Zinc in PDB 5zxl: Structure of Glda From E.Coli

All present enzymatic activity of Structure of Glda From E.Coli:
1.1.1.6;

The structure of Structure of Glda From E.Coli, PDB code: 5zxl was solved by J.Zhang, L.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.61 / 2.79
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	162.446, 162.446, 293.127, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.4

The structure of Structure of Glda From E.Coli also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of Glda From E.Coli (pdb code 5zxl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of Glda From E.Coli, PDB code: 5zxl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Glda From E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:93.5 occ:1.00 H2 A:GOL402 2.1 0.1 1.0 NE2 A:HIS271 2.3 69.3 1.0 NE2 A:HIS254 2.4 86.6 1.0 OD1 A:ASP171 2.4 75.5 1.0 O3 A:GOL402 2.6 84.9 1.0 HO2 A:GOL402 2.6 0.1 1.0 C2 A:GOL402 2.8 95.9 1.0 OD2 A:ASP171 3.0 75.5 1.0 CG A:ASP171 3.0 69.2 1.0 O2 A:GOL402 3.1 0.1 1.0 CD2 A:HIS271 3.1 63.2 1.0 C3 A:GOL402 3.2 83.9 1.0 HO3 A:GOL402 3.2 0.9 1.0 CD2 A:HIS254 3.3 73.3 1.0 CE1 A:HIS254 3.3 71.2 1.0 CE1 A:HIS271 3.4 58.6 1.0 OD1 A:ASP121 3.4 69.5 1.0 H32 A:GOL402 3.6 0.6 1.0 H31 A:GOL402 4.1 0.6 1.0 C1 A:GOL402 4.2 87.9 1.0 O1 A:GOL402 4.3 0.6 1.0 CG A:ASP121 4.3 72.4 1.0 CG A:HIS271 4.3 49.9 1.0 OD2 A:ASP121 4.4 74.3 1.0 CG2 A:VAL275 4.4 49.2 1.0 ND1 A:HIS271 4.4 55.4 1.0 ND1 A:HIS254 4.5 73.6 1.0 CG A:HIS254 4.5 80.1 1.0 CB A:ASP171 4.5 56.9 1.0 O A:HOH504 4.6 66.5 1.0 H11 A:GOL402 4.7 0.4 1.0 H12 A:GOL402 4.9 0.4 1.0

Zinc binding site 2 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Glda From E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.7 occ:1.00 O3 B:GOL402 2.0 0.7 1.0 NE2 B:HIS254 2.3 86.5 1.0 HO3 B:GOL402 2.6 0.2 1.0 OD1 B:ASP171 2.6 85.0 1.0 NE2 B:HIS271 2.7 80.5 1.0 C3 B:GOL402 3.0 92.2 1.0 CE1 B:HIS254 3.0 81.7 1.0 H32 B:GOL402 3.1 0.6 1.0 OD2 B:ASP171 3.2 70.9 1.0 OD1 B:ASP121 3.2 82.4 1.0 CG B:ASP171 3.2 73.4 1.0 CD2 B:HIS271 3.4 73.0 1.0 CD2 B:HIS254 3.5 81.6 1.0 H2 B:GOL402 3.6 0.2 1.0 H12 B:GOL402 3.6 0.5 1.0 C2 B:GOL402 3.8 96.9 1.0 CE1 B:HIS271 3.8 71.2 1.0 OD2 B:ASP121 3.8 87.7 1.0 H31 B:GOL402 3.9 0.6 1.0 CG B:ASP121 3.9 82.6 1.0 C1 B:GOL402 4.2 0.1 1.0 ND1 B:HIS254 4.3 78.8 1.0 H11 B:GOL402 4.5 0.5 1.0 CG B:HIS254 4.5 81.9 1.0 CG2 B:VAL275 4.6 59.5 1.0 CB B:ASP171 4.6 69.0 1.0 CG B:HIS271 4.7 74.8 1.0 ND1 B:HIS271 4.8 63.0 1.0 O B:ASP171 5.0 60.8 1.0

Zinc binding site 3 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Glda From E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:93.5 occ:1.00 NE2 C:HIS254 2.3 97.3 1.0 HO3 C:GOL402 2.4 0.3 1.0 H11 C:GOL402 2.4 0.5 1.0 OD1 C:ASP171 2.4 87.5 1.0 NE2 C:HIS271 2.5 77.8 1.0 O1 C:GOL402 2.6 82.8 1.0 HO1 C:GOL402 2.6 99.3 1.0 OD2 C:ASP171 2.9 73.1 1.0 C1 C:GOL402 2.9 93.8 1.0 CG C:ASP171 3.0 76.8 1.0 HO2 C:GOL402 3.1 0.8 1.0 CE1 C:HIS254 3.2 79.2 1.0 CD2 C:HIS271 3.3 71.5 1.0 O3 C:GOL402 3.4 0.3 1.0 CD2 C:HIS254 3.4 79.0 1.0 OD1 C:ASP121 3.4 85.8 1.0 CE1 C:HIS271 3.5 64.4 1.0 C2 C:GOL402 3.8 89.9 1.0 O2 C:GOL402 3.8 88.2 1.0 H12 C:GOL402 3.8 0.5 1.0 C3 C:GOL402 4.1 0.1 1.0 CG C:ASP121 4.2 88.2 1.0 OD2 C:ASP121 4.2 85.0 1.0 ND1 C:HIS254 4.4 82.7 1.0 H31 C:GOL402 4.4 0.7 1.0 CG C:HIS254 4.5 70.6 1.0 CB C:ASP171 4.5 62.7 1.0 CG2 C:VAL275 4.5 55.9 1.0 CG C:HIS271 4.5 60.7 1.0 ND1 C:HIS271 4.6 78.7 1.0 H2 C:GOL402 4.8 0.9 1.0 O C:ASP171 4.9 59.4 1.0

Zinc binding site 4 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Glda From E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:0.3 occ:1.00 O2 D:GOL405 1.9 0.1 1.0 NE2 D:HIS254 2.0 68.8 1.0 O3 D:GOL405 2.2 87.9 1.0 OD1 D:ASP171 2.3 80.3 1.0 NE2 D:HIS271 2.4 67.5 1.0 H2 D:GOL405 2.4 0.4 1.0 C2 D:GOL405 2.5 94.6 1.0 HO2 D:GOL405 2.6 0.2 1.0 CE1 D:HIS254 2.7 72.6 1.0 C3 D:GOL405 2.9 82.7 1.0 HO3 D:GOL405 2.9 0.4 1.0 CG D:ASP171 3.0 66.7 1.0 CD2 D:HIS271 3.1 69.0 1.0 CD2 D:HIS254 3.1 0.7 1.0 OD2 D:ASP171 3.2 68.8 1.0 H31 D:GOL405 3.4 99.1 1.0 CE1 D:HIS271 3.5 59.4 1.0 H32 D:GOL405 3.8 99.1 1.0 OD1 D:ASP121 3.8 70.9 1.0 ND1 D:HIS254 3.9 82.8 1.0 C1 D:GOL405 3.9 75.1 1.0 CG2 D:VAL275 4.1 46.9 1.0 CG D:HIS254 4.1 0.5 1.0 CG D:HIS271 4.4 48.0 1.0 H11 D:GOL405 4.4 90.1 1.0 CB D:ASP171 4.4 60.4 1.0 O1 D:GOL405 4.4 88.6 1.0 O D:HOH510 4.5 53.0 1.0 ND1 D:HIS271 4.5 65.0 1.0 CG D:ASP121 4.6 72.8 1.0 H12 D:GOL405 4.6 90.1 1.0 OD2 D:ASP121 4.6 75.0 1.0 O D:ASP171 4.8 53.4 1.0 CA D:ASP171 4.8 54.1 1.0

Zinc binding site 5 out of 5 in the Structure of Glda From E.Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Glda From E.Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:0.2 occ:1.00 NZ D:LYS274 2.9 53.7 1.0 NE2 D:HIS257 3.5 57.5 1.0 O D:HOH529 3.8 52.7 1.0 CA D:HIS271 4.0 48.2 1.0 CB D:HIS271 4.1 47.7 1.0 CE1 D:HIS257 4.1 45.5 1.0 N D:HIS271 4.1 54.6 1.0 CE D:LYS274 4.2 55.7 1.0 ND1 D:HIS271 4.2 65.0 1.0 CG2 D:THR261 4.5 43.7 1.0 CG D:HIS271 4.6 48.0 1.0 CD2 D:HIS257 4.7 57.9 1.0 O D:TYR269 4.8 52.0 1.0 C D:TYR270 4.9 51.1 1.0 CD D:LYS274 5.0 68.0 1.0

J.Zhang, A.N.Nanjaraj Urs, L.Lin, Y.Zhou, Y.Hu, G.Hua, Q.Gao, Z.Yuchi, Y.Zhang. Structure of Glycerol Dehydrogenase (Glda) From Escherichia Coli. Acta Crystallogr F Struct V. 75 176 2019BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30839292
DOI: 10.1107/S2053230X19000037