Zinc in PDB 7khe: Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp

Enzymatic activity of Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp

All present enzymatic activity of Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp:
2.7.7.6;

Other elements in 7khe:

The structure of Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp (pdb code 7khe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp, PDB code: 7khe:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7khe

Go back to Zinc Binding Sites List in 7khe
Zinc binding site 1 out of 3 in the Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.6
occ:1.00
SG D:CYS85 2.2 0.1 1.0
SG D:CYS72 2.2 0.4 1.0
SG D:CYS88 2.2 99.3 1.0
SG D:CYS70 2.3 0.7 1.0
CB D:CYS85 3.1 0.1 1.0
CB D:CYS70 3.2 0.7 1.0
N D:CYS72 3.4 0.4 1.0
CB D:CYS72 3.5 0.4 1.0
CB D:CYS88 3.8 99.3 1.0
CA D:CYS72 3.9 0.4 1.0
N D:GLY73 4.0 0.8 1.0
N D:CYS88 4.1 99.3 1.0
N D:LEU71 4.1 0.1 1.0
N D:LYS74 4.1 0.5 1.0
C D:CYS72 4.3 0.4 1.0
O D:CYS88 4.3 99.3 1.0
C D:CYS70 4.4 0.7 1.0
CA D:CYS70 4.4 0.7 1.0
CB D:LYS74 4.4 0.5 1.0
CA D:CYS88 4.4 99.3 1.0
C D:LEU71 4.5 0.1 1.0
CA D:CYS85 4.5 0.1 1.0
CA D:LEU71 4.8 0.1 1.0
CB D:LYS87 4.8 0.7 1.0
C D:CYS88 4.9 99.3 1.0
CA D:LYS74 4.9 0.5 1.0
CG2 D:VAL90 5.0 94.3 1.0
C D:CYS85 5.0 0.1 1.0
CA D:GLY73 5.0 0.8 1.0

Zinc binding site 2 out of 3 in 7khe

Go back to Zinc Binding Sites List in 7khe
Zinc binding site 2 out of 3 in the Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:0.7
occ:1.00
SG D:CYS898 2.0 73.4 1.0
SG D:CYS895 2.0 74.3 1.0
SG D:CYS814 2.1 82.5 1.0
SG D:CYS888 2.3 77.8 1.0
CB D:CYS895 3.0 74.3 1.0
CB D:CYS898 3.1 73.4 1.0
CB D:CYS888 3.4 77.8 1.0
NH2 D:ARG883 3.4 75.3 1.0
CB D:CYS814 3.5 82.5 1.0
CA D:CYS888 3.9 77.8 1.0
N D:CYS898 3.9 73.4 1.0
CA D:CYS895 4.0 74.3 1.0
N D:CYS895 4.0 74.3 1.0
CA D:CYS898 4.1 73.4 1.0
N D:CYS814 4.2 82.5 1.0
N D:ASP889 4.3 82.2 1.0
O D:CYS895 4.4 74.3 1.0
CG2 D:THR816 4.4 84.4 1.0
CZ D:ARG883 4.5 75.3 1.0
CA D:CYS814 4.5 82.5 1.0
C D:CYS895 4.5 74.3 1.0
C D:CYS888 4.6 77.8 1.0
NE D:ARG883 4.6 75.3 1.0

Zinc binding site 3 out of 3 in 7khe

Go back to Zinc Binding Sites List in 7khe
Zinc binding site 3 out of 3 in the Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:0.4
occ:1.00
SG M:CYS138 2.2 0.1 1.0
SG M:CYS135 2.3 0.1 1.0
SG M:CYS117 2.3 0.3 1.0
SG M:CYS114 2.4 0.1 1.0
CB M:CYS138 3.2 0.1 1.0
CB M:CYS114 3.4 0.1 1.0
CB M:CYS135 3.7 0.1 1.0
N M:CYS117 3.8 0.3 1.0
CB M:CYS117 3.8 0.3 1.0
CG1 M:VAL119 4.0 0.1 1.0
N M:CYS135 4.1 0.1 1.0
O M:CYS117 4.2 0.3 1.0
CA M:CYS117 4.3 0.3 1.0
N M:CYS138 4.3 0.1 1.0
CB M:SER116 4.3 0.3 1.0
CA M:CYS138 4.3 0.1 1.0
CA M:CYS135 4.5 0.1 1.0
C M:CYS117 4.7 0.3 1.0
C M:SER116 4.8 0.3 1.0
CA M:CYS114 4.8 0.1 1.0
O M:CYS135 4.9 0.1 1.0
N M:SER116 4.9 0.3 1.0
CA M:SER116 4.9 0.3 1.0

Reference:

Y.Shin, M.Z.Qayyum, K.S.Murakami. Escherichia Coli Rna Polymerase and RRNBP1 Promoter Pre-Open Complex with Dksa/Ppgpp To Be Published.
Page generated: Wed Dec 16 14:04:04 2020

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