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Zinc in PDB 7x75: Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three Zur Dimers

Enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three Zur Dimers

All present enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three Zur Dimers:
2.7.7.6;

Other elements in 7x75:

The structure of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three Zur Dimers also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three Zur Dimers (pdb code 7x75). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 20 binding sites of Zinc where determined in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three Zur Dimers, PDB code: 7x75:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 20 in 7x75

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Zinc binding site 1 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1402

b:91.2
occ:1.00
 SG D:CYS78 2.3 70.8 1.0
SG D:CYS62 2.3 77.3 1.0
SG D:CYS75 2.3 78.1 1.0
SG D:CYS60 2.3 69.9 1.0
CB D:CYS60 3.4 69.9 1.0
N D:CYS62 3.5 77.3 1.0
CB D:CYS62 3.5 77.3 1.0
CB D:CYS78 3.7 70.8 1.0
N D:CYS78 3.9 70.8 1.0
N D:TYR61 3.9 67.5 1.0
CB D:CYS75 3.9 78.1 1.0
CA D:CYS62 4.0 77.3 1.0
CB D:ARG77 4.3 83.9 1.0
CB D:LYS64 4.3 82.1 1.0
CA D:CYS78 4.3 70.8 1.0
C D:TYR61 4.5 67.5 1.0
N D:LYS64 4.5 82.1 1.0
CA D:CYS60 4.6 69.9 1.0
C D:CYS60 4.6 69.9 1.0
C D:CYS62 4.7 77.3 1.0
CA D:TYR61 4.7 67.5 1.0
N D:GLY63 4.7 81.3 1.0
N D:GLY79 4.8 66.0 1.0
C D:ARG77 4.9 83.9 1.0
C D:CYS78 5.0 70.8 1.0

Zinc binding site 2 out of 20 in 7x75

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Zinc binding site 2 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1403

b:90.2
occ:1.00
 SG D:CYS962 2.3 58.1 1.0
SG D:CYS972 2.3 51.5 1.0
SG D:CYS969 2.3 48.2 1.0
SG D:CYS886 2.3 68.7 1.0
CB D:CYS886 2.8 68.7 1.0
CB D:CYS972 3.2 51.5 1.0
CB D:CYS962 3.2 58.1 1.0
CA D:CYS962 3.6 58.1 1.0
CB D:CYS969 3.7 48.2 1.0
CA D:CYS886 3.8 68.7 1.0
N D:GLU963 4.1 70.4 1.0
N D:CYS969 4.2 48.2 1.0
C D:CYS962 4.3 58.1 1.0
CA D:CYS972 4.3 51.5 1.0
N D:CYS972 4.3 51.5 1.0
N D:CYS886 4.3 68.7 1.0
CA D:CYS969 4.5 48.2 1.0
CB D:SER964 4.8 59.6 1.0
N D:CYS962 4.9 58.1 1.0
C D:GLU963 4.9 70.4 1.0
O D:CYS969 4.9 48.2 1.0

Zinc binding site 3 out of 20 in 7x75

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Zinc binding site 3 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:196.4
occ:1.00
 SG G:CYS130 2.3 148.2 1.0
SG G:CYS90 2.3 151.2 1.0
SG G:CYS93 2.3 151.8 1.0
SG G:CYS133 2.3 145.5 1.0
CB G:CYS93 3.2 151.8 1.0
CB G:CYS130 3.4 148.2 1.0
CB G:CYS90 3.6 151.2 1.0
N G:CYS93 3.6 151.8 1.0
N G:CYS130 3.9 148.2 1.0
CA G:CYS93 4.0 151.8 1.0
CB G:CYS133 4.1 145.5 1.0
OD1 G:ASP132 4.1 145.0 1.0
CA G:CYS130 4.2 148.2 1.0
CB G:ALA92 4.3 148.6 1.0
NZ G:LYS95 4.5 150.1 1.0
C G:ALA92 4.6 148.6 1.0
OD2 G:ASP132 4.9 145.0 1.0
CG G:ASP132 4.9 145.0 1.0
CA G:ALA92 4.9 148.6 1.0
CA G:CYS133 4.9 145.5 1.0
N G:ALA92 5.0 148.6 1.0
N G:CYS133 5.0 145.5 1.0
C G:THR129 5.0 147.9 1.0
CA G:CYS90 5.0 151.2 1.0

Zinc binding site 4 out of 20 in 7x75

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Zinc binding site 4 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn202

b:226.2
occ:1.00
 NE2 G:HIS85 2.0 157.8 1.0
OD2 G:ASP65 2.0 150.1 1.0
NE2 G:HIS87 2.2 157.8 1.0
SG G:CYS79 2.3 156.9 1.0
CD2 G:HIS85 2.9 157.8 1.0
CE1 G:HIS85 2.9 157.8 1.0
CE1 G:HIS87 3.2 157.8 1.0
CG G:ASP65 3.2 150.1 1.0
CD2 G:HIS87 3.2 157.8 1.0
CB G:CYS79 3.3 156.9 1.0
ND1 G:HIS85 3.9 157.8 1.0
CG G:HIS85 4.0 157.8 1.0
CB G:ASP65 4.0 150.1 1.0
OD1 G:ASP65 4.1 150.1 1.0
ND1 G:HIS87 4.3 157.8 1.0
CG G:HIS87 4.4 157.8 1.0
CA G:CYS79 4.5 156.9 1.0
N G:CYS79 4.7 156.9 1.0
O G:HIS85 4.8 157.8 1.0
CG G:GLU98 4.9 159.0 1.0
OE2 G:GLU98 5.0 159.0 1.0
O G:ARG77 5.0 148.3 1.0

Zinc binding site 5 out of 20 in 7x75

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Zinc binding site 5 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn203

b:195.1
occ:1.00
 NE2 G:HIS86 2.1 157.8 1.0
NE2 G:HIS84 2.1 154.6 1.0
NE2 G:HIS122 2.3 154.4 1.0
CD2 G:HIS122 2.3 154.4 1.0
OE2 G:GLU105 2.5 142.2 1.0
OE1 G:GLU105 2.8 142.2 1.0
CD G:GLU105 2.9 142.2 1.0
CE1 G:HIS86 3.0 157.8 1.0
CE1 G:HIS84 3.1 154.6 1.0
CD2 G:HIS86 3.1 157.8 1.0
CD2 G:HIS84 3.1 154.6 1.0
CE1 G:HIS122 3.6 154.4 1.0
CG G:HIS122 3.6 154.4 1.0
ND1 G:HIS86 4.1 157.8 1.0
ND1 G:HIS122 4.2 154.4 1.0
CG G:HIS86 4.2 157.8 1.0
ND1 G:HIS84 4.2 154.6 1.0
CG G:HIS84 4.3 154.6 1.0
CG G:GLU105 4.3 142.2 1.0
CB G:HIS122 4.7 154.4 1.0
O G:HIS122 4.8 154.4 1.0

Zinc binding site 6 out of 20 in 7x75

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Zinc binding site 6 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:189.3
occ:1.00
 SG H:CYS93 2.3 152.2 1.0
SG H:CYS90 2.3 152.2 1.0
SG H:CYS133 2.3 148.2 1.0
SG H:CYS130 2.3 151.2 1.0
CB H:CYS130 2.5 151.2 1.0
CB H:CYS93 3.2 152.2 1.0
CB H:CYS90 3.5 152.2 1.0
NZ H:LYS95 3.6 149.8 1.0
N H:CYS93 3.7 152.2 1.0
OD1 H:ASP132 3.7 149.5 1.0
CB H:CYS133 3.9 148.2 1.0
CA H:CYS130 4.0 151.2 1.0
CA H:CYS93 4.1 152.2 1.0
CB H:ALA92 4.2 150.1 1.0
N H:CYS130 4.5 151.2 1.0
C H:ALA92 4.6 150.1 1.0
N H:CYS133 4.6 148.2 1.0
CA H:CYS133 4.7 148.2 1.0
CA H:ALA92 4.8 150.1 1.0
CG H:ASP132 4.9 149.5 1.0
CE H:LYS95 4.9 149.8 1.0
N H:ALA92 4.9 150.1 1.0
CA H:CYS90 4.9 152.2 1.0
C H:CYS130 4.9 151.2 1.0

Zinc binding site 7 out of 20 in 7x75

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Zinc binding site 7 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn202

b:167.6
occ:1.00
 NE2 H:HIS85 2.1 152.0 1.0
NE2 H:HIS87 2.2 151.3 1.0
SG H:CYS79 2.3 146.9 1.0
OD2 H:ASP65 3.0 147.4 1.0
CD2 H:HIS85 3.0 152.0 1.0
CE1 H:HIS85 3.1 152.0 1.0
CE1 H:HIS87 3.1 151.3 1.0
CD2 H:HIS87 3.2 151.3 1.0
CB H:ASP65 3.3 147.4 1.0
CB H:CYS79 3.5 146.9 1.0
CG H:ASP65 3.6 147.4 1.0
NH1 H:ARG77 4.1 147.7 1.0
ND1 H:HIS85 4.1 152.0 1.0
CG H:HIS85 4.1 152.0 1.0
ND1 H:HIS87 4.3 151.3 1.0
CG H:HIS87 4.3 151.3 1.0
CA H:ASP65 4.5 147.4 1.0
N H:ASP65 4.7 147.4 1.0
CA H:CYS79 4.8 146.9 1.0
OD1 H:ASP65 4.8 147.4 1.0
O H:HIS85 4.9 152.0 1.0
CG H:GLU98 4.9 148.8 1.0

Zinc binding site 8 out of 20 in 7x75

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Zinc binding site 8 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn203

b:213.3
occ:1.00
 NE2 H:HIS86 1.9 154.0 1.0
CE1 H:HIS122 1.9 152.9 1.0
NE2 H:HIS84 2.1 153.2 1.0
NE2 H:HIS122 2.3 152.9 1.0
CD2 H:HIS86 2.8 154.0 1.0
CE1 H:HIS86 2.8 154.0 1.0
CE1 H:HIS84 3.0 153.2 1.0
CD2 H:HIS84 3.1 153.2 1.0
ND1 H:HIS122 3.1 152.9 1.0
OE2 H:GLU105 3.2 144.7 1.0
CD2 H:HIS122 3.5 152.9 1.0
OE1 H:GLU100 3.8 148.3 1.0
ND1 H:HIS86 3.8 154.0 1.0
CG H:HIS86 3.8 154.0 1.0
CG H:HIS122 3.9 152.9 1.0
CD H:GLU105 4.1 144.7 1.0
ND1 H:HIS84 4.1 153.2 1.0
CG H:HIS84 4.2 153.2 1.0
OE1 H:GLU105 4.3 144.7 1.0
OE2 H:GLU100 4.6 148.3 1.0
CD H:GLU100 4.6 148.3 1.0
CG2 H:VAL104 4.8 142.0 1.0

Zinc binding site 9 out of 20 in 7x75

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Zinc binding site 9 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn201

b:204.9
occ:1.00
 SG K:CYS93 2.3 147.7 1.0
CB K:CYS130 2.3 149.3 1.0
SG K:CYS90 2.3 148.0 1.0
SG K:CYS130 2.3 149.3 1.0
SG K:CYS133 2.4 144.5 1.0
NZ K:LYS95 3.2 150.6 1.0
CB K:CYS93 3.6 147.7 1.0
CA K:CYS130 3.8 149.3 1.0
CB K:CYS90 3.8 148.0 1.0
N K:CYS93 3.8 147.7 1.0
CB K:CYS133 3.8 144.5 1.0
CB K:ALA92 4.0 143.1 1.0
OD1 K:ASP132 4.0 144.7 1.0
N K:CYS130 4.2 149.3 1.0
CA K:CYS93 4.4 147.7 1.0
CE K:LYS95 4.5 150.6 1.0
C K:ALA92 4.6 143.1 1.0
N K:CYS133 4.7 144.5 1.0
CA K:ALA92 4.7 143.1 1.0
CA K:CYS133 4.7 144.5 1.0
C K:CYS130 4.8 149.3 1.0
N K:ALA92 4.9 143.1 1.0

Zinc binding site 10 out of 20 in 7x75

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Zinc binding site 10 out of 20 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Three 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 Rnap-Promoter Open Complex with Three Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn202

b:224.5
occ:1.00
 OD2 K:ASP65 2.0 155.7 1.0
NE2 K:HIS85 2.3 155.9 1.0
SG K:CYS79 2.3 154.9 1.0
NE2 K:HIS87 2.3 157.0 1.0
CE1 K:HIS85 2.3 155.9 1.0
CB K:CYS79 2.9 154.9 1.0
CE1 K:HIS87 3.1 157.0 1.0
CG K:ASP65 3.3 155.7 1.0
ND1 K:HIS85 3.4 155.9 1.0
CD2 K:HIS85 3.4 155.9 1.0
CD2 K:HIS87 3.4 157.0 1.0
CG K:HIS85 4.0 155.9 1.0
OD1 K:ASP65 4.1 155.7 1.0
CB K:ASP65 4.2 155.7 1.0
ND1 K:HIS87 4.3 157.0 1.0
CA K:CYS79 4.4 154.9 1.0
CG K:HIS87 4.5 157.0 1.0
O K:THR81 4.8 148.8 1.0
CG K:GLU98 4.8 154.7 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 14:51:54 2024

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