Zinc in PDB 3aak: Crystal Structure of ZN2+-Bound Form of DES3-20ALG-2F122A

The structure of Crystal Structure of ZN2+-Bound Form of DES3-20ALG-2F122A, PDB code: 3aak was solved by T.Inuzuka, H.Suzuki, M.Kawasaki, H.Shibata, S.Wakatsuki, M.Maki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.24 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.266, 170.209, 46.911, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 29.8

The binding sites of Zinc atom in the Crystal Structure of ZN2+-Bound Form of DES3-20ALG-2F122A (pdb code 3aak). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of ZN2+-Bound Form of DES3-20ALG-2F122A, PDB code: 3aak:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of ZN2+-Bound Form of DES3-20ALG-2F122A


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 ZN2+-Bound Form of DES3-20ALG-2F122A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn991 b:69.8 occ:1.00 OD1 A:ASP36 2.0 64.3 1.0 OD2 A:ASP38 2.1 63.7 1.0 O A:VAL42 2.1 57.8 1.0 O A:HOH14 2.2 39.2 1.0 OE1 A:GLU47 2.6 54.3 1.0 OE2 A:GLU47 3.0 54.5 1.0 OG A:SER40 3.1 60.9 1.0 CG A:ASP38 3.1 63.8 1.0 CD A:GLU47 3.1 53.9 1.0 CG A:ASP36 3.2 64.9 1.0 C A:VAL42 3.2 57.8 1.0 OD1 A:ASP38 3.5 63.8 1.0 CB A:SER40 3.9 61.0 1.0 CA A:ILE43 4.0 56.8 1.0 OD2 A:ASP36 4.0 64.3 1.0 N A:ILE43 4.0 57.3 1.0 N A:SER40 4.0 61.6 1.0 CA A:ASP36 4.1 65.5 1.0 CB A:ASP36 4.2 65.5 1.0 N A:VAL42 4.2 58.5 1.0 CA A:VAL42 4.3 58.0 1.0 N A:SER44 4.4 56.3 1.0 C A:ASP36 4.4 65.5 1.0 N A:ASP38 4.4 64.3 1.0 CB A:ASP38 4.4 63.8 1.0 CA A:SER40 4.5 61.0 1.0 N A:ARG39 4.5 63.0 1.0 N A:LYS37 4.5 65.2 1.0 CG A:GLU47 4.6 53.8 1.0 C A:ILE43 4.7 56.6 1.0 N A:GLY41 4.7 60.1 1.0 CA A:ASP38 4.8 63.8 1.0 C A:ASP38 4.9 63.5 1.0 C A:SER40 5.0 60.6 1.0 OG A:SER44 5.0 56.5 1.0 O A:ASP36 5.0 65.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of ZN2+-Bound Form of DES3-20ALG-2F122A


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 ZN2+-Bound Form of DES3-20ALG-2F122A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn992 b:0.7 occ:1.00 OD1 A:ASP103 2.0 75.1 1.0 OG A:SER107 2.0 74.8 1.0 OD2 A:ASP105 2.1 76.8 1.0 OE1 A:GLU114 2.5 70.1 1.0 O A:HOH12 2.5 44.0 1.0 OE2 A:GLU114 3.0 69.9 1.0 O A:MET109 3.0 72.7 1.0 CD A:GLU114 3.1 69.7 1.0 CG A:ASP105 3.2 76.4 1.0 CG A:ASP103 3.2 75.2 1.0 CB A:SER107 3.5 74.9 1.0 OD1 A:ASP105 3.7 76.8 1.0 N A:SER107 3.8 75.0 1.0 C A:MET109 3.9 72.6 1.0 N A:ASN106 3.9 75.7 1.0 CA A:ASP103 3.9 75.3 1.0 OD2 A:ASP103 4.1 75.2 1.0 N A:ASP105 4.1 76.0 1.0 CB A:ASP103 4.1 75.2 1.0 N A:ARG104 4.2 75.8 1.0 CA A:SER107 4.2 74.8 1.0 C A:ASP103 4.3 75.5 1.0 OD2 A:ASP111 4.4 72.0 1.0 CB A:ASP105 4.4 76.0 1.0 N A:MET109 4.4 73.2 1.0 C A:ASP105 4.4 75.9 1.0 CA A:ASP105 4.5 76.0 1.0 CA A:ILE110 4.5 71.8 1.0 N A:ILE110 4.5 72.2 1.0 CA A:ASN106 4.6 75.4 1.0 O A:HOH13 4.6 40.2 1.0 N A:GLY108 4.6 74.3 1.0 CG A:GLU114 4.6 69.6 1.0 C A:ASN106 4.7 75.2 1.0 N A:ASP111 4.8 71.4 1.0 C A:SER107 4.8 74.6 1.0 CA A:MET109 4.8 72.8 1.0 O A:TYR102 4.9 74.7 1.0 CD1 A:ILE110 5.0 71.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of ZN2+-Bound Form of DES3-20ALG-2F122A


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 ZN2+-Bound Form of DES3-20ALG-2F122A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn993 b:38.8 occ:1.00 OD2 A:ASP173 1.9 40.4 1.0 OD2 A:ASP171 1.9 41.7 1.0 O A:HOH16 2.6 11.2 1.0 CG A:ASP171 2.7 42.3 1.0 OD1 A:ASP171 2.8 41.8 1.0 CG A:ASP173 2.9 40.8 1.0 O A:HOH15 3.0 15.9 1.0 OD1 A:ASP173 3.2 42.0 1.0 CB A:ASP171 4.2 43.0 1.0 CB A:ASP173 4.2 40.6 1.0 O A:TRP175 4.9 37.4 1.0

T.Inuzuka, H.Suzuki, M.Kawasaki, H.Shibata, S.Wakatsuki, M.Maki. Molecular Basis For Defect in Alix-Binding By Alternatively Spliced Isoform of Alg-2 (Alg-2DELTAGF122) and Structural Roles of F122 in Target Recognition Bmc Struct.Biol. V. 10 25 2010.
ISSN: ESSN 1472-6807
PubMed: 20691033
DOI: 10.1186/1472-6807-10-25