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Zinc in PDB 1tjl: Crystal Structure of Transcription Factor Dksa From E. Coli

Protein crystallography data

The structure of Crystal Structure of Transcription Factor Dksa From E. Coli, PDB code: 1tjl was solved by A.Perederina, V.Svetlov, M.N.Vassylyeva, I.Artsimovitch, S.Yokoyama, D.G.Vassylyev, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.95 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.319, 96.593, 117.477, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Transcription Factor Dksa From E. Coli (pdb code 1tjl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Transcription Factor Dksa From E. Coli, PDB code: 1tjl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1tjl

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Zinc binding site 1 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:31.9
occ:1.00
 SG A:CYS138 2.3 37.5 1.0
SG A:CYS114 2.3 33.3 1.0
SG A:CYS117 2.3 35.1 1.0
SG A:CYS135 2.4 36.7 1.0
CB A:CYS138 3.1 36.5 1.0
CB A:CYS114 3.3 31.1 1.0
CB A:CYS117 3.4 39.5 1.0
CB A:CYS135 3.5 34.1 1.0
N A:CYS117 3.5 40.9 1.0
CA A:CYS117 4.0 41.3 1.0
N A:CYS135 4.0 36.6 1.0
O A:CYS117 4.1 48.1 1.0
CB A:SER116 4.1 44.0 1.0
N A:CYS138 4.2 39.7 1.0
CA A:CYS138 4.2 38.5 1.0
CA A:CYS135 4.3 35.9 1.0
C A:CYS117 4.4 43.9 1.0
C A:SER116 4.5 41.3 1.0
CA A:SER116 4.7 42.0 1.0
N A:SER116 4.8 42.1 1.0
O A:CYS135 4.8 35.2 1.0
CA A:CYS114 4.8 33.2 1.0
CB A:VAL119 4.8 42.9 1.0
C A:CYS135 4.9 36.4 1.0

Zinc binding site 2 out of 10 in 1tjl

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Zinc binding site 2 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:32.6
occ:1.00
 SG B:CYS138 2.3 33.8 1.0
SG B:CYS117 2.3 33.1 1.0
SG B:CYS114 2.3 29.4 1.0
SG B:CYS135 2.4 34.0 1.0
CB B:CYS114 3.2 30.1 1.0
CB B:CYS138 3.2 32.0 1.0
CB B:CYS117 3.3 34.2 1.0
CB B:CYS135 3.5 33.9 1.0
N B:CYS117 3.6 34.4 1.0
OG B:SER116 3.6 38.1 1.0
CA B:CYS117 4.0 35.5 1.0
O B:CYS117 4.0 41.8 1.0
N B:CYS135 4.1 35.8 1.0
N B:CYS138 4.2 35.7 1.0
CA B:CYS138 4.3 33.3 1.0
C B:CYS117 4.4 37.1 1.0
CB B:SER116 4.4 33.4 1.0
CA B:CYS135 4.4 35.3 1.0
CB B:VAL119 4.6 35.7 1.0
C B:SER116 4.7 33.6 1.0
CA B:CYS114 4.7 30.1 1.0
N B:SER116 4.9 33.8 1.0
CA B:SER116 4.9 33.4 1.0
O B:CYS135 5.0 33.4 1.0

Zinc binding site 3 out of 10 in 1tjl

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Zinc binding site 3 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


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 Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:41.4
occ:1.00
 SG C:CYS114 2.3 41.4 1.0
SG C:CYS138 2.3 41.1 1.0
SG C:CYS135 2.3 41.3 1.0
SG C:CYS117 2.3 47.0 1.0
CB C:CYS114 3.2 46.9 1.0
CB C:CYS138 3.3 41.1 1.0
CB C:CYS135 3.4 43.2 1.0
CB C:CYS117 3.5 48.6 1.0
N C:CYS117 3.8 50.5 1.0
N C:CYS135 3.9 43.9 1.0
O C:CYS117 4.1 55.4 1.0
CA C:CYS117 4.2 51.4 1.0
N C:CYS138 4.2 43.5 1.0
CA C:CYS135 4.2 45.0 1.0
CA C:CYS138 4.4 42.5 1.0
CB C:SER116 4.5 47.7 1.0
C C:CYS117 4.5 53.0 1.0
CB C:VAL119 4.6 53.7 1.0
CA C:CYS114 4.7 49.8 1.0
O C:CYS135 4.8 46.9 1.0
C C:CYS135 4.8 46.4 1.0
C C:SER116 4.9 48.8 1.0

Zinc binding site 4 out of 10 in 1tjl

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Zinc binding site 4 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


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 Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:45.1
occ:1.00
 SG D:CYS138 2.3 46.5 1.0
SG D:CYS117 2.3 50.4 1.0
SG D:CYS114 2.3 47.9 1.0
SG D:CYS135 2.4 49.1 1.0
CB D:CYS138 3.2 44.1 1.0
CB D:CYS114 3.2 46.1 1.0
CB D:CYS117 3.4 50.7 1.0
N D:CYS117 3.6 51.7 1.0
CB D:CYS135 3.6 48.3 1.0
CA D:CYS117 4.0 52.1 1.0
O D:CYS117 4.0 56.6 1.0
O D:HOH221 4.1 34.8 1.0
N D:CYS135 4.1 48.6 1.0
N D:CYS138 4.2 43.9 1.0
CA D:CYS138 4.3 43.2 1.0
CB D:SER116 4.3 48.2 1.0
C D:CYS117 4.4 54.1 1.0
CA D:CYS135 4.5 48.0 1.0
CB D:VAL119 4.7 54.1 1.0
C D:SER116 4.7 50.4 1.0
CA D:CYS114 4.7 47.2 1.0
O D:HOH218 4.8 41.0 1.0
CA D:SER116 4.9 49.1 1.0
N D:SER116 4.9 47.9 1.0
OG D:SER116 5.0 48.9 1.0

Zinc binding site 5 out of 10 in 1tjl

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Zinc binding site 5 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


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 Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:49.5
occ:1.00
 SG E:CYS138 2.3 48.9 1.0
SG E:CYS135 2.4 45.2 1.0
SG E:CYS114 2.4 47.6 1.0
SG E:CYS117 2.4 45.8 1.0
CB E:CYS138 3.1 42.7 1.0
CB E:CYS135 3.3 43.5 1.0
CB E:CYS114 3.4 48.4 1.0
CB E:CYS117 3.7 46.9 1.0
N E:CYS135 3.8 43.2 1.0
N E:CYS138 3.9 38.5 1.0
CA E:CYS138 4.1 38.9 1.0
N E:CYS117 4.1 48.7 1.0
CA E:CYS135 4.2 42.1 1.0
O E:HOH223 4.4 60.1 1.0
O E:HOH236 4.5 48.7 1.0
CA E:CYS117 4.5 47.6 1.0
CB E:SER116 4.6 51.2 1.0
O E:CYS117 4.6 51.7 1.0
O E:CYS135 4.6 40.7 1.0
C E:CYS135 4.7 40.7 1.0
CB E:VAL119 4.9 47.8 1.0
CA E:CYS114 4.9 48.3 1.0
C E:CYS117 4.9 48.8 1.0
C E:LEU134 5.0 43.9 1.0

Zinc binding site 6 out of 10 in 1tjl

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Zinc binding site 6 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


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 Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn200

b:37.5
occ:1.00
 SG F:CYS138 2.3 39.0 1.0
SG F:CYS117 2.4 36.6 1.0
SG F:CYS135 2.4 35.2 1.0
SG F:CYS114 2.4 35.4 1.0
CB F:CYS138 3.2 36.5 1.0
CB F:CYS135 3.5 33.2 1.0
CB F:CYS114 3.5 33.4 1.0
N F:CYS117 3.5 43.8 1.0
CB F:CYS117 3.6 40.4 1.0
CB F:SER116 3.8 46.2 1.0
N F:CYS135 4.0 32.1 1.0
CA F:CYS117 4.1 43.3 1.0
N F:CYS138 4.2 35.6 1.0
CA F:CYS138 4.3 36.2 1.0
CA F:CYS135 4.3 32.1 1.0
OG F:SER116 4.4 46.6 1.0
O F:CYS117 4.4 49.6 1.0
C F:SER116 4.5 44.0 1.0
CA F:SER116 4.6 43.8 1.0
N F:SER116 4.7 43.0 1.0
C F:CYS117 4.7 46.1 1.0
O F:CYS135 4.8 30.4 1.0
C F:CYS135 4.9 33.0 1.0
CA F:CYS114 5.0 35.0 1.0

Zinc binding site 7 out of 10 in 1tjl

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Zinc binding site 7 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn200

b:36.4
occ:1.00
 SG G:CYS117 2.3 35.7 1.0
SG G:CYS114 2.3 34.1 1.0
SG G:CYS138 2.4 37.1 1.0
SG G:CYS135 2.4 33.3 1.0
CB G:CYS138 3.3 35.8 1.0
CB G:CYS114 3.3 32.7 1.0
CB G:CYS117 3.4 37.4 1.0
CB G:CYS135 3.5 31.4 1.0
N G:CYS117 3.5 39.5 1.0
CA G:CYS117 4.0 39.0 1.0
N G:CYS135 4.1 29.1 1.0
CB G:SER116 4.1 37.8 1.0
O G:CYS117 4.1 44.4 1.0
N G:CYS138 4.3 35.8 1.0
CA G:CYS135 4.4 30.6 1.0
CA G:CYS138 4.4 36.4 1.0
C G:CYS117 4.5 40.6 1.0
C G:SER116 4.5 39.0 1.0
CA G:SER116 4.7 38.2 1.0
N G:SER116 4.7 38.2 1.0
CA G:CYS114 4.7 33.0 1.0
OG G:SER116 4.9 39.5 1.0
CB G:VAL119 4.9 40.1 1.0
O G:CYS135 5.0 31.5 1.0

Zinc binding site 8 out of 10 in 1tjl

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Zinc binding site 8 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn200

b:51.3
occ:1.00
 SG H:CYS117 2.3 52.9 1.0
SG H:CYS114 2.3 47.4 1.0
SG H:CYS138 2.3 50.5 1.0
SG H:CYS135 2.4 49.5 1.0
CB H:CYS114 3.3 48.0 1.0
CB H:CYS117 3.3 53.7 1.0
CB H:CYS138 3.4 48.0 1.0
CB H:CYS135 3.4 48.2 1.0
N H:CYS117 3.7 53.3 1.0
O H:CYS117 4.0 57.2 1.0
CA H:CYS117 4.0 54.0 1.0
N H:CYS135 4.1 49.5 1.0
N H:CYS138 4.2 49.1 1.0
CA H:CYS135 4.3 49.4 1.0
CB H:VAL119 4.4 55.4 1.0
C H:CYS117 4.4 55.2 1.0
CA H:CYS138 4.4 48.2 1.0
CB H:SER116 4.6 52.5 1.0
CA H:CYS114 4.7 48.4 1.0
C H:SER116 4.8 53.6 1.0
O H:CYS135 4.9 50.3 1.0
C H:CYS135 4.9 49.9 1.0
CG1 H:VAL119 4.9 53.8 1.0
CG2 H:VAL119 4.9 56.9 1.0

Zinc binding site 9 out of 10 in 1tjl

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Zinc binding site 9 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:41.9
occ:1.00
 SG I:CYS114 2.3 43.7 1.0
SG I:CYS117 2.3 46.0 1.0
SG I:CYS135 2.3 43.8 1.0
SG I:CYS138 2.3 45.6 1.0
CB I:CYS114 3.1 43.4 1.0
CB I:CYS138 3.3 43.9 1.0
CB I:CYS135 3.3 44.1 1.0
CB I:CYS117 3.4 46.5 1.0
N I:CYS117 3.6 48.0 1.0
N I:CYS135 3.9 44.7 1.0
O I:CYS117 3.9 53.2 1.0
CA I:CYS117 4.0 48.2 1.0
CA I:CYS135 4.2 43.8 1.0
N I:CYS138 4.2 44.5 1.0
C I:CYS117 4.3 49.7 1.0
CA I:CYS138 4.4 43.4 1.0
CB I:SER116 4.4 46.2 1.0
CA I:CYS114 4.5 44.0 1.0
CB I:VAL119 4.5 45.9 1.0
O I:CYS135 4.7 44.3 1.0
C I:SER116 4.7 47.7 1.0
C I:CYS135 4.7 43.9 1.0
OG I:SER116 4.8 44.9 1.0
N I:SER116 4.9 46.6 1.0
CA I:SER116 4.9 46.8 1.0
C I:CYS114 5.0 45.4 1.0

Zinc binding site 10 out of 10 in 1tjl

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Zinc binding site 10 out of 10 in the Crystal Structure of Transcription Factor Dksa From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Transcription Factor Dksa From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:32.4
occ:1.00
 SG J:CYS138 2.3 35.0 1.0
SG J:CYS114 2.4 31.9 1.0
SG J:CYS135 2.4 31.9 1.0
SG J:CYS117 2.4 33.7 1.0
CB J:CYS138 3.2 37.6 1.0
CB J:CYS114 3.3 36.6 1.0
CB J:CYS135 3.4 35.6 1.0
CB J:CYS117 3.7 38.8 1.0
N J:CYS135 3.9 39.1 1.0
N J:CYS117 3.9 43.6 1.0
N J:CYS138 4.1 38.1 1.0
CA J:CYS135 4.2 37.7 1.0
CA J:CYS138 4.3 39.3 1.0
CA J:CYS117 4.4 42.1 1.0
O J:CYS117 4.4 45.5 1.0
CB J:SER116 4.4 46.6 1.0
O J:HOH243 4.5 28.6 1.0
O J:HOH220 4.6 38.2 1.0
O J:CYS135 4.7 38.3 1.0
C J:CYS135 4.8 38.5 1.0
CA J:CYS114 4.8 39.2 1.0
C J:CYS117 4.8 43.7 1.0
C J:LEU134 4.9 40.1 1.0
CB J:VAL119 5.0 46.7 1.0
C J:SER116 5.0 43.9 1.0
CG2 J:VAL119 5.0 48.9 1.0

Reference:

A.Perederina, V.Svetlov, M.N.Vassylyeva, T.H.Tahirov, S.Yokoyama, I.Artsimovitch, D.G.Vassylyev. Regulation Through the Secondary Channel--Structural Framework For Ppgpp-Dksa Synergism During Transcription Cell(Cambridge,Mass.) V. 118 297 2004.
ISSN: ISSN 0092-8674
PubMed: 15294156
DOI: 10.1016/J.CELL.2004.06.030
Page generated: Mon Jan 25 16:14:08 2021

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