Zinc in PDB 7vo9: Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)

Zinc Binding Sites:

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Binding sites:

The binding sites of Zinc atom in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) (pdb code 7vo9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers), PDB code: 7vo9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7vo9

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Zinc binding site 1 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:85.5
occ:1.00
 SG G:CYS93 2.3 70.5 1.0
SG G:CYS130 2.3 73.4 1.0
SG G:CYS90 2.3 71.9 1.0
SG G:CYS133 2.3 76.7 1.0
CB G:CYS130 3.2 73.4 1.0
CB G:CYS93 3.3 70.5 1.0
CB G:CYS133 3.4 76.7 1.0
CB G:CYS90 3.4 71.9 1.0
N G:CYS130 3.6 73.4 1.0
N G:CYS93 3.7 70.5 1.0
CA G:CYS93 4.0 70.5 1.0
CA G:CYS130 4.0 73.4 1.0
OD2 G:ASP132 4.5 77.1 1.0
OG1 G:THR129 4.5 70.4 1.0
CA G:CYS133 4.6 76.7 1.0
CB G:ALA92 4.7 65.0 1.0
N G:CYS133 4.7 76.7 1.0
C G:THR129 4.7 70.4 1.0
C G:ALA92 4.7 65.0 1.0
CA G:CYS90 4.8 71.9 1.0
OD1 G:ASP132 4.8 77.1 1.0
C G:CYS130 4.9 73.4 1.0
O G:CYS130 4.9 73.4 1.0
CG G:ASP132 5.0 77.1 1.0
CA G:THR129 5.0 70.4 1.0

Zinc binding site 2 out of 12 in 7vo9

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Zinc binding site 2 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn202

b:84.9
occ:1.00
 NE2 G:HIS85 1.7 52.6 1.0
NE2 G:HIS87 2.1 52.2 1.0
SG G:CYS79 2.3 55.3 1.0
CE1 G:HIS85 2.7 52.6 1.0
CD2 G:HIS85 2.7 52.6 1.0
OD2 G:ASP65 2.9 43.1 1.0
CE1 G:HIS87 3.0 52.2 1.0
CD2 G:HIS87 3.1 52.2 1.0
CG G:ASP65 3.4 43.1 1.0
CB G:CYS79 3.4 55.3 1.0
CB G:ASP65 3.7 43.1 1.0
ND1 G:HIS85 3.7 52.6 1.0
CG G:HIS85 3.7 52.6 1.0
ND1 G:HIS87 4.2 52.2 1.0
CG G:HIS87 4.2 52.2 1.0
OD1 G:ASP65 4.3 43.1 1.0
OE1 G:GLU98 4.6 56.6 1.0
CA G:CYS79 4.8 55.3 1.0
O G:HIS85 5.0 52.6 1.0

Zinc binding site 3 out of 12 in 7vo9

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Zinc binding site 3 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn203

b:80.9
occ:1.00
 NE2 G:HIS86 1.9 51.1 1.0
NE2 G:HIS84 2.0 55.5 1.0
NE2 G:HIS122 2.4 55.3 1.0
CE1 G:HIS86 2.8 51.1 1.0
CD2 G:HIS86 2.9 51.1 1.0
CE1 G:HIS84 3.0 55.5 1.0
CD2 G:HIS84 3.0 55.5 1.0
CE1 G:HIS122 3.2 55.3 1.0
CD2 G:HIS122 3.2 55.3 1.0
OE2 G:GLU105 3.3 61.7 1.0
ND1 G:HIS86 3.9 51.1 1.0
CG G:HIS86 4.0 51.1 1.0
O G:HIS122 4.0 55.3 1.0
ND1 G:HIS84 4.1 55.5 1.0
ND1 G:HIS122 4.1 55.3 1.0
CG G:HIS122 4.1 55.3 1.0
CG G:HIS84 4.1 55.5 1.0
CD G:GLU105 4.2 61.7 1.0
CG G:GLU105 4.6 61.7 1.0
O G:HIS85 4.6 52.6 1.0
C G:HIS122 4.9 55.3 1.0

Zinc binding site 4 out of 12 in 7vo9

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Zinc binding site 4 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:89.6
occ:1.00
 SG H:CYS90 2.3 65.5 1.0
SG H:CYS130 2.3 70.0 1.0
SG H:CYS93 2.3 67.5 1.0
SG H:CYS133 2.3 77.2 1.0
CB H:CYS130 3.3 70.0 1.0
CB H:CYS93 3.4 67.5 1.0
CB H:CYS90 3.4 65.5 1.0
CB H:CYS133 3.5 77.2 1.0
N H:CYS93 3.5 67.5 1.0
N H:CYS130 3.5 70.0 1.0
CA H:CYS93 4.0 67.5 1.0
CA H:CYS130 4.0 70.0 1.0
CB H:ALA92 4.1 63.2 1.0
C H:ALA92 4.4 63.2 1.0
OD1 H:ASP132 4.4 75.3 1.0
C H:THR129 4.6 69.6 1.0
CA H:ALA92 4.6 63.2 1.0
CA H:CYS133 4.7 77.2 1.0
N H:CYS133 4.8 77.2 1.0
N H:ALA92 4.8 63.2 1.0
CA H:THR129 4.8 69.6 1.0
CA H:CYS90 4.8 65.5 1.0
C H:CYS130 5.0 70.0 1.0
OD2 H:ASP132 5.0 75.3 1.0

Zinc binding site 5 out of 12 in 7vo9

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Zinc binding site 5 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn202

b:100.3
occ:1.00
 NE2 H:HIS87 2.0 60.5 1.0
NE2 H:HIS85 2.1 52.4 1.0
OD1 H:ASP65 2.1 56.9 1.0
SG H:CYS79 2.3 60.9 1.0
CE1 H:HIS87 2.9 60.5 1.0
CD2 H:HIS87 3.0 60.5 1.0
CE1 H:HIS85 3.0 52.4 1.0
CD2 H:HIS85 3.0 52.4 1.0
CG H:ASP65 3.1 56.9 1.0
CB H:CYS79 3.3 60.9 1.0
CB H:ASP65 3.5 56.9 1.0
ND1 H:HIS87 4.0 60.5 1.0
CG H:HIS87 4.0 60.5 1.0
ND1 H:HIS85 4.1 52.4 1.0
OD2 H:ASP65 4.2 56.9 1.0
CG H:HIS85 4.2 52.4 1.0
OE2 H:GLU98 4.6 55.0 1.0
CA H:CYS79 4.8 60.9 1.0
NH1 H:ARG77 5.0 60.2 1.0
CA H:ASP65 5.0 56.9 1.0

Zinc binding site 6 out of 12 in 7vo9

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Zinc binding site 6 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn203

b:64.3
occ:1.00
 NE2 H:HIS86 2.0 56.5 1.0
NE2 H:HIS122 2.0 57.8 1.0
NE2 H:HIS84 2.1 54.8 1.0
CE1 H:HIS86 2.9 56.5 1.0
CD2 H:HIS86 2.9 56.5 1.0
CE1 H:HIS122 3.0 57.8 1.0
CD2 H:HIS122 3.0 57.8 1.0
CD2 H:HIS84 3.0 54.8 1.0
CE1 H:HIS84 3.1 54.8 1.0
CD H:GLU105 3.3 69.5 1.0
OE1 H:GLU100 3.3 57.7 1.0
CG H:GLU105 3.4 69.5 1.0
OE1 H:GLU105 3.4 69.5 1.0
OE2 H:GLU105 3.9 69.5 1.0
ND1 H:HIS86 3.9 56.5 1.0
CG H:HIS86 4.0 56.5 1.0
ND1 H:HIS122 4.1 57.8 1.0
CG H:HIS122 4.1 57.8 1.0
ND1 H:HIS84 4.1 54.8 1.0
CD H:GLU100 4.2 57.7 1.0
CG H:HIS84 4.2 54.8 1.0
OE2 H:GLU100 4.2 57.7 1.0
CB H:GLU105 4.4 69.5 1.0
CG2 H:VAL104 4.6 63.5 1.0
O H:GLY101 4.7 60.4 1.0
O H:HIS122 4.9 57.8 1.0
CA H:GLU105 4.9 69.5 1.0

Zinc binding site 7 out of 12 in 7vo9

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Zinc binding site 7 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:74.8
occ:1.00
 SG M:CYS130 2.3 66.0 1.0
SG M:CYS133 2.3 76.0 1.0
SG M:CYS90 2.3 65.1 1.0
SG M:CYS93 2.3 65.0 1.0
CB M:CYS133 3.3 76.0 1.0
CB M:CYS130 3.3 66.0 1.0
CB M:CYS90 3.3 65.1 1.0
CB M:CYS93 3.3 65.0 1.0
N M:CYS130 3.5 66.0 1.0
N M:CYS93 3.6 65.0 1.0
CA M:CYS130 3.9 66.0 1.0
CA M:CYS93 4.0 65.0 1.0
N M:CYS133 4.2 76.0 1.0
O M:CYS130 4.3 66.0 1.0
CA M:CYS133 4.4 76.0 1.0
C M:CYS130 4.5 66.0 1.0
CB M:ALA92 4.6 67.8 1.0
C M:ALA92 4.6 67.8 1.0
C M:THR129 4.7 62.9 1.0
CA M:CYS90 4.7 65.1 1.0
CA M:THR129 5.0 62.9 1.0

Zinc binding site 8 out of 12 in 7vo9

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Zinc binding site 8 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:87.2
occ:1.00
 NE2 M:HIS87 2.0 52.4 1.0
NE2 M:HIS85 2.0 59.7 1.0
SG M:CYS79 2.3 55.8 1.0
OD2 M:ASP65 2.9 38.2 1.0
CE1 M:HIS85 3.0 59.7 1.0
CE1 M:HIS87 3.0 52.4 1.0
CD2 M:HIS85 3.0 59.7 1.0
CD2 M:HIS87 3.0 52.4 1.0
CB M:CYS79 3.4 55.8 1.0
CG M:ASP65 3.4 38.2 1.0
CG M:GLU98 3.6 66.1 1.0
NH1 M:ARG77 3.8 47.8 1.0
CD M:GLU98 3.8 66.1 1.0
CB M:ASP65 4.0 38.2 1.0
OE2 M:GLU98 4.0 66.1 1.0
ND1 M:HIS85 4.1 59.7 1.0
ND1 M:HIS87 4.1 52.4 1.0
OD1 M:ASP65 4.1 38.2 1.0
CG M:HIS85 4.1 59.7 1.0
CG M:HIS87 4.1 52.4 1.0
OE1 M:GLU98 4.4 66.1 1.0
CB M:GLU98 4.5 66.1 1.0
CA M:CYS79 4.6 55.8 1.0

Zinc binding site 9 out of 12 in 7vo9

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Zinc binding site 9 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn203

b:76.2
occ:1.00
 NE2 M:HIS86 2.0 53.3 1.0
NE2 M:HIS84 2.2 65.1 1.0
OE2 M:GLU105 2.2 59.9 1.0
NE2 M:HIS122 2.4 49.6 1.0
CD2 M:HIS84 2.8 65.1 1.0
CE1 M:HIS86 2.8 53.3 1.0
CD2 M:HIS86 2.9 53.3 1.0
CD M:GLU105 3.0 59.9 1.0
CG M:GLU105 3.1 59.9 1.0
CE1 M:HIS122 3.2 49.6 1.0
CE1 M:HIS84 3.4 65.1 1.0
CD2 M:HIS122 3.5 49.6 1.0
ND1 M:HIS86 3.8 53.3 1.0
CG M:HIS86 3.9 53.3 1.0
CG M:HIS84 4.1 65.1 1.0
OE1 M:GLU105 4.2 59.9 1.0
ND1 M:HIS84 4.3 65.1 1.0
ND1 M:HIS122 4.4 49.6 1.0
CG M:HIS122 4.6 49.6 1.0
CB M:GLU105 4.6 59.9 1.0
O M:GLY101 4.7 64.1 1.0
CG M:GLU100 4.7 67.3 1.0
N M:HIS86 4.9 53.3 1.0
C M:HIS85 5.0 59.7 1.0
CG2 M:VAL104 5.0 58.7 1.0

Zinc binding site 10 out of 12 in 7vo9

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Zinc binding site 10 out of 12 in the Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Streptomyces Coelicolor Zinc Uptake Regulator Complexed with Zinc and Dna (Dimer of Dimers) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:88.0
occ:1.00
 SG N:CYS93 2.3 66.7 1.0
SG N:CYS90 2.3 63.4 1.0
SG N:CYS130 2.3 70.5 1.0
N N:CYS130 3.1 70.5 1.0
CB N:CYS93 3.3 66.7 1.0
CB N:CYS130 3.3 70.5 1.0
CB N:CYS133 3.4 71.3 1.0
CB N:CYS90 3.4 63.4 1.0
SG N:CYS133 3.8 71.3 1.0
CA N:CYS130 3.8 70.5 1.0
N N:CYS93 3.9 66.7 1.0
C N:THR129 4.1 70.5 1.0
CG2 N:THR129 4.2 70.5 1.0
CA N:THR129 4.2 70.5 1.0
CA N:CYS93 4.3 66.7 1.0
CB N:ALA92 4.4 65.6 1.0
O N:CYS130 4.7 70.5 1.0
CA N:CYS133 4.7 71.3 1.0
C N:ALA92 4.8 65.6 1.0
C N:CYS130 4.8 70.5 1.0
CA N:CYS90 4.8 63.4 1.0
CB N:THR129 4.8 70.5 1.0
CD N:LYS95 4.8 67.6 1.0
NZ N:LYS95 5.0 67.6 1.0
O N:GLY128 5.0 67.2 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 12:42:55 2024

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