Zinc in PDB 8oki: Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5

Enzymatic activity of Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5

All present enzymatic activity of Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5:
2.7.7.6;

Other elements in 8oki:

The structure of Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 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 Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 (pdb code 8oki). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5, PDB code: 8oki:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8oki

Go back to Zinc Binding Sites List in 8oki
Zinc binding site 1 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5


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 Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:30.0
occ:1.00
 NE2 A:HIS70 2.1 0.8 1.0
SG A:CYS57 2.3 0.7 1.0
SG A:CYS60 2.3 0.7 1.0
SG A:CYS67 2.3 0.8 1.0
CE1 A:HIS70 2.8 0.8 1.0
CD2 A:HIS70 3.2 0.8 1.0
CB A:CYS57 3.3 0.7 1.0
CB A:CYS60 3.6 0.7 1.0
CB A:CYS67 3.7 0.8 1.0
ND1 A:HIS70 4.0 0.8 1.0
N A:CYS60 4.0 0.7 1.0
CG A:HIS70 4.2 0.8 1.0
CA A:CYS60 4.3 0.7 1.0
CA A:CYS67 4.5 0.8 1.0
CB A:THR59 4.6 0.6 1.0
N A:GLY69 4.6 0.9 1.0
CA A:CYS57 4.7 0.7 1.0
O A:GLY61 4.7 0.6 1.0
C A:CYS60 4.7 0.7 1.0
O A:CYS57 4.8 0.7 1.0
CD A:PRO68 4.8 0.8 1.0
CA A:GLY49 4.9 0.8 1.0
C A:THR59 4.9 0.6 1.0
C A:CYS67 4.9 0.8 1.0
CA A:GLY69 4.9 0.9 1.0
C A:CYS57 5.0 0.7 1.0

Zinc binding site 2 out of 6 in 8oki

Go back to Zinc Binding Sites List in 8oki
Zinc binding site 2 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5


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 Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:30.0
occ:1.00
 SG A:CYS100 2.3 0.7 1.0
SG A:CYS97 2.3 0.8 1.0
SG A:CYS144 2.3 0.7 1.0
SG A:CYS147 2.3 0.8 1.0
CB A:CYS144 3.0 0.7 1.0
CB A:CYS97 3.1 0.8 1.0
CB A:CYS100 3.4 0.7 1.0
CB A:CYS147 3.7 0.8 1.0
N A:CYS147 4.0 0.8 1.0
O A:CYS147 4.0 0.8 1.0
CA A:CYS147 4.3 0.8 1.0
N A:CYS100 4.3 0.7 1.0
CA A:CYS100 4.4 0.7 1.0
CA A:CYS144 4.5 0.7 1.0
CA A:CYS97 4.6 0.8 1.0
C A:CYS147 4.6 0.8 1.0
CB A:HIS146 4.8 0.7 1.0
C A:HIS146 4.9 0.7 1.0

Zinc binding site 3 out of 6 in 8oki

Go back to Zinc Binding Sites List in 8oki
Zinc binding site 3 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5


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 Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:30.0
occ:1.00
 SG B:CYS1059 2.3 0.8 1.0
SG B:CYS1077 2.3 0.8 1.0
SG B:CYS1062 2.3 30.0 1.0
SG B:CYS1080 2.3 0.7 1.0
CB B:CYS1059 3.2 0.8 1.0
CB B:CYS1077 3.3 0.8 1.0
CB B:CYS1062 3.3 30.0 1.0
CB B:CYS1080 3.6 0.7 1.0
O B:CYS1080 4.1 0.7 1.0
N B:CYS1062 4.1 30.0 1.0
CG1 B:VAL1079 4.2 0.8 1.0
N B:CYS1080 4.2 0.7 1.0
CA B:CYS1062 4.3 30.0 1.0
CA B:CYS1080 4.3 0.7 1.0
C B:CYS1080 4.5 0.7 1.0
CB B:GLU1082 4.5 0.7 1.0
CA B:CYS1059 4.6 0.8 1.0
CA B:CYS1077 4.7 0.8 1.0
C B:CYS1062 4.9 30.0 1.0
N B:GLY1063 4.9 0.9 1.0

Zinc binding site 4 out of 6 in 8oki

Go back to Zinc Binding Sites List in 8oki
Zinc binding site 4 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5


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 Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn101

b:30.0
occ:1.00
 SG I:CYS21 2.3 203.7 1.0
SG I:CYS18 2.3 202.0 1.0
SG I:CYS9 2.3 190.1 1.0
SG I:CYS6 2.3 204.5 1.0
CB I:CYS18 2.6 200.5 1.0
CB I:CYS6 3.3 194.8 1.0
CB I:CYS9 3.4 186.2 1.0
CB I:CYS21 3.5 201.9 1.0
NE2 I:HIS8 4.1 222.9 1.0
CA I:CYS18 4.1 200.8 1.0
N I:CYS21 4.3 198.0 1.0
CE1 I:HIS8 4.4 222.1 1.0
CG2 I:VAL20 4.4 190.2 1.0
CA I:CYS21 4.4 202.3 1.0
O I:SER23 4.6 202.3 1.0
O I:CYS21 4.6 211.1 1.0
CA I:CYS9 4.7 185.1 1.0
CA I:CYS6 4.7 194.6 1.0
CD2 I:HIS8 4.7 217.2 1.0
N I:CYS9 4.8 188.9 1.0
OG I:SER23 4.8 221.7 1.0
N I:CYS18 4.9 205.3 1.0
C I:CYS18 4.9 205.9 1.0
C I:CYS21 4.9 208.9 1.0

Zinc binding site 5 out of 6 in 8oki

Go back to Zinc Binding Sites List in 8oki
Zinc binding site 5 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5


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 Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:30.0
occ:1.00
 SG N:CYS45 2.3 0.6 1.0
SG N:CYS10 2.3 0.6 1.0
SG N:CYS7 2.3 0.6 1.0
SG N:CYS44 2.3 0.6 1.0
CB N:CYS7 3.3 0.6 1.0
CB N:CYS10 3.5 0.6 1.0
N N:CYS45 3.6 0.6 1.0
CB N:CYS45 3.7 0.6 1.0
C N:CYS44 3.8 0.6 1.0
CB N:CYS44 3.8 0.6 1.0
CA N:CYS45 3.8 0.6 1.0
N N:CYS10 3.9 0.6 1.0
O N:CYS44 4.1 0.6 1.0
NH2 N:ARG42 4.2 0.5 1.0
CA N:CYS10 4.2 0.6 1.0
CA N:CYS44 4.4 0.6 1.0
CA N:CYS7 4.7 0.6 1.0
CB N:LYS12 4.8 0.6 1.0
CB N:THR9 4.8 0.5 1.0
C N:CYS10 4.8 0.6 1.0
N N:GLY11 4.9 0.5 1.0
NE N:ARG42 5.0 0.5 1.0
C N:THR9 5.0 0.5 1.0
N N:LYS12 5.0 0.6 1.0

Zinc binding site 6 out of 6 in 8oki

Go back to Zinc Binding Sites List in 8oki
Zinc binding site 6 out of 6 in the Cryo-Em Structure of Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5


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 Pyrococcus Furiosus Transcription Elongation Complex Bound to SPT4/5 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:30.0
occ:1.00
 SG P:CYS11 2.3 84.7 1.0
SG P:CYS8 2.3 86.8 1.0
SG P:CYS30 2.3 82.8 1.0
SG P:CYS27 2.3 79.7 1.0
CB P:CYS8 2.8 86.8 1.0
CB P:CYS11 3.0 84.7 1.0
CB P:CYS27 3.2 79.7 1.0
CB P:CYS30 3.3 82.8 1.0
N P:CYS30 3.9 82.8 1.0
CA P:CYS11 4.2 84.7 1.0
N P:CYS11 4.2 84.7 1.0
CA P:CYS30 4.2 82.8 1.0
CB P:TYR29 4.2 81.8 1.0
CA P:CYS8 4.3 86.8 1.0
C P:TYR29 4.5 81.8 1.0
CA P:CYS27 4.7 79.7 1.0
CA P:TYR29 4.8 81.8 1.0
CD2 P:TYR29 4.8 81.8 1.0
CG P:TYR29 4.9 81.8 1.0
C P:CYS11 4.9 84.7 1.0
N P:TYR29 5.0 81.8 1.0
N P:GLY12 5.0 83.3 1.0

Reference:

D.M.Tarau, F.Grunberger, M.Pilsl, R.Reichelt, F.B.Heiss, S.Koenig, H.Urlaub, W.Hausner, C.Engel, D.Grohmann. Structural Basis of Archaeal Rna Polymerase Transcription Elongation and SPT4/5 Recruitment Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
Page generated: Thu Oct 31 08:49:53 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy