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

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

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

Other elements in 7vpd:

The structure of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One Zur Dimers 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 Streptomyces Coelicolor Rnap-Promoter Open Complex with One Zur Dimers (pdb code 7vpd). 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 Streptomyces Coelicolor Rnap-Promoter Open Complex with One Zur Dimers, PDB code: 7vpd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7vpd

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One 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 One Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1402

b:135.6
occ:1.00
 SG D:CYS78 2.3 107.6 1.0
SG D:CYS75 2.3 117.9 1.0
SG D:CYS60 2.3 109.5 1.0
SG D:CYS62 2.3 113.6 1.0
CB D:CYS60 3.1 109.5 1.0
N D:CYS62 3.4 113.6 1.0
CB D:CYS62 3.4 113.6 1.0
CB D:CYS78 3.6 107.6 1.0
N D:CYS78 3.8 107.6 1.0
N D:TYR61 3.8 98.8 1.0
CA D:CYS62 3.8 113.6 1.0
CB D:CYS75 3.9 117.9 1.0
N D:GLY63 4.2 116.8 1.0
CA D:CYS78 4.3 107.6 1.0
CA D:CYS60 4.3 109.5 1.0
N D:LYS64 4.3 117.7 1.0
O D:LYS64 4.4 117.7 1.0
CB D:ARG77 4.4 121.5 1.0
C D:TYR61 4.4 98.8 1.0
C D:CYS60 4.4 109.5 1.0
C D:CYS62 4.4 113.6 1.0
CB D:LYS64 4.5 117.7 1.0
CA D:TYR61 4.6 98.8 1.0
C D:ARG77 4.9 121.5 1.0
CA D:LYS64 4.9 117.7 1.0
C D:CYS78 4.9 107.6 1.0
CB D:TYR61 5.0 98.8 1.0

Zinc binding site 2 out of 8 in 7vpd

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One 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 One Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1403

b:103.9
occ:1.00
 SG D:CYS972 2.3 78.8 1.0
SG D:CYS962 2.3 82.7 1.0
SG D:CYS969 2.3 83.2 1.0
SG D:CYS886 2.3 90.5 1.0
CB D:CYS886 2.8 90.5 1.0
CB D:CYS972 3.0 78.8 1.0
CB D:CYS969 3.6 83.2 1.0
CB D:CYS962 3.6 82.7 1.0
CA D:CYS962 3.8 82.7 1.0
CA D:CYS886 3.8 90.5 1.0
N D:CYS972 4.1 78.8 1.0
CA D:CYS972 4.1 78.8 1.0
N D:CYS969 4.2 83.2 1.0
N D:GLU963 4.2 89.4 1.0
CA D:CYS969 4.4 83.2 1.0
N D:CYS886 4.4 90.5 1.0
C D:CYS962 4.5 82.7 1.0
N D:CYS962 4.9 82.7 1.0
O D:CYS969 4.9 83.2 1.0
CB D:SER964 4.9 84.4 1.0
C D:CYS969 5.0 83.2 1.0
C D:GLU963 5.0 89.4 1.0

Zinc binding site 3 out of 8 in 7vpd

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One 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 One Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:315.1
occ:1.00
 SG M:CYS133 2.3 234.7 1.0
SG M:CYS130 2.3 236.7 1.0
SG M:CYS93 2.3 237.2 1.0
SG M:CYS90 2.3 236.1 1.0
CB M:CYS93 3.1 237.2 1.0
CB M:CYS130 3.3 236.7 1.0
CB M:CYS90 3.5 236.1 1.0
N M:CYS130 3.6 236.7 1.0
N M:CYS93 3.8 237.2 1.0
CA M:CYS93 4.0 237.2 1.0
CA M:CYS130 4.0 236.7 1.0
CB M:CYS133 4.1 234.7 1.0
OD1 M:ASP132 4.3 232.4 1.0
CB M:ALA92 4.3 235.1 1.0
C M:ALA92 4.6 235.1 1.0
NZ M:LYS95 4.6 232.3 1.0
C M:THR129 4.7 235.9 1.0
OD2 M:ASP132 4.8 232.4 1.0
CA M:ALA92 4.9 235.1 1.0
CA M:CYS90 4.9 236.1 1.0
CA M:THR129 4.9 235.9 1.0
CG M:ASP132 5.0 232.4 1.0

Zinc binding site 4 out of 8 in 7vpd

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One 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 One Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:280.0
occ:1.00
 CB M:CYS79 2.3 239.4 1.0
SG M:CYS79 2.3 239.4 1.0
NE2 M:HIS85 2.3 238.9 1.0
NE2 M:HIS87 2.3 237.0 1.0
CD2 M:HIS85 2.6 238.9 1.0
CD2 M:HIS87 3.2 237.0 1.0
OD2 M:ASP65 3.3 236.4 1.0
CE1 M:HIS87 3.3 237.0 1.0
CE1 M:HIS85 3.5 238.9 1.0
CG M:GLU98 3.6 236.3 1.0
CA M:CYS79 3.7 239.4 1.0
CG M:HIS85 3.9 238.9 1.0
OE2 M:GLU98 4.0 236.3 1.0
NH1 M:ARG77 4.0 234.6 1.0
O M:THR81 4.1 235.7 1.0
ND1 M:HIS85 4.3 238.9 1.0
CD M:GLU98 4.3 236.3 1.0
C M:CYS79 4.3 239.4 1.0
CG M:HIS87 4.4 237.0 1.0
ND1 M:HIS87 4.4 237.0 1.0
CG M:ASP65 4.5 236.4 1.0
N M:SER80 4.6 234.5 1.0
N M:CYS79 4.7 239.4 1.0
N M:THR81 4.7 235.7 1.0
CB M:GLU98 4.8 236.3 1.0

Zinc binding site 5 out of 8 in 7vpd

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One 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 One Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn203

b:279.3
occ:1.00
 OE2 M:GLU105 2.1 234.5 1.0
NE2 M:HIS86 2.3 236.4 1.0
NE2 M:HIS122 2.3 239.2 1.0
NE2 M:HIS84 2.3 237.0 1.0
CE1 M:HIS86 2.6 236.4 1.0
CD2 M:HIS84 2.7 237.0 1.0
CD M:GLU105 2.9 234.5 1.0
OE1 M:GLU105 3.1 234.5 1.0
CE1 M:HIS122 3.1 239.2 1.0
CD2 M:HIS122 3.2 239.2 1.0
CD2 M:HIS86 3.4 236.4 1.0
CE1 M:HIS84 3.5 237.0 1.0
ND1 M:HIS86 3.7 236.4 1.0
CG M:HIS84 4.0 237.0 1.0
CG M:HIS86 4.1 236.4 1.0
ND1 M:HIS122 4.2 239.2 1.0
CG M:HIS122 4.2 239.2 1.0
CG M:GLU105 4.2 234.5 1.0
ND1 M:HIS84 4.3 237.0 1.0
CG2 M:VAL104 4.7 235.8 1.0
O M:HIS85 4.9 238.9 1.0

Zinc binding site 6 out of 8 in 7vpd

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One 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 One Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:267.6
occ:1.00
 SG N:CYS130 2.3 232.9 1.0
SG N:CYS133 2.3 231.6 1.0
SG N:CYS93 2.3 230.6 1.0
SG N:CYS90 2.3 233.9 1.0
CB N:CYS93 3.3 230.6 1.0
CB N:CYS90 3.6 233.9 1.0
N N:CYS130 3.7 232.9 1.0
N N:CYS93 3.7 230.6 1.0
CB N:CYS130 3.9 232.9 1.0
CB N:CYS133 4.1 231.6 1.0
CB N:ALA92 4.1 229.5 1.0
OD1 N:ASP132 4.1 232.8 1.0
CA N:CYS93 4.2 230.6 1.0
OD2 N:ASP132 4.2 232.8 1.0
CA N:CYS130 4.2 232.9 1.0
OG1 N:THR129 4.3 232.2 1.0
CG N:ASP132 4.5 232.8 1.0
N N:CYS133 4.5 231.6 1.0
C N:ALA92 4.6 229.5 1.0
O N:CYS130 4.6 232.9 1.0
C N:CYS130 4.6 232.9 1.0
C N:THR129 4.7 232.2 1.0
CA N:THR129 4.7 232.2 1.0
CA N:CYS133 4.8 231.6 1.0
CA N:ALA92 4.8 229.5 1.0
CA N:CYS90 5.0 233.9 1.0
N N:ALA92 5.0 229.5 1.0

Zinc binding site 7 out of 8 in 7vpd

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with One 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 One Zur Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:280.5
occ:1.00
 OD2 N:ASP65 2.0 236.7 1.0
SG N:CYS79 2.3 238.3 1.0
NE2 N:HIS87 2.3 239.3 1.0
NE2 N:HIS85 2.3 236.8 1.0
CB N:CYS79 2.6 238.3 1.0
CD2 N:HIS85 2.8 236.8 1.0
CE1 N:HIS87 3.1 239.3 1.0
CG N:ASP65 3.2 236.7 1.0
CD2 N:HIS87 3.4 239.3 1.0
CE1 N:HIS85 3.5 236.8 1.0
OE1 N:GLU98 3.6 236.0 1.0
CB N:ASP65 4.0 236.7 1.0
CA N:CYS79 4.0 238.3 1.0
CG N:HIS85 4.1 236.8 1.0
CB N:GLU98 4.1 236.0 1.0
OD1 N:ASP65 4.1 236.7 1.0
ND1 N:HIS87 4.2 239.3 1.0
CD N:GLU98 4.3 236.0 1.0
ND1 N:HIS85 4.4 236.8 1.0
CG N:HIS87 4.4 239.3 1.0
NH1 N:ARG77 4.4 235.2 1.0
N N:CYS79 4.5 238.3 1.0
CG N:GLU98 4.8 236.0 1.0

Zinc binding site 8 out of 8 in 7vpd

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

b:291.0
occ:1.00
 OE2 N:GLU105 2.0 244.9 1.0
NE2 N:HIS86 2.3 239.0 1.0
NE2 N:HIS122 2.3 240.0 1.0
NE2 N:HIS84 2.3 236.4 1.0
CD N:GLU105 2.6 244.9 1.0
OE1 N:GLU105 2.7 244.9 1.0
CE1 N:HIS86 2.9 239.0 1.0
CD2 N:HIS122 3.0 240.0 1.0
CE1 N:HIS84 3.0 236.4 1.0
CD2 N:HIS86 3.4 239.0 1.0
CE1 N:HIS122 3.4 240.0 1.0
CD2 N:HIS84 3.4 236.4 1.0
CG2 N:VAL104 3.4 239.3 1.0
CG N:GLU105 4.0 244.9 1.0
ND1 N:HIS86 4.1 239.0 1.0
ND1 N:HIS84 4.2 236.4 1.0
CG N:HIS122 4.3 240.0 1.0
CG N:HIS86 4.3 239.0 1.0
ND1 N:HIS122 4.4 240.0 1.0
CG N:HIS84 4.5 236.4 1.0
CB N:VAL104 4.7 239.3 1.0
N N:GLU105 4.8 244.9 1.0
CB N:GLU105 5.0 244.9 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 12:43:03 2024

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