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Zinc in PDB 4jk2: X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp)

Enzymatic activity of X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp)

All present enzymatic activity of X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp):
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp), PDB code: 4jk2 was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 4.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 185.323, 205.411, 309.581, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 32.2

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp) (pdb code 4jk2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp), PDB code: 4jk2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4jk2

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Zinc binding site 1 out of 4 in the X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp)


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 Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:54.5
occ:1.00
 SG D:CYS85 2.4 38.8 1.0
SG D:CYS70 2.4 37.4 1.0
SG D:CYS72 2.4 53.2 1.0
SG D:CYS88 2.9 0.5 1.0
CB D:CYS85 2.9 27.2 1.0
CB D:CYS70 3.1 14.5 1.0
N D:CYS72 3.8 90.7 1.0
CB D:CYS72 3.9 35.0 1.0
N D:LEU71 4.1 4.8 1.0
O D:CYS88 4.1 0.4 1.0
N D:GLY73 4.1 7.2 1.0
N D:LYS74 4.4 0.0 1.0
CA D:CYS72 4.4 94.0 1.0
CA D:CYS70 4.4 4.2 1.0
CA D:CYS85 4.4 2.8 1.0
CB D:LYS74 4.5 83.0 1.0
CB D:CYS88 4.5 0.3 1.0
C D:CYS70 4.6 20.6 1.0
N D:CYS88 4.7 0.6 1.0
CD1 D:TYR75 4.7 38.7 1.0
CG D:LYS74 4.7 0.6 1.0
C D:LEU71 4.8 15.5 1.0
C D:CYS72 4.8 0.6 1.0
CA D:LEU71 4.9 7.1 1.0
CA D:CYS88 5.0 0.7 1.0
C D:CYS88 5.0 0.8 1.0

Zinc binding site 2 out of 4 in 4jk2

Go back to Zinc Binding Sites List in 4jk2
Zinc binding site 2 out of 4 in the X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp)


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 Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:8.6
occ:1.00
 CB D:CYS895 2.3 34.4 1.0
SG D:CYS888 2.3 0.2 1.0
SG D:CYS898 2.3 17.5 1.0
SG D:CYS814 2.7 1.4 1.0
SG D:CYS895 3.1 42.3 1.0
CB D:CYS888 3.1 2.0 1.0
CB D:CYS898 3.3 13.6 1.0
CA D:CYS895 3.6 42.8 1.0
CA D:CYS888 3.7 63.4 1.0
N D:CYS895 3.9 43.1 1.0
CB D:CYS814 4.3 1.3 1.0
C D:CYS888 4.4 78.7 1.0
N D:ASP889 4.5 88.8 1.0
C D:CYS895 4.5 51.8 1.0
CA D:CYS898 4.5 18.3 1.0
O D:GLY815 4.5 0.6 1.0
N D:CYS898 4.6 17.6 1.0
O D:CYS895 4.7 68.9 1.0
NH2 D:ARG883 4.8 21.2 1.0
N D:CYS814 4.8 31.3 1.0
N D:CYS888 4.9 90.6 1.0
N D:THR890 5.0 58.2 1.0
CB D:THR890 5.0 17.3 1.0

Zinc binding site 3 out of 4 in 4jk2

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Zinc binding site 3 out of 4 in the X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp)


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 Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1501

b:60.2
occ:1.00
 SG I:CYS88 2.4 0.9 1.0
SG I:CYS72 2.4 34.3 1.0
SG I:CYS70 2.5 59.6 1.0
SG I:CYS85 3.0 4.2 1.0
CB I:CYS70 3.0 9.5 1.0
N I:CYS72 3.1 63.2 1.0
CB I:CYS85 3.5 12.2 1.0
N I:LEU71 3.5 33.8 1.0
CB I:CYS72 3.6 36.5 1.0
CA I:CYS72 3.9 61.9 1.0
N I:GLY73 4.0 97.1 1.0
C I:LEU71 4.0 27.2 1.0
C I:CYS70 4.1 65.4 1.0
CA I:LEU71 4.1 4.6 1.0
CB I:CYS88 4.2 0.0 1.0
CA I:CYS70 4.2 68.2 1.0
CB I:LEU71 4.2 1.0 1.0
O I:CYS88 4.2 83.0 1.0
C I:CYS72 4.5 53.6 1.0
N I:CYS88 4.7 94.9 1.0
N I:LYS74 4.8 68.4 1.0
CA I:CYS88 4.9 99.6 1.0
CA I:CYS85 5.0 62.8 1.0

Zinc binding site 4 out of 4 in 4jk2

Go back to Zinc Binding Sites List in 4jk2
Zinc binding site 4 out of 4 in the X-Ray Crystal Structure of Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp)


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 Escherichia Coli SIGMA70 Holoenzyme in Complex with Guanosine Pentaphosphate (Pppgpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1502

b:49.6
occ:1.00
 CB I:CYS895 2.1 0.8 1.0
SG I:CYS888 2.3 64.9 1.0
SG I:CYS898 2.3 5.5 1.0
SG I:CYS814 2.7 22.9 1.0
SG I:CYS895 2.9 0.3 1.0
CB I:CYS898 3.2 0.1 1.0
CB I:CYS888 3.3 50.3 1.0
CA I:CYS895 3.5 49.9 1.0
N I:CYS895 3.9 92.7 1.0
CA I:CYS888 4.1 0.4 1.0
C I:CYS895 4.3 43.5 1.0
N I:CYS898 4.3 30.0 1.0
CB I:CYS814 4.3 63.6 1.0
CA I:CYS898 4.4 23.5 1.0
O I:CYS895 4.5 55.9 1.0
O I:GLY815 4.6 8.3 1.0
NH2 I:ARG883 4.7 32.6 1.0
N I:CYS814 4.7 61.1 1.0
C I:CYS888 4.8 0.1 1.0
CB I:THR890 4.9 36.8 1.0
N I:ASP889 4.9 65.4 1.0
CA I:CYS814 5.0 59.1 1.0

Reference:

U.Mechold, K.Potrykus, H.Murphy, K.S.Murakami, M.Cashel. Differential Regulation By Ppgpp Versus Pppgpp in Escherichia Coli. Nucleic Acids Res. V. 41 6175 2013.
ISSN: ISSN 0305-1048
PubMed: 23620295
DOI: 10.1093/NAR/GKT302
Page generated: Wed Aug 20 19:12:31 2025

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