Zinc in PDB 6ofu: X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12

The structure of X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12, PDB code: 6ofu was solved by B.J.Dopkins, J.B.Thoden, J.P.Huddleston, T.Narindoshvili, B.Fose, F.M.Rachel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.74 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.763, 85.663, 84.268, 90.00, 109.88, 90.00
R / Rfree (%)	14.1 / 18.2

The structure of X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12 (pdb code 6ofu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12, PDB code: 6ofu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.6 occ:1.00 NE2 A:HIS82 2.0 26.9 1.0 ND1 A:HIS206 2.0 29.1 1.0 NE2 A:HIS178 2.1 46.0 1.0 O A:HOH1242 2.3 35.9 1.0 O A:HOH1134 2.3 34.2 1.0 CD2 A:HIS82 3.0 27.4 1.0 CE1 A:HIS206 3.0 31.1 1.0 CE1 A:HIS178 3.0 54.6 1.0 CE1 A:HIS82 3.0 30.5 1.0 CG A:HIS206 3.0 26.9 1.0 CD2 A:HIS178 3.1 53.2 1.0 CB A:HIS206 3.4 26.9 1.0 ND1 A:HIS178 4.1 50.0 1.0 ND1 A:HIS82 4.1 26.2 1.0 CG A:HIS82 4.1 24.8 1.0 NE2 A:HIS206 4.1 24.0 1.0 CD2 A:HIS206 4.2 29.5 1.0 CG A:HIS178 4.2 53.3 1.0 ND2 A:ASN228 4.2 25.0 1.0 OD2 A:ASP81 4.3 26.4 1.0 CA A:HIS206 4.3 23.3 1.0 OD1 A:ASP81 4.4 17.9 1.0 N A:GLY207 4.7 33.1 1.0 CG A:ASP81 4.7 20.9 1.0 CG2 A:VAL137 4.8 42.1 1.0 C A:HIS206 4.9 28.4 1.0

Zinc binding site 2 out of 5 in the X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:26.4 occ:1.00 NE2 B:HIS178 2.1 23.8 1.0 NE2 B:HIS82 2.1 22.8 1.0 OE1 B:GLU133 2.2 20.8 1.0 ND1 B:HIS206 2.2 22.6 1.0 O B:HOH533 2.3 22.3 1.0 OE2 B:GLU133 2.3 25.3 1.0 CD B:GLU133 2.5 20.7 1.0 CE1 B:HIS206 3.1 23.5 1.0 CE1 B:HIS178 3.1 29.6 1.0 CE1 B:HIS82 3.1 24.1 1.0 CD2 B:HIS178 3.1 34.1 1.0 CD2 B:HIS82 3.1 20.7 1.0 CG B:HIS206 3.4 22.3 1.0 CB B:HIS206 3.8 20.8 1.0 CG B:GLU133 4.0 19.6 1.0 O B:HOH608 4.0 44.3 1.0 OD2 B:ASP103 4.1 21.9 1.0 ND1 B:HIS178 4.2 30.9 1.0 ND1 B:HIS82 4.2 22.2 1.0 CG B:HIS178 4.2 31.9 1.0 CG B:HIS82 4.3 20.1 1.0 NE2 B:HIS206 4.3 19.8 1.0 O B:HOH416 4.3 30.1 1.0 CD2 B:HIS206 4.4 22.5 1.0 CG B:ASP103 4.7 22.1 1.0 CB B:GLU133 4.8 17.9 1.0 OD1 B:ASP103 5.0 19.4 1.0

Zinc binding site 3 out of 5 in the X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:60.3 occ:1.00 CE1 C:HIS82 2.2 22.5 0.5 NE2 C:HIS82 2.3 23.4 0.5 O C:HOH559 2.4 47.3 1.0 O C:HOH578 2.4 46.5 1.0 O C:HOH451 2.5 40.2 1.0 NE2 C:HIS82 3.0 21.8 0.5 ND1 C:HIS206 3.1 43.8 1.0 CE1 C:HIS82 3.2 23.1 0.5 CD2 C:HIS82 3.3 22.6 0.5 ND1 C:HIS82 3.3 22.6 0.5 O C:HOH606 3.4 47.0 1.0 CG C:HIS206 3.4 36.8 1.0 CB C:HIS206 3.4 34.6 1.0 ZN C:ZN302 3.9 58.7 1.0 CE1 C:HIS206 4.0 39.4 1.0 ND2 C:ASN228 4.0 28.1 1.0 CD2 C:HIS82 4.2 21.8 0.5 OD2 C:ASP81 4.3 25.4 1.0 ND1 C:HIS82 4.4 22.6 0.5 CG C:HIS82 4.4 20.3 0.5 CD2 C:HIS206 4.4 35.6 1.0 CG C:HIS82 4.4 20.0 0.5 CA C:HIS206 4.4 30.8 1.0 OD1 C:ASP81 4.6 20.3 1.0 NE2 C:HIS206 4.6 32.0 1.0 CG C:ASN228 4.8 25.3 1.0 CB C:ASN228 4.8 22.5 1.0 N C:GLY207 4.9 41.4 1.0 CG C:ASP81 4.9 23.4 1.0

Zinc binding site 4 out of 5 in the X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:58.7 occ:1.00 OE1 C:GLU133 2.2 36.8 1.0 NE2 C:HIS82 2.3 21.8 0.5 CE1 C:HIS82 2.3 23.1 0.5 O C:HOH606 2.4 47.0 1.0 O C:HOH418 2.5 30.6 1.0 ND1 C:HIS206 2.7 43.8 1.0 CD C:GLU133 2.8 31.9 1.0 OE2 C:GLU133 2.8 37.8 1.0 CD2 C:HIS82 3.2 21.8 0.5 NE2 C:HIS82 3.2 23.4 0.5 ND1 C:HIS82 3.3 22.6 0.5 CE1 C:HIS206 3.4 39.4 1.0 CE1 C:HIS82 3.4 22.5 0.5 OD2 C:ASP103 3.6 27.6 1.0 CG C:HIS206 3.8 36.8 1.0 ZN C:ZN301 3.9 60.3 1.0 CB C:HIS206 4.1 34.6 1.0 O C:HOH551 4.1 39.4 1.0 CG C:GLU133 4.3 23.4 1.0 CE C:MET101 4.3 23.4 1.0 CG C:HIS82 4.4 20.0 0.5 CD2 C:HIS82 4.4 22.6 0.5 CG C:ASP103 4.4 26.9 1.0 ND1 C:HIS82 4.5 22.6 0.5 CG C:HIS82 4.5 20.3 0.5 NE2 C:HIS206 4.6 32.0 1.0 CD2 C:HIS206 4.8 35.6 1.0 CB C:GLU133 4.8 23.9 1.0 OD1 C:ASP103 4.9 23.3 1.0

Zinc binding site 5 out of 5 in the X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of the Ydji Aldolase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:40.7 occ:1.00 OE1 D:GLU133 2.2 29.2 1.0 ND1 D:HIS206 2.2 31.0 1.0 NE2 D:HIS82 2.3 22.0 1.0 OE2 D:GLU133 2.6 35.6 1.0 CD D:GLU133 2.7 26.4 1.0 O D:HOH587 2.7 44.3 1.0 O D:HOH416 2.8 29.3 1.0 CE1 D:HIS206 3.0 29.7 1.0 CD2 D:HIS82 3.2 22.3 1.0 CE1 D:HIS82 3.3 24.0 1.0 CG D:HIS206 3.3 25.5 1.0 O D:HOH505 3.4 23.4 1.0 CB D:HIS206 3.8 25.3 1.0 OD2 D:ASP103 4.1 23.1 1.0 CG D:GLU133 4.2 21.9 1.0 NE2 D:HIS206 4.2 23.6 1.0 CE D:MET101 4.3 26.4 1.0 CD2 D:HIS206 4.4 30.0 1.0 CG D:HIS82 4.4 19.7 1.0 ND1 D:HIS82 4.4 25.0 1.0 O D:HOH495 4.6 40.8 1.0 CG D:ASP103 4.8 23.0 1.0 CB D:GLU133 4.8 20.2 1.0

J.P.Huddleston, J.B.Thoden, B.J.Dopkins, T.Narindoshvili, B.J.Fose, H.M.Holden, F.M.Raushel. Structural and Functional Characterization of Ydji, An Aldolase of Unknown Specificity Inescherichia COLIK12. Biochemistry V. 58 3340 2019.
ISSN: ISSN 0006-2960
PubMed: 31322866
DOI: 10.1021/ACS.BIOCHEM.9B00326