Zinc in PDB 9bct: Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna

Enzymatic activity of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna

All present enzymatic activity of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna:
2.7.7.6;

Other elements in 9bct:

The structure of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna (pdb code 9bct). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna, PDB code: 9bct:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9bct

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:114.7
occ:1.00
 NE2 A:HIS73 2.1 65.3 1.0
SG A:CYS63 2.3 87.5 1.0
SG A:CYS60 2.3 76.3 1.0
SG A:CYS70 2.3 82.7 1.0
CE1 A:HIS73 2.9 62.4 1.0
CB A:CYS60 3.1 75.1 1.0
CD2 A:HIS73 3.2 65.1 1.0
CB A:CYS63 3.4 72.2 1.0
CB A:CYS70 3.6 76.0 1.0
N A:CYS63 3.7 73.6 1.0
ND1 A:HIS73 4.0 58.2 1.0
CA A:CYS63 4.1 71.8 1.0
CG A:HIS73 4.2 62.5 1.0
CA A:CYS70 4.4 78.1 1.0
CA A:CYS60 4.6 71.8 1.0
CD A:PRO71 4.6 68.3 1.0
CA A:GLY52 4.6 65.3 1.0
CB A:THR62 4.7 66.3 1.0
C A:CYS63 4.7 75.3 1.0
N A:GLY72 4.7 72.2 1.0
N A:GLY64 4.7 71.0 1.0
C A:THR62 4.8 73.0 1.0
C A:CYS70 4.9 79.3 1.0
N A:ALA65 4.9 73.3 1.0
N A:THR62 4.9 69.8 1.0
N A:PRO71 4.9 69.9 1.0
C A:CYS60 5.0 71.6 1.0

Zinc binding site 2 out of 8 in 9bct

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:141.2
occ:1.00
 SG A:CYS147 2.3 105.7 1.0
SG A:CYS100 2.3 103.2 1.0
SG A:CYS150 2.3 109.5 1.0
CB A:CYS103 2.6 97.9 1.0
CB A:CYS100 2.7 88.3 1.0
CB A:CYS147 3.1 98.3 1.0
N A:CYS103 3.3 97.8 1.0
CA A:CYS103 3.5 97.3 1.0
CB A:CYS150 3.6 98.8 1.0
SG A:CYS103 3.9 108.1 1.0
N A:GLY104 4.2 88.0 1.0
CA A:CYS100 4.2 86.0 1.0
C A:CYS103 4.3 98.4 1.0
N A:CYS150 4.3 102.0 1.0
CA A:CYS147 4.6 97.2 1.0
CA A:CYS150 4.6 101.0 1.0
C A:GLU102 4.6 94.3 1.0
NE2 A:GLN154 4.6 86.6 1.0
C A:CYS100 4.7 86.7 1.0
N A:ARG105 4.8 83.4 1.0
N A:GLU102 4.9 91.5 1.0
N A:CYS100 4.9 83.0 1.0
O A:ARG105 5.0 86.1 1.0

Zinc binding site 3 out of 8 in 9bct

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:133.2
occ:1.00
 CB B:CYS1086 2.1 86.5 1.0
SG B:CYS1068 2.3 79.3 1.0
SG B:CYS1065 2.3 85.5 1.0
SG B:CYS1083 2.3 81.2 1.0
SG B:CYS1086 2.3 94.2 1.0
CB B:CYS1083 3.3 78.4 1.0
CB B:CYS1065 3.4 70.2 1.0
CA B:CYS1086 3.5 80.2 1.0
CB B:CYS1068 3.9 77.4 1.0
N B:CYS1086 4.0 83.6 1.0
N B:CYS1068 4.0 75.0 1.0
CB B:SER1067 4.2 78.3 1.0
C B:CYS1086 4.2 83.2 1.0
CB B:GLU1088 4.3 88.9 1.0
N B:GLY1087 4.5 83.5 1.0
CA B:CYS1068 4.6 78.5 1.0
CA B:CYS1083 4.7 74.9 1.0
CA B:CYS1065 4.8 69.5 1.0
O B:GLY1087 4.8 90.2 1.0
C B:SER1067 4.8 77.7 1.0
CA B:SER1067 4.8 76.6 1.0
N B:SER1067 4.9 74.0 1.0
O B:CYS1086 4.9 87.2 1.0
O B:CYS1083 5.0 81.2 1.0

Zinc binding site 4 out of 8 in 9bct

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:91.9
occ:1.00
 SG N:CYS45 2.3 59.5 1.0
SG N:CYS10 2.3 62.0 1.0
SG N:CYS44 2.3 56.8 1.0
SG N:CYS7 2.3 50.5 1.0
N N:CYS45 3.2 51.2 1.0
CB N:CYS7 3.3 42.7 1.0
CB N:CYS44 3.6 46.7 1.0
CB N:CYS45 3.6 50.7 1.0
CA N:CYS45 3.7 43.5 1.0
C N:CYS44 3.8 49.1 1.0
N N:CYS10 3.9 47.6 1.0
CB N:CYS10 4.0 53.6 1.0
CB N:THR9 4.1 53.3 1.0
NE N:ARG42 4.1 43.8 1.0
CA N:CYS44 4.3 44.8 1.0
CG2 N:THR9 4.4 58.5 1.0
CA N:CYS10 4.5 47.8 1.0
NH2 N:ARG42 4.5 45.2 1.0
O N:CYS44 4.6 52.9 1.0
N N:THR9 4.7 47.6 1.0
CA N:CYS7 4.7 38.1 1.0
CB N:ARG42 4.7 44.0 1.0
CA N:THR9 4.8 43.3 1.0
C N:THR9 4.8 56.8 1.0
CB N:LYS12 4.8 46.8 1.0
CZ N:ARG42 4.8 48.6 1.0
N N:CYS44 4.8 45.2 1.0

Zinc binding site 5 out of 8 in 9bct

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:117.5
occ:1.00
 SG P:CYS8 2.3 78.5 1.0
SG P:CYS27 2.3 71.0 1.0
SG P:CYS11 2.3 80.4 1.0
SG P:CYS30 2.3 70.7 1.0
CB P:CYS8 3.0 61.2 1.0
CB P:CYS27 3.1 65.4 1.0
CB P:CYS11 3.3 65.6 1.0
CB P:CYS30 3.8 73.7 1.0
N P:CYS11 4.0 66.6 1.0
N P:CYS30 4.1 68.7 1.0
CA P:CYS11 4.2 66.9 1.0
CB P:SER32 4.3 63.2 1.0
CA P:CYS8 4.5 57.9 1.0
CA P:CYS30 4.5 67.8 1.0
CA P:CYS27 4.6 66.3 1.0
CB P:TYR29 4.6 66.4 1.0
N P:GLY12 4.7 58.6 1.0
OG P:SER32 4.8 58.3 1.0
C P:CYS11 4.9 68.8 1.0
N P:SER32 4.9 66.3 1.0
O P:CYS27 4.9 75.0 1.0
C P:CYS27 5.0 69.9 1.0

Zinc binding site 6 out of 8 in 9bct

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn101

b:157.7
occ:1.00
 SG I:CYS22 2.3 136.4 1.0
SG I:CYS10 2.3 92.8 1.0
SG I:CYS19 2.3 117.2 1.0
SG I:CYS7 2.3 112.2 1.0
CB I:CYS7 3.1 102.3 1.0
CB I:CYS22 3.4 127.5 1.0
CB I:CYS19 3.7 117.6 1.0
CB I:CYS10 3.7 91.3 1.0
N I:CYS10 4.0 88.0 1.0
N I:CYS22 4.2 128.4 1.0
CA I:CYS22 4.4 128.6 1.0
CA I:CYS10 4.4 93.5 1.0
CA I:CYS7 4.6 101.6 1.0
CB I:TYR12 4.7 84.9 1.0
CB I:HIS9 4.9 96.8 1.0
C I:CYS10 4.9 97.4 1.0
C I:CYS22 4.9 129.8 1.0
N I:GLY23 4.9 127.4 1.0
N I:HIS11 4.9 87.7 1.0
CB I:SER24 4.9 125.1 1.0
N I:TYR12 5.0 78.2 1.0
CA I:CYS19 5.0 116.2 1.0
N I:HIS9 5.0 88.9 1.0

Zinc binding site 7 out of 8 in 9bct

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn701

b:131.9
occ:1.00
 OD2 J:ASP257 2.1 86.4 1.0
OD2 J:ASP364 2.2 82.3 1.0
NE2 J:HIS258 2.3 65.2 1.0
NE2 J:HIS615 2.3 80.0 1.0
CD2 J:HIS258 2.6 61.0 1.0
CE1 J:HIS615 3.1 77.6 1.0
CE1 J:HIS253 3.2 72.4 1.0
CG J:ASP257 3.2 81.4 1.0
CD2 J:HIS615 3.3 80.5 1.0
CG J:ASP364 3.4 77.2 1.0
CE1 J:HIS258 3.4 69.4 1.0
NE2 J:HIS253 3.6 70.7 1.0
OD1 J:ASP257 3.7 80.1 1.0
CG J:HIS258 3.8 63.0 1.0
ND1 J:HIS258 4.2 73.8 1.0
ND1 J:HIS615 4.2 76.3 1.0
CB J:ASP364 4.2 74.9 1.0
OD1 J:ASP364 4.3 82.1 1.0
CG J:HIS615 4.3 77.1 1.0
CB J:ASP257 4.3 69.9 1.0
ND1 J:HIS253 4.4 66.9 1.0
N J:ASP364 4.9 79.4 1.0
CD2 J:HIS253 4.9 61.7 1.0
CB J:HIS258 5.0 61.7 1.0

Zinc binding site 8 out of 8 in 9bct

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 44 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn701

b:157.7
occ:1.00
 NE2 M:HIS615 2.3 82.4 1.0
NE2 M:HIS258 2.3 64.8 1.0
OD2 M:ASP257 2.4 80.2 1.0
OD2 M:ASP364 2.4 76.5 1.0
OD1 M:ASP364 2.8 75.7 1.0
CD2 M:HIS258 2.8 61.5 1.0
CG M:ASP364 2.8 77.6 1.0
CE1 M:HIS615 2.9 77.4 1.0
NE2 M:HIS253 3.3 80.6 1.0
CD2 M:HIS615 3.3 77.9 1.0
CE1 M:HIS258 3.5 65.0 1.0
CG M:ASP257 3.6 73.7 1.0
CE1 M:HIS253 3.6 71.2 1.0
ND1 M:HIS615 4.0 74.5 1.0
CG M:HIS258 4.1 59.1 1.0
CB M:ASP364 4.2 75.8 1.0
CG M:HIS615 4.2 74.6 1.0
CB M:ASP257 4.3 65.2 1.0
ND1 M:HIS258 4.4 64.7 1.0
OD1 M:ASP257 4.5 73.9 1.0
CD2 M:HIS253 4.6 69.7 1.0
ND1 M:HIS253 4.9 60.4 1.0

Reference:

L.You, R.H.Ebright. Structural Basis of Archaeal Ftta-Dependent Transcription Termination To Be Published.
Page generated: Thu Oct 31 14:40:03 2024

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