Atomistry » Zinc » PDB 3b7r-3bo5 » 3bl5
Atomistry »
  Zinc »
    PDB 3b7r-3bo5 »
      3bl5 »

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

Protein crystallography data

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

Other elements in 3bl5:

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

Zinc Binding Sites:

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 3bl5

Go back to Zinc Binding Sites List in 3bl5
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 3bl5

Go back to Zinc Binding Sites List in 3bl5
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 3bl5

Go back to Zinc Binding Sites List in 3bl5
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 3bl5

Go back to Zinc Binding Sites List in 3bl5
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 3bl5

Go back to Zinc Binding Sites List in 3bl5
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 3bl5

Go back to Zinc Binding Sites List in 3bl5
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

Reference:

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
Page generated: Thu Oct 24 11:32:30 2024

Last articles

Mg in 6CA4
Mg in 6C90
Mg in 6CA0
Mg in 6C9Y
Mg in 6C8Z
Mg in 6C8P
Mg in 6C8N
Mg in 6C8O
Mg in 6C8D
Mg in 6C8L
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy