Zinc in PDB 9bcu: Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 52 Nt Rna

Enzymatic activity of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 52 Nt Rna

All present enzymatic activity of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 52 Nt Rna:
2.7.7.6;

Other elements in 9bcu:

The structure of Cryo-Em Structure of Thermococcus Kodakarensis Ftta-Dependent Transcription Pre-Termination Complex Containing 52 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 52 Nt Rna (pdb code 9bcu). 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 52 Nt Rna, PDB code: 9bcu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:93.7
occ:1.00
 NE2 A:HIS73 2.1 51.9 1.0
SG A:CYS70 2.3 60.9 1.0
SG A:CYS63 2.3 82.2 1.0
SG A:CYS60 2.3 58.3 1.0
CD2 A:HIS73 2.6 46.1 1.0
CB A:CYS63 3.1 60.0 1.0
CE1 A:HIS73 3.3 45.0 1.0
CB A:CYS60 3.3 56.0 1.0
N A:CYS63 3.7 61.9 1.0
CG A:HIS73 3.8 42.4 1.0
CB A:CYS70 3.9 56.9 1.0
CA A:CYS63 4.0 62.3 1.0
CA A:GLY52 4.1 48.2 1.0
ND1 A:HIS73 4.1 47.1 1.0
N A:GLY72 4.4 47.5 1.0
N A:GLY52 4.5 45.7 1.0
CB A:THR62 4.5 48.5 1.0
C A:THR62 4.6 55.8 1.0
CD A:PRO71 4.6 45.9 1.0
CA A:GLY72 4.7 41.9 1.0
CA A:CYS70 4.7 55.3 1.0
CA A:CYS60 4.8 54.6 1.0
C A:GLY72 4.8 45.7 1.0
N A:PRO71 4.9 47.3 1.0
C A:CYS70 4.9 58.1 1.0
CA A:THR62 4.9 54.2 1.0
N A:THR62 5.0 54.5 1.0

Zinc binding site 2 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:108.1
occ:1.00
 CB A:CYS103 2.0 72.5 1.0
SG A:CYS147 2.3 88.0 1.0
SG A:CYS150 2.3 84.0 1.0
SG A:CYS103 2.3 77.5 1.0
SG A:CYS100 2.3 78.1 1.0
CB A:CYS147 3.0 73.8 1.0
CB A:CYS100 3.1 66.4 1.0
CA A:CYS103 3.4 69.5 1.0
CB A:CYS150 3.8 73.4 1.0
N A:CYS103 3.9 67.9 1.0
N A:CYS150 4.1 74.2 1.0
C A:CYS103 4.2 67.6 1.0
N A:GLY104 4.4 65.8 1.0
CB A:HIS149 4.4 71.5 1.0
CA A:CYS147 4.5 73.7 1.0
CA A:CYS150 4.5 75.5 1.0
CA A:CYS100 4.6 62.5 1.0
NE2 A:GLN154 4.7 66.2 1.0
N A:ARG105 4.8 62.1 1.0
C A:HIS149 4.9 72.3 1.0
C A:CYS147 5.0 76.4 1.0
N A:HIS149 5.0 70.6 1.0
CB A:ALA152 5.0 70.2 1.0

Zinc binding site 3 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:93.0
occ:1.00
 SG B:CYS1068 2.3 51.2 1.0
SG B:CYS1083 2.3 63.2 1.0
SG B:CYS1086 2.3 64.8 1.0
SG B:CYS1065 2.3 52.5 1.0
CB B:CYS1086 2.9 59.8 1.0
CB B:CYS1083 3.2 53.0 1.0
CB B:CYS1065 3.3 44.6 1.0
CB B:CYS1068 3.8 51.9 1.0
N B:CYS1068 3.9 45.7 1.0
CA B:CYS1086 3.9 58.4 1.0
N B:CYS1086 4.0 57.1 1.0
CB B:SER1067 4.3 55.4 1.0
N B:GLY1087 4.3 65.8 1.0
C B:CYS1086 4.4 60.5 1.0
CA B:CYS1068 4.5 49.4 1.0
CB B:GLU1088 4.6 61.2 1.0
CA B:CYS1083 4.6 53.1 1.0
O B:GLY1087 4.7 73.1 1.0
CA B:CYS1065 4.8 38.6 1.0
CB B:HIS1070 4.9 38.9 1.0
C B:SER1067 4.9 56.5 1.0
CG1 B:VAL1085 4.9 51.7 1.0
N B:SER1067 4.9 51.9 1.0
C B:GLY1087 4.9 67.0 1.0
CA B:SER1067 5.0 52.7 1.0

Zinc binding site 4 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:73.9
occ:1.00
 SG N:CYS45 2.3 39.6 1.0
SG N:CYS10 2.3 45.2 1.0
SG N:CYS44 2.3 40.5 1.0
SG N:CYS7 2.3 35.7 1.0
N N:CYS45 3.2 27.1 1.0
CB N:CYS7 3.3 27.2 1.0
CB N:CYS45 3.6 34.2 1.0
CB N:CYS44 3.6 32.2 1.0
CA N:CYS45 3.7 31.4 1.0
C N:CYS44 3.9 29.4 1.0
N N:CYS10 3.9 32.7 1.0
CB N:CYS10 3.9 37.1 1.0
CB N:THR9 4.1 43.9 1.0
NE N:ARG42 4.2 35.1 1.0
CA N:CYS44 4.3 29.3 1.0
CA N:CYS10 4.5 31.8 1.0
O N:CYS44 4.6 45.7 1.0
NH2 N:ARG42 4.7 36.4 1.0
OG1 N:THR9 4.8 46.5 1.0
CA N:CYS7 4.8 27.8 1.0
CB N:ARG42 4.8 33.6 1.0
N N:THR9 4.8 38.5 1.0
C N:THR9 4.8 36.0 1.0
CA N:THR9 4.8 27.1 1.0
CB N:LYS12 4.8 28.7 1.0
CG2 N:THR9 4.8 42.6 1.0
N N:CYS44 4.9 32.6 1.0
CZ N:ARG42 5.0 31.9 1.0

Zinc binding site 5 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:107.1
occ:1.00
 SG P:CYS8 2.3 62.4 1.0
SG P:CYS30 2.3 65.2 1.0
SG P:CYS11 2.3 73.2 1.0
SG P:CYS27 2.3 57.6 1.0
CB P:CYS8 3.0 50.5 1.0
CB P:CYS27 3.1 50.7 1.0
CB P:CYS11 3.2 53.6 1.0
CB P:CYS30 3.8 58.5 1.0
N P:CYS11 3.9 58.7 1.0
N P:CYS30 4.1 59.2 1.0
CA P:CYS11 4.1 57.5 1.0
CA P:CYS30 4.5 55.7 1.0
CA P:CYS8 4.5 48.8 1.0
CB P:SER32 4.5 50.6 1.0
CA P:CYS27 4.6 49.9 1.0
CB P:TYR29 4.6 51.1 1.0
N P:GLY12 4.7 54.3 1.0
C P:CYS11 4.8 57.1 1.0
N P:SER32 4.9 49.6 1.0

Zinc binding site 6 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn101

b:168.4
occ:1.00
 SG I:CYS10 2.3 129.1 1.0
SG I:CYS7 2.3 125.5 1.0
SG I:CYS22 2.3 134.8 1.0
SG I:CYS19 2.3 131.2 1.0
CB I:CYS7 3.1 121.3 1.0
CB I:CYS10 3.7 120.5 1.0
CB I:CYS19 3.8 131.1 1.0
N I:CYS10 3.9 120.2 1.0
CB I:CYS22 3.9 133.5 1.0
N I:CYS22 4.0 133.3 1.0
CB I:SER24 4.2 130.3 1.0
CA I:CYS10 4.4 121.2 1.0
CB I:HIS9 4.4 122.3 1.0
CA I:CYS22 4.4 134.7 1.0
N I:SER24 4.5 132.2 1.0
CB I:VAL21 4.6 127.3 1.0
CA I:CYS7 4.6 121.2 1.0
OG I:SER24 4.6 128.4 1.0
N I:GLY23 4.7 130.6 1.0
ND1 I:HIS9 4.8 123.2 1.0
C I:CYS22 4.8 134.2 1.0
C I:HIS9 4.9 121.0 1.0
N I:HIS9 4.9 119.0 1.0
CA I:HIS9 5.0 120.7 1.0
CA I:SER24 5.0 131.3 1.0
CB I:TYR12 5.0 106.5 1.0

Zinc binding site 7 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn701

b:117.1
occ:1.00
 OD2 J:ASP257 2.1 72.0 1.0
OD2 J:ASP364 2.1 63.5 1.0
NE2 J:HIS615 2.3 60.8 1.0
NE2 J:HIS258 2.3 50.2 1.0
CE1 J:HIS615 2.8 57.3 1.0
CD2 J:HIS258 2.8 46.9 1.0
CG J:ASP257 3.2 67.3 1.0
CG J:ASP364 3.4 59.8 1.0
CD2 J:HIS615 3.4 60.0 1.0
CE1 J:HIS258 3.5 57.6 1.0
OD1 J:ASP257 3.7 71.6 1.0
CE1 J:HIS253 3.7 55.8 1.0
ND1 J:HIS615 3.9 57.7 1.0
OD1 J:ASP364 4.0 64.6 1.0
NE2 J:HIS253 4.1 51.8 1.0
CG J:HIS258 4.1 50.0 1.0
CG J:HIS615 4.2 56.2 1.0
ND1 J:HIS258 4.4 59.9 1.0
CB J:ASP364 4.4 55.4 1.0
CB J:ASP257 4.4 56.8 1.0
ND1 J:HIS253 5.0 53.8 1.0

Zinc binding site 8 out of 8 in 9bcu

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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 52 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 52 Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn701

b:133.6
occ:1.00
 NE2 M:HIS258 2.3 63.9 1.0
NE2 M:HIS615 2.3 79.4 1.0
OD2 M:ASP364 2.3 80.0 1.0
OD1 M:ASP257 2.7 73.3 1.0
OD1 M:ASP364 2.8 77.4 1.0
CE1 M:HIS615 2.8 74.2 1.0
CG M:ASP364 2.8 76.8 1.0
CD2 M:HIS258 3.0 61.4 1.0
CD2 M:HIS615 3.4 74.1 1.0
CE1 M:HIS258 3.4 62.9 1.0
NE2 M:HIS253 3.7 70.4 1.0
CG M:ASP257 3.9 73.5 1.0
ND1 M:HIS615 3.9 73.8 1.0
CE1 M:HIS253 4.1 65.6 1.0
CB M:ASP364 4.2 72.4 1.0
CG M:HIS615 4.2 72.5 1.0
CG M:HIS258 4.3 60.8 1.0
ND1 M:HIS258 4.4 65.7 1.0
OD2 M:ASP257 4.5 77.2 1.0
CB M:ASP257 4.9 68.7 1.0

Reference:

L.You, R.H.Ebright. Structural Basis of Archaeal Ftta-Dependent Transcription Termination To Be Published.
Page generated: Thu Oct 31 14:40:04 2024

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