B:TYR121 4.7 58.3 1.0 CD2 B:PHE94 4.7 44.9 1.0 C B:PHE94 4.7 47.3 1.0 C B:CYS119 4.8 46.2 1.0 N B:PRO120 4.9 43.9 1.0 O B:CYS92 5.0 46.0 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:34.4 occ:1.00 NE2 B:HIS138 2.2 55.8 1.0 SG B:CYS130 2.2 51.1 1.0 SG B:CYS143 2.3 55.6 1.0 SG B:CYS127 2.3 50.3 1.0 CD2 B:HIS138 3.1 52.4 1.0 CB B:CYS143 3.1 58.6 1.0 CB B:CYS127 3.1 46.5 1.0 CE1 B:HIS138 3.2 55.8 1.0 CB B:CYS130 3.3 53.3 1.0 N B:CYS130 3.8 47.7 1.0 CA B:CYS143 3.8 54.7 1.0 CA B:CYS130 4.0 53.3 1.0 CG B:HIS138 4.3 51.6 1.0 ND1 B:HIS138 4.3 47.8 1.0 CD B:PRO144 4.4 74.6 1.0 CB B:LEU129 4.5 56.1 1.0 CA B:CYS127 4.6 48.4 1.0 C B:LEU129 4.6 49.6 1.0 CB B:ALA132 4.6 50.2 1.0 C B:CYS130 4.7 51.5 1.0 C B:CYS143 4.7 63.5 1.0 CB B:MET145 4.8 0.3 1.0 N B:GLY131 4.8 52.3 1.0 N B:ALA132 4.8 53.7 1.0 N B:PRO144 4.9 70.5 1.0 N B:LEU129 4.9 49.9 1.0 CA B:LEU129 4.9 53.8 1.0 N B:CYS143 4.9 62.9 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:39.0 occ:1.00 NE2 C:HIS108 2.2 42.9 1.0 SG C:CYS92 2.3 46.0 1.0 SG C:CYS95 2.3 47.2 1.0 SG C:CYS119 2.4 44.2 1.0 CD2 C:HIS108 3.1 43.9 1.0 CB C:CYS92 3.2 48.1 1.0 CE1 C:HIS108 3.2 42.1 1.0 CB C:CYS119 3.3 44.3 1.0 CB C:CYS95 3.4 47.7 1.0 N C:CYS95 3.8 50.9 1.0 CA C:CYS119 4.1 44.0 1.0 CA C:CYS95 4.1 50.8 1.0 CG C:HIS108 4.3 44.4 1.0 ND1 C:HIS108 4.3 44.4 1.0 CD C:PRO120 4.5 51.0 1.0 CD2 C:PHE94 4.6 48.6 1.0 CA C:CYS92 4.6 47.6 1.0 CB C:PHE94 4.6 51.4 1.0 C C:PHE94 4.8 51.1 1.0 C C:CYS119 4.8 48.0 1.0 CD1 C:TYR121 4.9 52.6 1.0 N C:PRO120 4.9 47.6 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:40.8 occ:1.00 SG C:CYS127 2.2 54.2 1.0 NE2 C:HIS138 2.2 61.1 1.0 SG C:CYS143 2.3 59.6 1.0 SG C:CYS130 2.3 56.9 1.0 CB C:CYS127 3.0 52.1 1.0 CB C:CYS143 3.1 59.6 1.0 CE1 C:HIS138 3.2 64.5 1.0 CD2 C:HIS138 3.2 59.0 1.0 CB C:CYS130 3.3 55.8 1.0 N C:CYS130 3.7 56.2 1.0 CA C:CYS143 3.8 64.2 1.0 CA C:CYS130 4.0 58.7 1.0 O C:HOH168 4.1 43.0 1.0 CD C:PRO144 4.3 73.8 1.0 ND1 C:HIS138 4.3 59.1 1.0 CB C:LEU129 4.4 60.7 1.0 CG C:HIS138 4.4 59.7 1.0 CA C:CYS127 4.5 53.0 1.0 C C:LEU129 4.6 58.5 1.0 CB C:ALA132 4.6 50.8 1.0 C C:CYS130 4.7 54.3 1.0 C C:CYS143 4.7 62.4 1.0 N C:GLY131 4.8 54.1 1.0 N C:PRO144 4.8 76.2 1.0 CA C:LEU129 4.8 56.3 1.0 N C:LEU129 4.9 61.4 1.0 C C:CYS127 4.9 55.5 1.0 N C:CYS143 4.9 66.4 1.0 N C:ALA132 4.9 57.5 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Nanos


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 Nanos within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:35.1 occ:1.00 NE2 D:HIS97 2.1 50.1 1.0 SG A:CYS151 2.3 54.9 1.0 CE1 D:HIS97 3.1 50.9 1.0 CB A:CYS151 3.1 53.3 1.0 CD2 D:HIS97 3.1 51.4 1.0 ND1 D:HIS97 4.2 46.2 1.0 CG D:HIS97 4.3 48.3 1.0 CA A:CYS151 4.3 58.1 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Nanos


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Nanos within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:37.9 occ:1.00 NE2 D:HIS108 2.1 45.3 1.0 SG D:CYS95 2.3 46.6 1.0 SG D:CYS92 2.3 43.7 1.0 SG D:CYS119 2.3 46.2 1.0 CD2 D:HIS108 3.1 45.0 1.0 CE1 D:HIS108 3.1 44.6 1.0 CB D:CYS92 3.2 45.7 1.0 CB D:CYS119 3.2 43.6 1.0 CB D:CYS95 3.3 42.8 1.0 N D:CYS95 3.8 44.3 1.0 CA D:CYS119 4.0 42.2 1.0 CA D:CYS95 4.1 43.7 1.0 ND1 D:HIS108 4.2 42.5 1.0 CG D:HIS108 4.3 44.7 1.0 CB D:PHE94 4.5 48.2 1.0 CA D:CYS92 4.6 45.2 1.0 CD D:PRO120 4.6 49.6 1.0 CD1 D:TYR121 4.7 55.7 1.0 CD2 D:PHE94 4.7 53.1 1.0 C D:CYS119 4.7 48.4 1.0 C D:PHE94 4.8 46.2 1.0 N D:PRO120 4.9 48.8 1.0 C D:CYS92 4.9 47.0 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Nanos


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Nanos within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:52.9 occ:1.00 SG D:CYS130 2.0 81.6 1.0 NE2 D:HIS138 2.1 73.1 1.0 SG D:CYS127 2.3 82.3 1.0 SG D:CYS143 2.4 98.9 1.0 CB D:CYS127 3.1 72.3 1.0 CD2 D:HIS138 3.1 69.3 1.0 CE1 D:HIS138 3.1 77.2 1.0 CB D:CYS143 3.2 97.3 1.0 CB D:CYS130 3.2 90.3 1.0 N D:CYS130 3.6 91.9 1.0 CA D:CYS143 3.9 92.1 1.0 CA D:CYS130 4.0 92.2 1.0 ND1 D:HIS138 4.2 76.1 1.0 CG D:HIS138 4.2 72.4 1.0 CB D:LEU129 4.4 0.4 1.0 CD D:PRO144 4.4 0.4 1.0 CA D:CYS127 4.5 81.1 1.0 CB D:ALA132 4.6 76.7 1.0 C D:LEU129 4.6 98.0 1.0 N D:PRO144 4.7 0.8 1.0 C D:CYS130 4.7 92.3 1.0 N D:GLY131 4.7 91.1 1.0 C D:CYS143 4.7 95.6 1.0 N D:ALA132 4.8 81.2 1.0 CA D:LEU129 4.9 97.7 1.0 N D:LEU129 5.0 93.0 1.0

H.Hashimoto, K.Hara, A.Hishiki, S.Kawaguchi, N.Shichijo, K.Nakamura, S.Unzai, Y.Tamaru, T.Shimizu, M.Sato. Crystal Structure of Zinc-Finger Domain of Nanos and Its Functional Implications Embo Rep. V. 11 848 2010.
ISSN: ISSN 1469-221X
PubMed: 20948543
DOI: 10.1038/EMBOR.2010.155