Zinc in PDB 1k4p: Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions

The structure of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions, PDB code: 1k4p was solved by D.-I.Liao, Y.-J.Zheng, P.V.Viitanen, D.B.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.725, 88.530, 43.994, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions (pdb code 1k4p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions, PDB code: 1k4p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions


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 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:8.0 occ:0.76 OE2 A:GLU181 2.0 9.9 1.0 O A:HOH1091 2.0 12.8 1.0 OE1 A:GLU183 2.1 10.0 1.0 O A:HOH1068 2.1 13.4 1.0 O A:HOH1069 2.1 12.8 1.0 O A:HOH1067 2.3 11.4 1.0 CD A:GLU181 3.1 9.1 1.0 CD A:GLU183 3.1 10.9 1.0 OE1 A:GLU181 3.4 14.9 1.0 OE2 A:GLU183 3.4 12.0 1.0 CG A:GLU181 4.3 8.5 1.0 CG A:GLU183 4.4 10.6 1.0 CA A:GLU183 4.5 6.2 1.0 N A:GLY184 4.5 6.8 1.0 CB A:GLU183 4.7 7.7 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions


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 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:7.1 occ:0.94 OE2 A:GLU37 1.9 9.2 1.0 O A:HOH1219 1.9 23.4 1.0 ND1 A:HIS153 2.1 6.3 1.0 O A:HOH1024 2.2 8.1 1.0 O2 A:SO41001 2.3 7.6 1.0 CD A:GLU37 2.9 10.2 1.0 CE1 A:HIS153 2.9 6.1 1.0 OE1 A:GLU37 3.1 14.6 1.0 CG A:HIS153 3.2 5.0 1.0 S A:SO41001 3.4 7.1 1.0 ZN A:ZN1005 3.5 10.5 0.6 ZN A:ZN1006 3.5 10.7 0.5 O3 A:SO41001 3.5 10.4 1.0 CB A:HIS153 3.6 4.8 1.0 OD2 A:ASP41 4.1 6.6 1.0 NH1 A:ARG36 4.1 7.8 1.0 NE2 A:HIS153 4.1 5.8 1.0 O4 A:SO41001 4.2 10.4 1.0 OD1 A:ASP41 4.2 11.1 1.0 CG A:GLU37 4.2 8.8 1.0 CD2 A:HIS153 4.2 5.4 1.0 N A:HIS153 4.3 5.0 1.0 CG A:ASP41 4.4 8.7 1.0 O A:HOH1174 4.4 31.2 1.0 O A:HOH1073 4.5 18.9 1.0 OE1 A:GLU39 4.5 10.6 1.0 O1 A:SO41001 4.6 7.6 1.0 CA A:HIS153 4.6 4.8 1.0 OE2 A:GLU174 4.8 42.1 1.0 CB A:GLU37 4.8 7.0 1.0 OD2 A:ASP32 5.0 8.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions


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 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:10.5 occ:0.60 O A:HOH1219 2.0 23.4 1.0 O A:HOH1111 2.1 16.1 1.0 OD1 A:ASP41 2.2 11.1 1.0 OE2 A:GLU174 2.5 42.1 1.0 CG A:ASP41 3.0 8.7 1.0 CD A:GLU174 3.2 13.3 1.0 OD2 A:ASP41 3.2 6.6 1.0 O A:HOH1024 3.3 8.1 1.0 ZN A:ZN1004 3.5 7.1 0.9 CG A:GLU174 3.5 6.8 1.0 O A:HOH1086 3.7 19.4 1.0 CD1 A:ILE172 3.9 6.2 1.0 OE1 A:GLU174 4.0 9.1 1.0 O A:HOH1107 4.1 16.7 1.0 N A:GLU174 4.1 4.2 1.0 O3 A:SO41001 4.1 10.4 1.0 ND1 A:HIS153 4.3 6.3 1.0 ZN A:ZN1006 4.3 10.7 0.5 C A:SER173 4.4 4.2 1.0 CG1 A:ILE172 4.4 4.3 1.0 CB A:HIS153 4.4 4.8 1.0 CB A:ASP41 4.5 5.8 1.0 CA A:SER173 4.5 3.7 1.0 CG A:HIS153 4.6 5.0 1.0 CA A:GLU174 4.6 5.1 1.0 CB A:GLU174 4.6 7.8 1.0 O A:HOH1073 4.8 18.9 1.0 N A:SER173 4.8 3.3 1.0 O2 A:SO41001 4.8 7.6 1.0 CB A:ILE172 5.0 4.3 1.0 O A:SER173 5.0 5.4 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions


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 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:10.7 occ:0.49 OE1 A:GLU37 1.9 14.6 1.0 O A:HOH1073 2.2 18.9 1.0 O A:HOH1174 2.4 31.2 1.0 ZN A:ZN1007 2.5 11.8 0.5 CD A:GLU37 3.0 10.2 1.0 O A:HOH1219 3.2 23.4 1.0 ZN A:ZN1004 3.5 7.1 0.9 OE2 A:GLU37 3.6 9.2 1.0 OE2 A:GLU174 3.7 42.1 1.0 O A:HOH1024 3.8 8.1 1.0 OE1 A:GLU39 4.0 10.6 1.0 O3 A:SO41001 4.1 10.4 1.0 O A:HOH1086 4.2 19.4 1.0 CG A:GLU37 4.3 8.8 1.0 ZN A:ZN1005 4.3 10.5 0.6 O4 A:SO41001 4.4 10.4 1.0 O2 A:SO41001 4.4 7.6 1.0 S A:SO41001 4.5 7.1 1.0 CD A:GLU174 4.8 13.3 1.0 CG A:GLU174 5.0 6.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions


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 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:11.8 occ:0.48 ZN A:ZN1006 2.5 10.7 0.5 O A:HOH1174 3.1 31.2 1.0 O A:HOH1073 3.5 18.9 1.0 OH A:TYR94 3.6 22.6 1.0 O A:HOH1086 3.8 19.4 1.0 OE2 A:GLU174 4.0 42.1 1.0 OE1 A:GLU37 4.3 14.6 1.0 OG1 A:THR92 4.7 23.4 1.0 O A:HOH1219 4.7 23.4 1.0 CZ A:TYR94 4.8 13.4 1.0

D.I.Liao, Y.J.Zheng, P.V.Viitanen, D.B.Jordan. Structural Definition of the Active Site and Catalytic Mechanism of 3,4-Dihydroxy-2-Butanone-4-Phosphate Synthase. Biochemistry V. 41 1795 2002.
ISSN: ISSN 0006-2960
PubMed: 11827524
DOI: 10.1021/BI015652U