Zinc in PDB 3bl5: Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis

The structure of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis, PDB code: 3bl5 was solved by N.Cicmil, R.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.057, 75.542, 131.023, 90.00, 94.73, 90.00
R / Rfree (%)	22.2 / 27.2

The structure of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis (pdb code 3bl5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis, PDB code: 3bl5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:0.7 occ:1.00 SG A:CYS198 2.3 97.9 1.0 SG A:CYS201 2.3 88.8 1.0 SG A:CYS195 2.4 0.7 1.0 SG A:CYS186 2.4 90.9 1.0 CB A:CYS186 3.1 90.7 1.0 N A:CYS195 3.3 0.6 1.0 N A:TYR187 3.3 93.0 1.0 CA A:CYS186 3.4 89.4 1.0 CB A:CYS195 3.4 0.7 1.0 OD1 A:ASN188 3.4 99.4 1.0 CB A:CYS198 3.7 100.0 1.0 CB A:CYS201 3.8 89.5 1.0 C A:CYS186 3.8 91.2 1.0 CA A:CYS195 3.8 0.7 1.0 N A:GLY196 4.1 0.7 1.0 C A:GLY194 4.1 0.6 1.0 CA A:GLY194 4.2 0.7 1.0 N A:CYS198 4.2 0.3 1.0 CA A:TYR187 4.5 95.0 1.0 N A:ASN188 4.5 96.7 1.0 CG A:ASN188 4.5 98.5 1.0 C A:CYS195 4.5 0.6 1.0 CA A:CYS198 4.6 99.5 1.0 N A:CYS201 4.6 90.3 1.0 N A:CYS186 4.7 86.8 1.0 N A:GLU197 4.7 0.5 1.0 CA A:CYS201 4.7 89.8 1.0 CB A:TYR187 4.8 95.6 1.0 C A:TYR187 4.8 95.9 1.0 CB A:ASN188 5.0 97.4 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:96.0 occ:1.00 SG B:CYS186 2.2 89.5 1.0 SG B:CYS201 2.4 93.9 1.0 SG B:CYS198 2.4 0.3 1.0 SG B:CYS195 2.4 0.7 1.0 CB B:CYS186 3.0 93.5 1.0 N B:CYS195 3.2 0.1 1.0 CA B:CYS186 3.3 93.1 1.0 CB B:CYS195 3.3 0.2 1.0 N B:TYR187 3.3 95.4 1.0 OD1 B:ASN188 3.4 0.7 1.0 CB B:CYS198 3.8 0.3 1.0 CB B:CYS201 3.8 93.7 1.0 C B:CYS186 3.8 94.4 1.0 CA B:CYS195 3.8 0.2 1.0 C B:GLY194 4.0 0.5 1.0 N B:GLY196 4.1 0.5 1.0 CA B:GLY194 4.1 0.5 1.0 N B:CYS198 4.3 0.6 1.0 N B:ASN188 4.4 98.1 1.0 CG B:ASN188 4.5 99.9 1.0 CA B:TYR187 4.5 96.9 1.0 C B:CYS195 4.5 0.5 1.0 N B:CYS201 4.6 94.7 1.0 N B:CYS186 4.6 91.3 1.0 CA B:CYS198 4.6 0.2 1.0 N B:GLU197 4.7 0.7 1.0 CA B:CYS201 4.8 93.8 1.0 CB B:TYR187 4.8 96.9 1.0 C B:TYR187 4.8 97.5 1.0 CB B:ASN188 4.9 99.5 1.0 O B:CYS186 5.0 94.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:63.0 occ:1.00 SG C:CYS195 2.1 66.1 1.0 SG C:CYS201 2.3 64.4 1.0 SG C:CYS198 2.3 58.1 1.0 SG C:CYS186 2.3 61.9 1.0 CB C:CYS201 3.0 68.6 1.0 CB C:CYS186 3.2 62.1 1.0 CB C:CYS195 3.2 66.2 1.0 N C:CYS195 3.4 65.2 1.0 CB C:CYS198 3.5 62.3 1.0 CA C:CYS186 3.6 63.0 1.0 N C:GLY196 3.6 66.9 1.0 CA C:CYS195 3.6 66.5 1.0 N C:CYS198 3.9 64.8 1.0 C C:CYS195 4.0 66.8 1.0 N C:TYR187 4.1 65.3 1.0 CA C:CYS201 4.2 68.9 1.0 CA C:CYS198 4.2 62.9 1.0 ND2 C:ASN188 4.2 69.6 1.0 N C:CYS201 4.3 69.5 1.0 C C:CYS186 4.3 63.3 1.0 N C:GLU197 4.4 66.6 1.0 C C:GLY194 4.4 65.6 1.0 O C:CYS198 4.4 62.3 1.0 CA C:GLY196 4.6 66.5 1.0 C C:CYS198 4.7 63.1 1.0 N C:CYS186 4.8 63.3 1.0 CA C:GLY194 4.8 66.8 1.0 N C:ASN188 4.8 67.5 1.0 C C:GLU197 4.9 66.3 1.0 C C:GLY196 4.9 66.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:75.2 occ:1.00 SG D:CYS195 2.1 72.5 1.0 SG D:CYS186 2.2 73.4 1.0 SG D:CYS198 2.3 68.1 1.0 SG D:CYS201 2.3 73.1 1.0 CB D:CYS201 3.0 71.4 1.0 CB D:CYS186 3.2 69.2 1.0 CB D:CYS195 3.2 69.9 1.0 CB D:CYS198 3.4 69.1 1.0 N D:CYS195 3.5 68.5 1.0 N D:GLY196 3.6 71.6 1.0 CA D:CYS186 3.6 67.7 1.0 CA D:CYS195 3.7 69.3 1.0 N D:CYS198 3.8 72.3 1.0 C D:CYS195 4.0 70.8 1.0 N D:TYR187 4.1 68.5 1.0 CA D:CYS201 4.1 71.4 1.0 CA D:CYS198 4.1 70.5 1.0 ND2 D:ASN188 4.2 68.3 1.0 N D:CYS201 4.2 70.0 1.0 N D:GLU197 4.3 71.7 1.0 C D:CYS186 4.3 67.6 1.0 O D:CYS198 4.4 69.4 1.0 C D:GLY194 4.4 69.5 1.0 CA D:GLY196 4.6 71.0 1.0 C D:CYS198 4.6 69.2 1.0 C D:GLU197 4.8 74.0 1.0 N D:CYS186 4.8 68.4 1.0 C D:GLY196 4.8 71.1 1.0 CA D:GLY194 4.9 70.5 1.0 N D:ASN188 4.9 70.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn300 b:0.7 occ:1.00 SG E:CYS195 2.2 0.7 1.0 SG E:CYS201 2.3 97.5 1.0 SG E:CYS198 2.3 0.7 1.0 SG E:CYS186 2.6 94.1 1.0 CB E:CYS186 2.9 93.1 1.0 N E:CYS195 3.1 0.6 1.0 CA E:CYS186 3.4 92.6 1.0 CB E:CYS201 3.4 97.2 1.0 CB E:CYS195 3.5 0.7 1.0 CB E:CYS198 3.6 0.7 1.0 N E:GLY196 3.6 0.7 1.0 CA E:CYS195 3.7 0.4 1.0 ND2 E:ASN188 3.8 0.1 1.0 N E:CYS198 4.0 0.7 1.0 N E:TYR187 4.1 96.5 1.0 C E:GLY194 4.1 0.7 1.0 C E:CYS195 4.1 0.0 1.0 C E:CYS186 4.2 94.5 1.0 CA E:GLY194 4.2 0.7 1.0 CA E:CYS198 4.3 0.6 1.0 N E:GLU197 4.4 0.7 1.0 O E:CYS198 4.5 0.9 1.0 N E:CYS186 4.5 90.3 1.0 CA E:CYS201 4.6 98.1 1.0 CA E:GLY196 4.7 0.3 1.0 N E:CYS201 4.7 98.4 1.0 C E:CYS198 4.8 0.5 1.0 C E:GLU197 4.9 0.7 1.0 O E:ASP193 5.0 0.7 1.0 CG E:ASN188 5.0 0.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn300 b:0.7 occ:1.00 SG F:CYS198 2.7 0.7 1.0 SG F:CYS201 2.9 0.7 1.0 N F:CYS195 2.9 0.7 1.0 SG F:CYS195 3.0 0.5 1.0 SG F:CYS186 3.0 0.7 1.0 N F:GLY196 3.1 0.7 1.0 CB F:CYS201 3.1 0.7 1.0 CB F:CYS186 3.4 0.7 1.0 CA F:CYS186 3.6 0.7 1.0 CA F:CYS195 3.6 0.7 1.0 CB F:CYS195 3.7 0.4 1.0 C F:CYS195 3.7 0.7 1.0 C F:GLY194 3.9 0.7 1.0 CB F:CYS198 4.0 0.7 1.0 CA F:GLY194 4.0 0.7 1.0 N F:CYS201 4.0 0.7 1.0 CA F:GLY196 4.1 0.7 1.0 ND2 F:ASN188 4.1 0.7 1.0 N F:CYS198 4.2 0.7 1.0 CA F:CYS201 4.2 0.7 1.0 N F:TYR187 4.3 0.3 1.0 N F:GLU197 4.3 0.7 1.0 C F:CYS186 4.4 0.6 1.0 CA F:CYS198 4.6 0.7 1.0 C F:GLY196 4.6 0.7 1.0 N F:CYS186 4.7 0.7 1.0 O F:CYS198 4.7 0.7 1.0 O F:CYS195 4.9 0.7 1.0 O F:ASP193 4.9 0.7 1.0 O F:GLY194 5.0 0.5 1.0

N.Cicmil, R.H.Huang. Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in Preq(1) Biosynthesis. Proteins V. 72 1084 2008.
ISSN: ISSN 0887-3585
PubMed: 18491386
DOI: 10.1002/PROT.22098