Zinc in PDB 3w5k: Crystal Structure of SNAIL1 and Importin Beta Complex

The structure of Crystal Structure of SNAIL1 and Importin Beta Complex, PDB code: 3w5k was solved by S.Choi, E.Yamashita, N.Yasuhara, J.Song, S.Y.Son, Y.H.Won, Y.S.Shin, T.Sekimoto, I.Y.Park, Y.Yoneda, S.J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	228.210, 77.528, 72.019, 90.00, 100.96, 90.00
R / Rfree (%)	21.5 / 26.4

The binding sites of Zinc atom in the Crystal Structure of SNAIL1 and Importin Beta Complex (pdb code 3w5k). 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 SNAIL1 and Importin Beta Complex, PDB code: 3w5k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of SNAIL1 and Importin Beta 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 SNAIL1 and Importin Beta Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:0.1 occ:1.00 NE2 B:HIS172 2.1 0.9 1.0 SG B:CYS156 2.2 0.5 1.0 NE2 B:HIS176 2.2 0.6 1.0 SG B:CYS159 2.3 0.6 1.0 NZ B:LYS161 2.5 0.6 1.0 CE1 B:HIS176 2.8 0.3 1.0 CD2 B:HIS172 2.8 0.3 1.0 CD2 B:HIS176 3.2 0.1 1.0 CE1 B:HIS172 3.2 0.1 1.0 CB B:CYS156 3.3 0.3 1.0 N B:CYS159 3.6 0.1 1.0 CE B:LYS161 3.7 0.7 1.0 CB B:CYS159 3.8 0.6 1.0 ND1 B:HIS176 3.8 0.8 1.0 CB B:TYR158 3.9 0.7 1.0 CG B:HIS176 4.0 0.8 1.0 CG B:HIS172 4.1 0.0 1.0 CA B:CYS159 4.1 0.3 1.0 ND1 B:HIS172 4.2 0.6 1.0 C B:TYR158 4.2 0.4 1.0 CA B:TYR158 4.5 1.0 1.0 CA B:CYS156 4.7 0.5 1.0 N B:TYR158 4.7 0.1 1.0 C B:CYS159 4.7 0.8 1.0 O B:CYS156 4.9 0.7 1.0 C B:CYS156 5.0 0.8 1.0 CD B:LYS161 5.0 0.7 1.0 N B:ASN160 5.0 0.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of SNAIL1 and Importin Beta 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 SNAIL1 and Importin Beta Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:0.1 occ:1.00 NE2 B:HIS198 2.0 98.5 1.0 NE2 B:HIS202 2.1 0.1 1.0 SG B:CYS185 2.3 0.4 1.0 SG B:CYS182 2.3 0.8 1.0 CD2 B:HIS198 2.8 96.8 1.0 CD2 B:HIS202 2.9 0.0 1.0 CE1 B:HIS198 3.1 96.0 1.0 CE1 B:HIS202 3.2 1.0 1.0 CB B:THR184 3.4 0.8 1.0 CB B:CYS182 3.5 0.5 1.0 CB B:CYS185 3.8 0.2 1.0 C B:THR184 3.8 0.2 1.0 CG2 B:THR184 3.9 0.2 1.0 N B:CYS185 3.9 0.1 1.0 CG B:HIS198 4.0 94.7 1.0 CA B:THR184 4.0 0.5 1.0 ND1 B:HIS198 4.1 93.4 1.0 CG B:HIS202 4.2 0.9 1.0 N B:THR184 4.2 0.2 1.0 O B:THR184 4.2 0.3 1.0 ND1 B:HIS202 4.3 0.2 1.0 OG1 B:THR184 4.4 0.3 1.0 CA B:CYS185 4.5 0.1 1.0 CG2 B:VAL199 4.5 93.7 1.0 CA B:VAL199 4.9 99.3 1.0 CA B:CYS182 5.0 0.9 1.0 O B:HIS198 5.0 90.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of SNAIL1 and Importin Beta 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 SNAIL1 and Importin Beta Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:0.2 occ:1.00 NE2 B:HIS230 2.0 0.2 1.0 NE2 B:HIS226 2.1 84.5 1.0 SG B:CYS213 2.2 0.8 1.0 SG B:CYS210 2.5 0.3 1.0 CE1 B:HIS230 2.9 0.5 1.0 CB B:CYS213 3.0 98.0 1.0 CE1 B:HIS226 3.0 76.4 1.0 CD2 B:HIS230 3.0 0.1 1.0 CD2 B:HIS226 3.1 78.7 1.0 CB B:CYS210 3.4 84.9 1.0 N B:CYS213 3.5 0.8 1.0 CA B:CYS213 3.8 0.4 1.0 ND1 B:HIS230 4.1 0.4 1.0 CB B:HIS212 4.1 0.6 1.0 ND1 B:HIS226 4.1 65.6 1.0 CG B:HIS230 4.1 0.5 1.0 CG B:HIS226 4.2 68.8 1.0 C B:HIS212 4.3 0.8 1.0 C B:CYS213 4.5 0.7 1.0 CA B:HIS212 4.6 0.1 1.0 N B:SER214 4.8 0.2 1.0 N B:HIS212 4.8 0.4 1.0 CA B:CYS210 4.8 93.1 1.0 CG B:HIS212 4.8 0.6 1.0 CD2 B:HIS212 4.8 0.2 1.0 CB B:ARG215 4.9 0.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of SNAIL1 and Importin Beta 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 SNAIL1 and Importin Beta Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:57.6 occ:1.00 NE2 B:HIS254 2.1 47.4 1.0 SG B:CYS241 2.2 54.0 1.0 SG B:CYS238 2.3 62.1 1.0 SG B:CYS259 2.3 70.0 1.0 CE1 B:HIS254 3.0 45.4 1.0 CD2 B:HIS254 3.1 47.4 1.0 CB B:CYS238 3.2 37.1 1.0 CB B:CYS259 3.3 75.1 1.0 CB B:CYS241 3.3 59.3 1.0 N B:CYS241 3.7 57.2 1.0 CA B:CYS259 4.0 69.6 1.0 CA B:CYS241 4.1 61.2 1.0 ND1 B:HIS254 4.1 56.9 1.0 O B:HOH601 4.2 55.0 1.0 CG B:HIS254 4.2 57.6 1.0 CB B:ALA240 4.4 47.7 1.0 C B:ALA240 4.6 55.4 1.0 CA B:CYS238 4.7 47.0 1.0 NH1 B:ARG243 4.8 68.8 1.0 C B:CYS241 4.8 66.3 1.0 O A:HOH932 4.8 58.0 1.0 CA B:ALA240 4.8 51.5 1.0 CG B:GLN255 4.9 85.2 1.0 N B:ALA240 4.9 58.1 1.0 N B:CYS259 4.9 70.3 1.0 N B:ALA242 5.0 53.0 1.0 C B:CYS259 5.0 69.4 1.0

S.Choi, E.Yamashita, N.Yasuhara, J.Song, S.Y.Son, Y.H.Won, H.R.Hong, Y.S.Shin, T.Sekimoto, I.Y.Park, Y.Yoneda, S.J.Lee. Structural Basis For the Selective Nuclear Import of the C2H2 Zinc-Finger Protein Snail By Importin Beta. Acta Crystallogr.,Sect.D V. 70 1050 2014.
ISSN: ISSN 0907-4449
PubMed: 24699649
DOI: 10.1107/S1399004714000972