Zinc in PDB 7vpz: Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer

Enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer

All present enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer:
2.7.7.6;

Other elements in 7vpz:

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

Zinc binding site 1 out of 8 in 7vpz

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1402

b:167.6
occ:1.00
SG D:CYS78 2.3 149.9 1.0
SG D:CYS62 2.3 153.6 1.0
SG D:CYS75 2.3 158.5 1.0
SG D:CYS60 2.3 157.2 1.0
CB D:CYS60 3.0 157.2 1.0
CB D:CYS62 3.6 153.6 1.0
N D:CYS62 3.6 153.6 1.0
CB D:CYS78 3.8 149.9 1.0
CB D:CYS75 3.9 158.5 1.0
N D:TYR61 3.9 141.7 1.0
N D:CYS78 4.0 149.9 1.0
CA D:CYS62 4.1 153.6 1.0
CB D:LYS64 4.2 155.8 1.0
CA D:CYS60 4.2 157.2 1.0
C D:CYS60 4.3 157.2 1.0
CB D:ARG77 4.4 163.1 1.0
CA D:CYS78 4.5 149.9 1.0
N D:LYS64 4.5 155.8 1.0
C D:TYR61 4.6 141.7 1.0
C D:CYS62 4.7 153.6 1.0
CA D:TYR61 4.8 141.7 1.0
N D:TYR65 4.8 161.0 1.0
N D:GLY63 4.8 159.8 1.0
CA D:LYS64 4.9 155.8 1.0
O D:CYS75 4.9 158.5 1.0

Zinc binding site 2 out of 8 in 7vpz

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1403

b:180.9
occ:1.00
SG D:CYS972 2.3 129.4 1.0
SG D:CYS962 2.3 126.4 1.0
SG D:CYS969 2.3 130.3 1.0
SG D:CYS886 2.3 143.1 1.0
CB D:CYS886 2.6 143.1 1.0
CB D:CYS962 3.2 126.4 1.0
CB D:CYS972 3.3 129.4 1.0
CA D:CYS886 3.5 143.1 1.0
CA D:CYS962 3.6 126.4 1.0
CB D:CYS969 3.7 130.3 1.0
N D:GLU963 4.0 138.6 1.0
N D:CYS886 4.2 143.1 1.0
N D:CYS969 4.3 130.3 1.0
C D:CYS962 4.3 126.4 1.0
N D:CYS972 4.4 129.4 1.0
CA D:CYS972 4.4 129.4 1.0
CA D:CYS969 4.5 130.3 1.0
C D:CYS886 4.7 143.1 1.0
C D:GLU963 4.9 138.6 1.0
O D:CYS969 4.9 130.3 1.0
N D:GLY887 4.9 143.5 1.0
N D:CYS962 4.9 126.4 1.0
O D:GLU963 4.9 138.6 1.0
C D:CYS969 5.0 130.3 1.0
NE D:ARG957 5.0 139.7 1.0

Zinc binding site 3 out of 8 in 7vpz

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:425.3
occ:1.00
SG M:CYS93 2.3 382.8 1.0
SG M:CYS90 2.3 387.0 1.0
SG M:CYS133 2.3 371.7 1.0
SG M:CYS130 2.3 381.9 1.0
CB M:CYS130 3.2 381.9 1.0
CB M:CYS93 3.3 382.8 1.0
N M:CYS130 3.5 381.9 1.0
CB M:CYS90 3.5 387.0 1.0
CA M:CYS130 4.0 381.9 1.0
N M:CYS93 4.0 382.8 1.0
CB M:CYS133 4.1 371.7 1.0
CA M:CYS93 4.2 382.8 1.0
OD1 M:ASP132 4.3 369.4 1.0
CB M:ALA92 4.5 378.6 1.0
C M:THR129 4.6 377.2 1.0
C M:ALA92 4.7 378.6 1.0
CA M:THR129 4.7 377.2 1.0
OD2 M:ASP132 4.8 369.4 1.0
CA M:CYS90 4.9 387.0 1.0
CG M:ASP132 4.9 369.4 1.0
C M:CYS130 5.0 381.9 1.0

Zinc binding site 4 out of 8 in 7vpz

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:389.8
occ:1.00
SG M:CYS79 2.3 382.8 1.0
NE2 M:HIS85 2.3 379.9 1.0
NE2 M:HIS87 2.3 380.7 1.0
CB M:CYS79 2.3 382.8 1.0
CD2 M:HIS85 2.7 379.9 1.0
OD2 M:ASP65 2.8 385.1 1.0
CD2 M:HIS87 3.1 380.7 1.0
CE1 M:HIS87 3.4 380.7 1.0
CE1 M:HIS85 3.5 379.9 1.0
CA M:CYS79 3.8 382.8 1.0
CG M:GLU98 3.9 377.4 1.0
CG M:ASP65 4.0 385.1 1.0
CG M:HIS85 4.0 379.9 1.0
NH1 M:ARG77 4.0 389.5 1.0
O M:THR81 4.2 371.2 1.0
OE2 M:GLU98 4.3 377.4 1.0
CG M:HIS87 4.3 380.7 1.0
ND1 M:HIS85 4.4 379.9 1.0
ND1 M:HIS87 4.4 380.7 1.0
C M:CYS79 4.5 382.8 1.0
CD M:GLU98 4.6 377.4 1.0
N M:CYS79 4.7 382.8 1.0
CB M:ASP65 4.8 385.1 1.0
OD1 M:ASP65 4.9 385.1 1.0
N M:SER80 4.9 369.5 1.0

Zinc binding site 5 out of 8 in 7vpz

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn203

b:432.2
occ:1.00
OE2 M:GLU105 2.1 402.8 1.0
NE2 M:HIS86 2.3 386.1 1.0
NE2 M:HIS84 2.3 379.0 1.0
NE2 M:HIS122 2.3 389.1 1.0
CE1 M:HIS86 2.6 386.1 1.0
CD M:GLU105 2.7 402.8 1.0
CD2 M:HIS84 2.8 379.0 1.0
OE1 M:GLU105 2.9 402.8 1.0
CE1 M:HIS122 3.1 389.1 1.0
CD2 M:HIS122 3.2 389.1 1.0
CD2 M:HIS86 3.4 386.1 1.0
CE1 M:HIS84 3.5 379.0 1.0
ND1 M:HIS86 3.7 386.1 1.0
CG M:HIS84 4.0 379.0 1.0
CG M:GLU105 4.1 402.8 1.0
CG M:HIS86 4.1 386.1 1.0
ND1 M:HIS122 4.1 389.1 1.0
CG M:HIS122 4.2 389.1 1.0
ND1 M:HIS84 4.3 379.0 1.0
CG2 M:VAL104 4.9 396.7 1.0

Zinc binding site 6 out of 8 in 7vpz

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:442.1
occ:1.00
SG N:CYS133 2.3 395.1 1.0
SG N:CYS130 2.3 399.2 1.0
SG N:CYS93 2.3 401.1 1.0
SG N:CYS90 2.3 398.0 1.0
OD1 N:ASP132 3.2 393.0 1.0
CB N:CYS93 3.4 401.1 1.0
CB N:CYS90 3.6 398.0 1.0
N N:CYS130 3.7 399.2 1.0
CB N:CYS130 3.9 399.2 1.0
N N:CYS93 3.9 401.1 1.0
CB N:CYS133 4.1 395.1 1.0
CG N:ASP132 4.2 393.0 1.0
CA N:CYS130 4.2 399.2 1.0
CB N:ALA92 4.3 399.8 1.0
CA N:CYS93 4.3 401.1 1.0
OG1 N:THR129 4.4 394.1 1.0
OD2 N:ASP132 4.4 393.0 1.0
N N:CYS133 4.6 395.1 1.0
O N:CYS130 4.6 399.2 1.0
C N:CYS130 4.7 399.2 1.0
C N:ALA92 4.7 399.8 1.0
C N:THR129 4.7 394.1 1.0
CA N:THR129 4.8 394.1 1.0
CA N:CYS133 4.8 395.1 1.0
CA N:ALA92 4.9 399.8 1.0
CA N:CYS90 5.0 398.0 1.0

Zinc binding site 7 out of 8 in 7vpz

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:410.9
occ:1.00
OD2 N:ASP65 1.9 388.4 1.0
NE2 N:HIS85 2.3 388.3 1.0
NE2 N:HIS87 2.3 386.4 1.0
SG N:CYS79 2.3 384.6 1.0
CD2 N:HIS85 2.7 388.3 1.0
CB N:CYS79 2.9 384.6 1.0
CE1 N:HIS87 3.0 386.4 1.0
CG N:ASP65 3.1 388.4 1.0
CD2 N:HIS87 3.4 386.4 1.0
CE1 N:HIS85 3.5 388.3 1.0
OE1 N:GLU98 3.8 385.9 1.0
CB N:ASP65 4.0 388.4 1.0
OD1 N:ASP65 4.0 388.4 1.0
CG N:HIS85 4.0 388.3 1.0
ND1 N:HIS87 4.1 386.4 1.0
CB N:GLU98 4.1 385.9 1.0
CA N:CYS79 4.3 384.6 1.0
ND1 N:HIS85 4.4 388.3 1.0
CG N:HIS87 4.4 386.4 1.0
CD N:GLU98 4.5 385.9 1.0
NH1 N:ARG77 4.6 386.3 1.0
N N:CYS79 4.7 384.6 1.0
CG N:GLU98 4.9 385.9 1.0

Zinc binding site 8 out of 8 in 7vpz

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer


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 One Zur Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn203

b:431.0
occ:1.00
OE2 N:GLU105 1.9 401.0 1.0
NE2 N:HIS122 2.3 381.0 1.0
NE2 N:HIS86 2.3 387.8 1.0
NE2 N:HIS84 2.3 383.8 1.0
CD N:GLU105 2.5 401.0 1.0
OE1 N:GLU105 2.5 401.0 1.0
CE1 N:HIS86 3.0 387.8 1.0
CE1 N:HIS84 3.1 383.8 1.0
CD2 N:HIS122 3.1 381.0 1.0
CE1 N:HIS122 3.4 381.0 1.0
CD2 N:HIS86 3.4 387.8 1.0
CD2 N:HIS84 3.4 383.8 1.0
CG2 N:VAL104 3.4 392.6 1.0
CG N:GLU105 3.8 401.0 1.0
ND1 N:HIS86 4.1 387.8 1.0
ND1 N:HIS84 4.3 383.8 1.0
CG N:HIS122 4.3 381.0 1.0
CG N:HIS86 4.4 387.8 1.0
ND1 N:HIS122 4.4 381.0 1.0
CG N:HIS84 4.5 383.8 1.0
CB N:VAL104 4.7 392.6 1.0
N N:GLU105 4.7 401.0 1.0
CB N:GLU105 4.8 401.0 1.0
CA N:GLU105 4.9 401.0 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 12:45:00 2024

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