Zinc in PDB 2zrt: Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2

The structure of Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2, PDB code: 2zrt was solved by H.Suzuki, M.Kawasaki, T.Kakiuchi, 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)	115.47 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.806, 147.537, 230.735, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 22.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 (pdb code 2zrt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 37 binding sites of Zinc where determined in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2, PDB code: 2zrt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn990 b:0.5 occ:1.00 OD1 A:ASP105 2.0 0.5 1.0 O A:MET109 2.4 0.4 1.0 CG A:ASP105 2.8 0.6 1.0 OD2 A:ASP103 3.0 0.6 1.0 OD2 A:ASP105 3.1 0.7 1.0 O A:ASP103 3.3 0.3 1.0 OE2 A:GLU114 3.4 0.5 1.0 CG A:GLU114 3.5 0.3 1.0 C A:MET109 3.5 0.4 1.0 OD1 A:ASP111 3.5 0.2 1.0 CG A:ASP103 3.8 0.9 1.0 CD A:GLU114 3.9 0.6 1.0 CG A:ASP111 3.9 0.2 1.0 N A:ASP111 4.0 0.5 1.0 CA A:ILE110 4.0 0.6 1.0 OD2 A:ASP111 4.0 0.8 1.0 CB A:GLU114 4.1 0.0 1.0 N A:ILE110 4.2 0.5 1.0 CB A:ASP105 4.2 0.6 1.0 OG A:SER107 4.2 0.5 1.0 OD1 A:ASP103 4.3 0.7 1.0 C A:ASP103 4.3 0.2 1.0 C A:ILE110 4.4 0.6 1.0 N A:ASP105 4.6 0.5 1.0 CA A:MET109 4.6 0.3 1.0 CA A:ASP103 4.8 0.1 1.0 CB A:ASP111 4.9 0.4 1.0 CB A:MET109 4.9 0.4 1.0 CB A:ASP103 4.9 0.1 1.0 CA A:ASP105 4.9 0.7 1.0 N A:MET109 5.0 0.1 1.0

Zinc binding site 2 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn991 b:0.2 occ:1.00 OD1 A:ASP169 2.0 91.0 1.0 OD1 A:ASP173 2.3 85.4 1.0 O A:TRP175 2.5 80.9 1.0 CG A:ASP169 3.2 91.5 1.0 CG A:ASP173 3.2 85.5 1.0 C A:TRP175 3.3 80.9 1.0 ZN A:ZN992 3.4 0.3 1.0 CB A:ASP171 3.4 88.8 1.0 OD2 A:ASP173 3.7 85.4 1.0 OD2 A:ASP169 3.9 91.0 1.0 CA A:ASP169 4.0 92.0 1.0 N A:TRP175 4.0 82.3 1.0 N A:ILE176 4.1 80.0 1.0 OD1 A:ASP171 4.2 89.1 1.0 CB A:ASP169 4.2 92.0 1.0 CA A:TRP175 4.2 81.5 1.0 CA A:ILE176 4.2 79.2 1.0 N A:ASP173 4.2 86.1 1.0 N A:ASP171 4.2 89.3 1.0 CA A:ASP171 4.3 88.7 1.0 CG A:ASP171 4.3 89.0 1.0 N A:GLN172 4.3 87.7 1.0 CB A:ASP173 4.4 85.5 1.0 C A:ASP169 4.4 91.5 1.0 CB A:TRP175 4.5 81.8 1.0 CG2 A:ILE176 4.7 79.2 1.0 C A:ASP171 4.7 88.3 1.0 CA A:ASP173 4.7 85.5 1.0 N A:THR170 4.8 90.8 1.0 N A:GLY174 4.8 84.4 1.0 O A:ASP169 4.9 91.4 1.0 C A:ASP173 5.0 85.0 1.0

Zinc binding site 3 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn992 b:0.3 occ:1.00 OD1 A:ASP171 2.3 89.1 1.0 OD2 A:ASP173 2.7 85.4 1.0 CG A:ASP171 2.8 89.0 1.0 CB A:ASP171 3.1 88.8 1.0 CG A:ASP173 3.2 85.5 1.0 ZN A:ZN991 3.4 0.2 1.0 OD1 A:ASP173 3.5 85.4 1.0 OD2 A:ASP171 3.7 89.4 1.0 O A:TRP175 4.2 80.9 1.0 CB A:ASP173 4.2 85.5 1.0 CA A:ASP171 4.6 88.7 1.0

Zinc binding site 4 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 ZN2+-Bound Form of DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn990 b:95.3 occ:1.00 OD2 B:ASP38 2.0 76.0 1.0 OD1 B:ASP36 2.2 75.2 1.0 O B:VAL42 2.3 70.6 1.0 OE1 B:GLU47 2.5 64.8 1.0 OG B:SER40 2.7 73.4 1.0 CG B:ASP38 2.8 76.2 1.0 OD1 B:ASP38 3.1 77.0 1.0 OE2 B:GLU47 3.1 64.8 1.0 CD B:GLU47 3.1 64.8 1.0 CG B:ASP36 3.4 75.5 1.0 C B:VAL42 3.5 70.6 1.0 CB B:SER40 3.5 73.4 1.0 N B:SER40 3.8 74.0 1.0 OG B:SER44 3.8 70.2 1.0 OD2 B:ASP36 4.2 75.5 1.0 CB B:ASP38 4.2 75.8 1.0 N B:ARG39 4.2 75.4 1.0 CA B:SER40 4.2 73.3 1.0 N B:SER44 4.2 69.7 1.0 N B:VAL42 4.3 71.2 1.0 N B:ASP38 4.3 76.0 1.0 N B:ILE43 4.3 70.3 1.0 CA B:ILE43 4.3 70.2 1.0 CA B:ASP36 4.4 75.7 1.0 CB B:ASP36 4.4 75.7 1.0 CA B:VAL42 4.4 70.9 1.0 C B:ASP36 4.5 75.9 1.0 CG B:GLU47 4.6 65.4 1.0 N B:LYS37 4.6 76.0 1.0 CA B:ASP38 4.6 75.8 1.0 N B:GLY41 4.7 72.4 1.0 C B:ILE43 4.7 70.0 1.0 C B:ASP38 4.7 75.6 1.0 C B:ARG39 4.8 74.6 1.0 C B:SER40 4.9 72.8 1.0 CA B:ARG39 4.9 75.2 1.0 CB B:SER44 5.0 69.7 1.0

Zinc binding site 5 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 ZN2+-Bound Form of DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn991 b:75.5 occ:1.00 O B:MET109 1.8 59.8 1.0 OE1 B:GLU114 1.9 59.1 1.0 OD2 B:ASP103 2.0 59.8 1.0 OD2 B:ASP105 2.4 62.4 1.0 CD B:GLU114 2.7 60.0 1.0 OG B:SER107 2.9 61.0 1.0 OE2 B:GLU114 2.9 59.1 1.0 C B:MET109 3.0 59.9 1.0 CG B:ASP103 3.1 59.8 1.0 ZN B:ZN993 3.2 0.7 1.0 CG B:ASP105 3.4 61.9 1.0 OD1 B:ASP105 3.7 62.1 1.0 CA B:ILE110 3.7 59.9 1.0 N B:ILE110 3.8 59.9 1.0 CA B:ASP103 3.8 60.1 1.0 N B:ASP111 3.8 59.7 1.0 CB B:ASP103 3.9 60.0 1.0 OD1 B:ASP103 4.0 59.9 1.0 CB B:SER107 4.1 61.0 1.0 CG B:GLU114 4.1 60.5 1.0 CA B:MET109 4.2 60.3 1.0 N B:MET109 4.2 60.5 1.0 C B:ILE110 4.3 59.9 1.0 N B:SER107 4.3 61.1 1.0 C B:ASP103 4.4 60.4 1.0 N B:ARG104 4.6 61.0 1.0 N B:ASP105 4.6 61.5 1.0 CB B:GLU114 4.7 60.6 1.0 NE2 B:GLN145 4.7 62.2 1.0 CB B:ASP105 4.7 61.7 1.0 CA B:SER107 4.8 61.0 1.0 N B:ASN106 4.8 61.4 1.0 CB B:ILE110 4.9 59.8 1.0 CG B:ASP111 5.0 59.3 1.0 CB B:ASP111 5.0 59.6 1.0 CA B:ASP105 5.0 61.6 1.0 C B:ASP105 5.0 61.5 1.0 CA B:ASP111 5.0 59.7 1.0

Zinc binding site 6 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 ZN2+-Bound Form of DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn992 b:95.9 occ:1.00 OD1 B:ASP169 2.3 65.9 1.0 OD2 B:ASP171 2.5 68.0 1.0 O B:TRP175 2.5 75.3 1.0 CB B:ASP173 2.7 70.8 1.0 OD2 B:ASP173 3.0 70.9 1.0 CG B:ASP173 3.1 71.1 1.0 ZN B:ZN994 3.2 0.1 1.0 N B:ASP173 3.4 70.3 1.0 CG B:ASP169 3.4 66.1 1.0 C B:TRP175 3.5 75.2 1.0 CG B:ASP171 3.6 67.7 1.0 CA B:ASP173 3.6 70.9 1.0 N B:TRP175 4.0 74.0 1.0 OD1 B:ASP171 4.0 67.5 1.0 OD2 B:ASP169 4.1 66.0 1.0 CA B:TRP175 4.2 74.6 1.0 CB B:TRP175 4.2 74.5 1.0 OD1 B:ASP173 4.2 71.9 1.0 N B:GLY174 4.3 71.9 1.0 CB B:ASP169 4.5 66.3 1.0 C B:ASP173 4.5 71.3 1.0 CA B:ASP169 4.5 66.5 1.0 N B:GLN172 4.5 69.1 1.0 C B:GLN172 4.5 69.9 1.0 N B:ILE176 4.6 75.9 1.0 N B:ASP171 4.8 67.7 1.0 C B:ASP171 4.8 68.6 1.0 C B:ASP169 4.8 66.7 1.0 CA B:ILE176 4.8 76.6 1.0 CB B:ASP171 4.9 68.0 1.0 CA B:GLN172 4.9 69.6 1.0

Zinc binding site 7 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 ZN2+-Bound Form of DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn993 b:0.7 occ:1.00 OD1 B:ASP105 2.4 62.1 1.0 CG B:ASP105 3.0 61.9 1.0 OD2 B:ASP105 3.0 62.4 1.0 OD2 B:ASP111 3.2 59.0 1.0 CB B:ASP111 3.2 59.6 1.0 NE2 B:GLN145 3.2 62.2 1.0 ZN B:ZN991 3.2 75.5 1.0 CG B:ASP111 3.3 59.3 1.0 OG B:SER107 3.5 61.0 1.0 OE1 B:GLU114 3.9 59.1 1.0 N B:ASP111 3.9 59.7 1.0 CA B:ASP111 4.1 59.7 1.0 CB B:SER107 4.1 61.0 1.0 OD1 B:ASP111 4.2 59.5 1.0 CD B:GLU114 4.2 60.0 1.0 OE2 B:GLU114 4.2 59.1 1.0 O B:MET109 4.2 59.8 1.0 CB B:ASP105 4.4 61.7 1.0 CD B:GLN145 4.4 62.4 1.0 CG B:GLN145 4.7 63.0 1.0 OD2 B:ASP103 5.0 59.8 1.0 C B:ILE110 5.0 59.9 1.0

Zinc binding site 8 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 ZN2+-Bound Form of DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn994 b:0.1 occ:1.00 OD2 B:ASP173 1.8 70.9 1.0 OD1 B:ASP171 3.0 67.5 1.0 CG B:ASP173 3.1 71.1 1.0 ZN B:ZN992 3.2 95.9 1.0 OD2 B:ASP171 3.4 68.0 1.0 CG B:ASP171 3.6 67.7 1.0 CB B:ASP173 3.9 70.8 1.0 OD1 B:ASP173 3.9 71.9 1.0 CB B:TRP175 5.0 74.5 1.0 O B:TRP175 5.0 75.3 1.0

Zinc binding site 9 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 ZN2+-Bound Form of DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn990 b:86.7 occ:1.00 O C:VAL42 2.2 76.7 1.0 OE2 C:GLU47 2.4 72.2 1.0 OD2 C:ASP38 2.4 77.6 1.0 OG C:SER40 2.4 77.6 1.0 OD1 C:ASP36 2.6 75.2 1.0 OD1 C:ASP38 3.0 77.8 1.0 CG C:ASP38 3.1 77.4 1.0 CG C:ASP36 3.1 74.9 1.0 OD2 C:ASP36 3.3 76.3 1.0 CD C:GLU47 3.4 72.3 1.0 C C:VAL42 3.4 76.7 1.0 CB C:SER40 3.6 77.5 1.0 OE1 C:GLU47 3.8 71.7 1.0 N C:SER40 4.0 77.4 1.0 CA C:SER40 4.2 77.5 1.0 N C:VAL42 4.3 76.9 1.0 N C:ILE43 4.3 76.5 1.0 CA C:ILE43 4.3 76.2 1.0 CB C:ASP36 4.3 74.2 1.0 N C:SER44 4.4 76.0 1.0 C C:SER40 4.4 77.4 1.0 CA C:VAL42 4.4 76.8 1.0 CA C:ASP36 4.5 74.2 1.0 CB C:ASP38 4.5 77.0 1.0 O C:SER40 4.6 77.6 1.0 CG C:GLU47 4.6 72.5 1.0 N C:ARG39 4.8 77.3 1.0 C C:ASP36 4.8 74.7 1.0 C C:ILE43 4.9 76.2 1.0 N C:ASP38 4.9 76.5 1.0 N C:GLY41 4.9 77.3 1.0 C C:ASP38 4.9 77.2 1.0 C C:GLY41 4.9 77.0 1.0 CD1 C:ILE43 5.0 76.7 1.0

Zinc binding site 10 out of 37 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2


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 ZN2+-Bound Form of DES3-23ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn991 b:80.3 occ:1.00 O C:MET109 2.0 68.4 1.0 OD1 C:ASP105 2.1 64.5 1.0 OG C:SER107 2.1 67.0 1.0 OE1 C:GLU114 2.2 70.0 1.0 OD2 C:ASP103 2.3 60.6 1.0 OD2 C:ASP111 2.9 70.8 1.0 CD C:GLU114 3.0 69.7 1.0 C C:MET109 3.1 68.5 1.0 CG C:ASP105 3.2 64.7 1.0 CG C:ASP103 3.3 60.4 1.0 CB C:SER107 3.3 66.8 1.0 OE2 C:GLU114 3.4 70.1 1.0 OD2 C:ASP105 3.6 64.9 1.0 CA C:ASP103 3.8 60.2 1.0 ZN C:ZN993 3.8 0.4 1.0 CA C:ILE110 3.8 68.5 1.0 N C:ILE110 3.9 68.5 1.0 N C:SER107 3.9 66.3 1.0 CB C:ASP103 3.9 60.2 1.0 CG C:ASP111 4.0 69.7 1.0 N C:ASP111 4.1 68.7 1.0 N C:MET109 4.1 68.3 1.0 CA C:MET109 4.2 68.6 1.0 CA C:SER107 4.2 66.7 1.0 OD1 C:ASP103 4.2 60.0 1.0 C C:ASP103 4.2 61.0 1.0 CG C:GLU114 4.3 69.1 1.0 OD1 C:ASP111 4.3 70.7 1.0 C C:ILE110 4.4 68.5 1.0 NE2 C:GLN145 4.4 65.8 1.0 CB C:ASP105 4.4 64.5 1.0 N C:ASP105 4.5 64.0 1.0 O C:ASP103 4.6 61.1 1.0 N C:ASN106 4.7 65.2 1.0 CB C:MET109 4.7 69.2 1.0 N C:ARG104 4.7 62.0 1.0 C C:SER107 4.8 67.0 1.0 CA C:ASP105 4.8 64.5 1.0 CB C:GLU114 4.8 68.7 1.0 N C:GLY108 4.8 67.2 1.0 C C:ASP105 4.8 64.8 1.0

H.Suzuki, M.Kawasaki, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki. Crystallization and X-Ray Diffraction Analysis of N-Terminally Truncated Human Alg-2 Acta Crystallogr.,Sect.F V. 64 974 2008.
ISSN: ESSN 1744-3091
PubMed: 18997320
DOI: 10.1107/S1744309108030297