Zinc in PDB 7x74: Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.

Enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.

All present enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.:
2.7.7.6;

Other elements in 7x74:

The structure of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. (pdb code 7x74). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers., PDB code: 7x74:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 7x74

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Zinc binding site 1 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1402

b:107.8
occ:1.00
 SG D:CYS78 2.3 89.6 1.0
SG D:CYS75 2.3 93.0 1.0
SG D:CYS62 2.3 92.6 1.0
SG D:CYS60 2.3 89.9 1.0
N D:CYS62 3.1 92.6 1.0
CB D:CYS62 3.3 92.6 1.0
CB D:CYS60 3.3 89.9 1.0
CA D:CYS62 3.6 92.6 1.0
CB D:CYS78 3.6 89.6 1.0
N D:TYR61 3.8 81.2 1.0
N D:CYS78 3.9 89.6 1.0
CB D:CYS75 3.9 93.0 1.0
N D:GLY63 4.0 101.0 1.0
C D:CYS60 4.0 89.9 1.0
C D:TYR61 4.1 81.2 1.0
C D:CYS62 4.2 92.6 1.0
CA D:CYS60 4.2 89.9 1.0
CA D:CYS78 4.3 89.6 1.0
N D:LYS64 4.3 102.9 1.0
CA D:TYR61 4.4 81.2 1.0
CB D:ARG77 4.4 105.0 1.0
CB D:LYS64 4.5 102.9 1.0
O D:CYS60 4.6 89.9 1.0
CB D:TYR61 4.9 81.2 1.0
N D:GLY79 4.9 83.9 1.0
O D:CYS75 4.9 93.0 1.0
C D:ARG77 4.9 105.0 1.0
C D:CYS78 4.9 89.6 1.0
CB D:VAL80 5.0 77.9 1.0

Zinc binding site 2 out of 14 in 7x74

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Zinc binding site 2 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1403

b:150.7
occ:1.00
 SG D:CYS972 2.3 74.6 1.0
SG D:CYS969 2.3 66.8 1.0
SG D:CYS886 2.3 89.2 1.0
SG D:CYS962 2.3 75.3 1.0
CB D:CYS886 2.8 89.2 1.0
CB D:CYS972 3.1 74.6 1.0
CB D:CYS962 3.4 75.3 1.0
CB D:CYS969 3.4 66.8 1.0
CA D:CYS886 3.8 89.2 1.0
CA D:CYS962 4.0 75.3 1.0
N D:CYS972 4.1 74.6 1.0
N D:CYS969 4.1 66.8 1.0
CA D:CYS972 4.2 74.6 1.0
CA D:CYS969 4.3 66.8 1.0
N D:CYS886 4.3 89.2 1.0
N D:GLU963 4.4 88.7 1.0
C D:CYS962 4.6 75.3 1.0
O D:CYS969 4.6 66.8 1.0
C D:CYS969 4.7 66.8 1.0
O D:GLU963 4.9 88.7 1.0

Zinc binding site 3 out of 14 in 7x74

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Zinc binding site 3 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:283.0
occ:1.00
 SG G:CYS130 2.3 181.2 1.0
SG G:CYS90 2.3 190.6 1.0
SG G:CYS93 2.3 191.2 1.0
SG G:CYS133 2.3 174.2 1.0
CB G:CYS93 3.1 191.2 1.0
CB G:CYS130 3.5 181.2 1.0
N G:CYS93 3.6 191.2 1.0
CB G:CYS90 3.7 190.6 1.0
N G:CYS130 3.9 181.2 1.0
CA G:CYS93 4.0 191.2 1.0
CB G:CYS133 4.1 174.2 1.0
OD1 G:ASP132 4.1 172.5 1.0
CA G:CYS130 4.3 181.2 1.0
CB G:ALA92 4.3 181.9 1.0
NZ G:LYS95 4.5 187.6 1.0
C G:ALA92 4.6 181.9 1.0
OD2 G:ASP132 4.9 172.5 1.0
CA G:ALA92 4.9 181.9 1.0
CG G:ASP132 4.9 172.5 1.0
N G:ALA92 4.9 181.9 1.0
CA G:CYS133 4.9 174.2 1.0
N G:CYS133 5.0 174.2 1.0

Zinc binding site 4 out of 14 in 7x74

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Zinc binding site 4 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn202

b:256.2
occ:1.00
 NE2 G:HIS85 2.3 196.9 1.0
NE2 G:HIS87 2.3 191.8 1.0
CE1 G:HIS87 2.3 191.8 1.0
SG G:CYS79 2.3 192.0 1.0
CE1 G:HIS85 2.5 196.9 1.0
CB G:CYS79 3.3 192.0 1.0
CD2 G:HIS85 3.5 196.9 1.0
ND1 G:HIS87 3.6 191.8 1.0
ND1 G:HIS85 3.7 196.9 1.0
CD2 G:HIS87 3.7 191.8 1.0
CB G:ASP65 4.1 182.3 1.0
OD2 G:ASP65 4.1 182.3 1.0
CG G:HIS85 4.2 196.9 1.0
CG G:HIS87 4.3 191.8 1.0
O G:THR81 4.3 189.2 1.0
CG G:ASP65 4.4 182.3 1.0
CG G:GLU98 4.6 191.9 1.0
CA G:CYS79 4.7 192.0 1.0
N G:CYS79 5.0 192.0 1.0

Zinc binding site 5 out of 14 in 7x74

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Zinc binding site 5 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn203

b:271.0
occ:1.00
 NE2 G:HIS122 2.3 188.9 1.0
NE2 G:HIS86 2.3 192.6 1.0
NE2 G:HIS84 2.3 197.4 1.0
CD2 G:HIS122 2.3 188.9 1.0
CE1 G:HIS84 2.6 197.4 1.0
OE2 G:GLU105 2.8 182.0 1.0
OE1 G:GLU105 2.9 182.0 1.0
CD2 G:HIS86 3.0 192.6 1.0
CD G:GLU105 3.1 182.0 1.0
CE1 G:HIS86 3.3 192.6 1.0
CE1 G:HIS122 3.6 188.9 1.0
CD2 G:HIS84 3.6 197.4 1.0
CG G:HIS122 3.6 188.9 1.0
ND1 G:HIS84 3.9 197.4 1.0
CG G:HIS86 4.2 192.6 1.0
ND1 G:HIS122 4.2 188.9 1.0
ND1 G:HIS86 4.3 192.6 1.0
CG G:HIS84 4.4 197.4 1.0
CG G:GLU105 4.5 182.0 1.0
CB G:HIS122 4.8 188.9 1.0
O G:HIS122 4.8 188.9 1.0
O G:HIS85 5.0 196.9 1.0

Zinc binding site 6 out of 14 in 7x74

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Zinc binding site 6 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:260.7
occ:1.00
 SG H:CYS93 2.3 190.3 1.0
SG H:CYS90 2.3 190.7 1.0
SG H:CYS133 2.3 182.1 1.0
SG H:CYS130 2.3 187.3 1.0
CB H:CYS130 2.5 187.3 1.0
CB H:CYS93 3.2 190.3 1.0
CB H:CYS90 3.5 190.7 1.0
NZ H:LYS95 3.6 186.8 1.0
OD1 H:ASP132 3.7 180.6 1.0
N H:CYS93 3.7 190.3 1.0
CB H:CYS133 3.9 182.1 1.0
CA H:CYS130 3.9 187.3 1.0
CA H:CYS93 4.1 190.3 1.0
CB H:ALA92 4.2 185.3 1.0
N H:CYS130 4.5 187.3 1.0
N H:CYS133 4.5 182.1 1.0
C H:ALA92 4.6 185.3 1.0
CA H:CYS133 4.7 182.1 1.0
CA H:ALA92 4.8 185.3 1.0
CG H:ASP132 4.9 180.6 1.0
CE H:LYS95 4.9 186.8 1.0
CA H:CYS90 4.9 190.7 1.0
C H:CYS130 4.9 187.3 1.0
N H:ALA92 4.9 185.3 1.0

Zinc binding site 7 out of 14 in 7x74

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Zinc binding site 7 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn202

b:208.0
occ:1.00
 NE2 H:HIS85 2.2 181.8 1.0
NE2 H:HIS87 2.2 182.2 1.0
SG H:CYS79 2.3 179.9 1.0
CD2 H:HIS85 3.1 181.8 1.0
CE1 H:HIS85 3.1 181.8 1.0
CE1 H:HIS87 3.1 182.2 1.0
CD2 H:HIS87 3.2 182.2 1.0
CB H:ASP65 3.2 180.9 1.0
OD2 H:ASP65 3.3 180.9 1.0
CB H:CYS79 3.4 179.9 1.0
CG H:ASP65 3.7 180.9 1.0
ND1 H:HIS85 4.2 181.8 1.0
CG H:HIS85 4.2 181.8 1.0
ND1 H:HIS87 4.3 182.2 1.0
CG H:HIS87 4.3 182.2 1.0
CA H:ASP65 4.4 180.9 1.0
N H:ASP65 4.7 180.9 1.0
CA H:CYS79 4.7 179.9 1.0
NH1 H:ARG77 4.9 180.8 1.0
O H:HIS85 4.9 181.8 1.0
OD1 H:ASP65 4.9 180.9 1.0
CG H:GLU98 5.0 180.6 1.0

Zinc binding site 8 out of 14 in 7x74

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Zinc binding site 8 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


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 Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn203

b:258.9
occ:1.00
 NE2 H:HIS86 2.1 181.6 1.0
NE2 H:HIS84 2.2 182.0 1.0
OE2 H:GLU105 2.2 173.9 1.0
NE2 H:HIS122 2.3 184.7 1.0
CD2 H:HIS122 2.3 184.7 1.0
OE1 H:GLU105 2.9 173.9 1.0
CD H:GLU105 2.9 173.9 1.0
CE1 H:HIS86 3.0 181.6 1.0
CD2 H:HIS86 3.0 181.6 1.0
CE1 H:HIS84 3.1 182.0 1.0
CD2 H:HIS84 3.2 182.0 1.0
CE1 H:HIS122 3.5 184.7 1.0
CG H:HIS122 3.5 184.7 1.0
OE2 H:GLU100 3.6 175.4 1.0
OE1 H:GLU100 3.9 175.4 1.0
ND1 H:HIS86 4.0 181.6 1.0
ND1 H:HIS122 4.1 184.7 1.0
CG H:HIS86 4.1 181.6 1.0
CD H:GLU100 4.1 175.4 1.0
ND1 H:HIS84 4.2 182.0 1.0
CG H:HIS84 4.3 182.0 1.0
CG H:GLU105 4.3 173.9 1.0
CG2 H:VAL104 4.6 171.8 1.0
CB H:HIS122 4.6 184.7 1.0

Zinc binding site 9 out of 14 in 7x74

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Zinc binding site 9 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:269.2
occ:1.00
 SG M:CYS133 2.3 182.2 1.0
SG M:CYS130 2.3 187.6 1.0
SG M:CYS93 2.3 185.8 1.0
SG M:CYS90 2.3 187.0 1.0
CB M:CYS93 3.1 185.8 1.0
CB M:CYS130 3.2 187.6 1.0
CB M:CYS90 3.5 187.0 1.0
N M:CYS130 3.6 187.6 1.0
N M:CYS93 3.8 185.8 1.0
CA M:CYS93 4.0 185.8 1.0
CA M:CYS130 4.0 187.6 1.0
CB M:CYS133 4.1 182.2 1.0
OD1 M:ASP132 4.3 179.2 1.0
CB M:ALA92 4.3 182.1 1.0
C M:ALA92 4.5 182.1 1.0
NZ M:LYS95 4.6 184.2 1.0
C M:THR129 4.7 183.4 1.0
OD2 M:ASP132 4.8 179.2 1.0
CA M:ALA92 4.9 182.1 1.0
CA M:CYS90 4.9 187.0 1.0
CA M:THR129 4.9 183.4 1.0
CG M:ASP132 4.9 179.2 1.0

Zinc binding site 10 out of 14 in 7x74

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Zinc binding site 10 out of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with Two Zur Dimers. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:219.8
occ:1.00
 CB M:CYS79 2.2 184.7 1.0
SG M:CYS79 2.3 184.7 1.0
NE2 M:HIS85 2.3 186.3 1.0
NE2 M:HIS87 2.3 187.5 1.0
CD2 M:HIS85 2.6 186.3 1.0
OD2 M:ASP65 3.2 183.2 1.0
CD2 M:HIS87 3.2 187.5 1.0
CE1 M:HIS87 3.3 187.5 1.0
CE1 M:HIS85 3.5 186.3 1.0
CA M:CYS79 3.6 184.7 1.0
CG M:GLU98 3.7 183.6 1.0
OG1 M:THR81 3.8 179.2 1.0
CG M:HIS85 3.9 186.3 1.0
OE2 M:GLU98 4.1 183.6 1.0
O M:THR81 4.1 179.2 1.0
C M:CYS79 4.3 184.7 1.0
ND1 M:HIS85 4.3 186.3 1.0
NH1 M:ARG77 4.3 186.2 1.0
ND1 M:HIS87 4.4 187.5 1.0
CD M:GLU98 4.4 183.6 1.0
CG M:HIS87 4.4 187.5 1.0
CG M:ASP65 4.4 183.2 1.0
N M:SER80 4.6 176.9 1.0
N M:CYS79 4.7 184.7 1.0
N M:THR81 4.7 179.2 1.0
CB M:GLU98 4.9 183.6 1.0
O M:CYS79 5.0 184.7 1.0
CB M:THR81 5.0 179.2 1.0

Reference:

X.Yang, Y.Wang, G.Liu, Z.Deng, S.Lin, J.Zheng. Structural Basis of Streptomyces Transcription Activation By Zinc Uptake Regulator. Nucleic Acids Res. V. 50 8363 2022.
ISSN: ESSN 1362-4962
PubMed: 35871291
DOI: 10.1093/NAR/GKAC627
Page generated: Wed Oct 30 14:42:46 2024

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