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Zinc in PDB 3qsu: Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna

Protein crystallography data

The structure of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna, PDB code: 3qsu was solved by R.Brennan, N.Horstmann, T.M.Link, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.20 / 2.20
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 156.397, 156.397, 34.646, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 25.5

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Zinc atom in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna (pdb code 3qsu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 29 binding sites of Zinc where determined in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna, PDB code: 3qsu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 29 in 3qsu

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Zinc binding site 1 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn78

b:72.0
occ:1.00
NE2 A:HIS53 2.1 60.7 1.0
O A:HOH134 2.7 64.5 1.0
CE1 A:HIS53 2.8 57.3 1.0
CD2 A:HIS53 3.4 54.8 1.0
ND1 A:HIS53 4.0 55.8 1.0
OE1 H:GLU66 4.1 73.9 1.0
CG A:HIS53 4.3 53.5 1.0
SD A:MET32 4.8 62.5 1.0
OG1 H:THR64 4.9 60.2 1.0

Zinc binding site 2 out of 29 in 3qsu

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Zinc binding site 2 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn79

b:63.0
occ:1.00
ND1 A:HIS58 2.3 39.6 1.0
O A:HOH83 2.3 39.0 1.0
O A:HOH82 2.5 50.6 1.0
O A:HOH84 2.5 44.9 1.0
CE1 A:HIS58 3.3 41.4 1.0
CG A:HIS58 3.3 40.8 1.0
CB A:HIS58 3.6 39.0 1.0
NE2 A:HIS58 4.4 41.0 1.0
CD2 A:HIS58 4.5 40.7 1.0
N A:HIS58 4.6 39.9 1.0
CD1 A:TYR56 4.7 43.0 1.0
CA A:HIS58 4.7 36.6 1.0
CG A:TYR56 5.0 41.4 1.0

Zinc binding site 3 out of 29 in 3qsu

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Zinc binding site 3 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn78

b:73.9
occ:1.00
NE2 B:HIS53 2.3 52.1 1.0
NZ B:LYS51 3.1 64.7 1.0
CD2 B:HIS53 3.2 51.7 1.0
CE1 B:HIS53 3.3 55.5 1.0
CE B:LYS51 3.3 60.3 1.0
CE B:MET32 4.1 60.6 1.0
O R:HOH155 4.1 65.2 1.0
ND1 B:HIS53 4.4 53.0 1.0
CG B:HIS53 4.4 50.6 1.0
OG1 A:THR64 4.5 56.0 1.0
CG2 A:THR64 4.6 49.7 1.0
CD B:LYS51 4.8 60.5 1.0
CB A:THR64 4.9 53.7 1.0

Zinc binding site 4 out of 29 in 3qsu

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Zinc binding site 4 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn79

b:57.2
occ:1.00
ND1 B:HIS58 2.2 35.7 1.0
O B:HOH84 2.3 54.5 1.0
O B:HOH83 2.4 47.5 1.0
O B:HOH82 2.6 39.7 1.0
CG B:HIS58 3.1 36.0 1.0
CE1 B:HIS58 3.2 38.4 1.0
CB B:HIS58 3.4 38.0 1.0
NE2 B:HIS58 4.3 38.1 1.0
CD2 B:HIS58 4.3 37.5 1.0
N B:HIS58 4.4 32.8 1.0
CA B:HIS58 4.5 38.0 1.0
CD1 B:TYR56 4.8 38.9 1.0
CD1 B:TYR42 5.0 52.6 1.0

Zinc binding site 5 out of 29 in 3qsu

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Zinc binding site 5 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn78

b:96.2
occ:1.00
NE2 H:HIS53 2.4 62.6 1.0
CD2 H:HIS53 3.3 57.1 1.0
CE1 H:HIS53 3.4 62.9 1.0
CG H:HIS53 4.4 53.3 1.0
ND1 H:HIS53 4.4 59.5 1.0
CD H:LYS51 4.5 68.0 1.0
OG H:SER48 4.7 69.8 1.0
CB H:SER48 4.8 66.5 1.0
CG H:LYS51 4.9 71.0 1.0
CG2 I:THR64 4.9 58.0 1.0
SD H:MET32 4.9 67.4 1.0
OG1 I:THR64 5.0 54.3 1.0
CG H:MET32 5.0 62.9 1.0

Zinc binding site 6 out of 29 in 3qsu

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Zinc binding site 6 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn79

b:60.9
occ:1.00
ND1 H:HIS58 2.2 37.5 1.0
O H:HOH108 2.5 47.9 1.0
O H:HOH80 2.7 38.1 1.0
CE1 H:HIS58 3.2 39.8 1.0
CG H:HIS58 3.2 39.8 1.0
CB H:HIS58 3.5 38.9 1.0
NE2 H:HIS58 4.3 39.3 1.0
CD2 H:HIS58 4.3 36.8 1.0
N H:HIS58 4.5 41.3 1.0
CA H:HIS58 4.6 38.2 1.0
CD1 H:TYR56 4.7 38.8 1.0
CD1 H:TYR42 4.7 59.1 1.0
CB H:TYR56 4.9 37.9 1.0

Zinc binding site 7 out of 29 in 3qsu

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Zinc binding site 7 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn78

b:55.2
occ:1.00
NE2 I:HIS53 2.1 46.1 1.0
O I:HOH88 2.3 48.7 1.0
O I:HOH119 2.4 54.7 1.0
O I:HOH87 2.4 54.1 1.0
CE1 I:HIS53 3.1 45.4 1.0
CD2 I:HIS53 3.1 43.6 1.0
ND1 I:HIS53 4.2 43.4 1.0
CG I:HIS53 4.3 42.5 1.0
OG1 K:THR64 4.5 46.9 1.0
CE I:MET32 4.5 51.9 1.0
CG2 K:THR64 4.8 44.7 1.0
CB I:LYS51 4.9 46.7 1.0
CB K:THR64 4.9 41.5 1.0

Zinc binding site 8 out of 29 in 3qsu

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Zinc binding site 8 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn79

b:54.5
occ:1.00
ND1 I:HIS58 2.2 34.1 1.0
O I:HOH112 2.5 34.1 1.0
O I:HOH83 2.5 37.4 1.0
O I:HOH82 2.9 46.9 1.0
CE1 I:HIS58 3.1 33.4 1.0
CG I:HIS58 3.2 35.7 1.0
CB I:HIS58 3.5 36.8 1.0
O I:HOH131 3.8 43.5 1.0
NE2 I:HIS58 4.3 33.5 1.0
CD2 I:HIS58 4.3 35.0 1.0
N I:HIS58 4.4 36.9 1.0
CA I:HIS58 4.6 35.1 1.0
CD1 I:TYR42 4.6 48.9 1.0
CD1 I:TYR56 4.6 31.9 1.0
CB I:TYR56 4.6 34.2 1.0
CG I:TYR56 4.8 32.8 1.0

Zinc binding site 9 out of 29 in 3qsu

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Zinc binding site 9 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn78

b:55.9
occ:1.00
ND1 K:HIS58 2.2 31.0 1.0
O K:HOH86 2.7 30.7 1.0
O K:HOH85 2.7 46.1 1.0
O K:HOH175 2.7 41.4 1.0
O K:HOH128 2.7 42.1 1.0
CE1 K:HIS58 3.1 32.3 1.0
CG K:HIS58 3.2 34.9 1.0
CB K:HIS58 3.5 33.5 1.0
NE2 K:HIS58 4.2 32.5 1.0
CD2 K:HIS58 4.3 34.1 1.0
N K:HIS58 4.5 32.8 1.0
CD1 K:TYR56 4.6 32.6 1.0
CA K:HIS58 4.7 33.7 1.0
CB K:TYR56 4.9 33.2 1.0
CG K:TYR56 4.9 32.3 1.0

Zinc binding site 10 out of 29 in 3qsu

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Zinc binding site 10 out of 29 in the Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Staphylococcus Aureus Hfq in Complex with A7 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn79

b:86.5
occ:1.00
NE2 K:HIS53 2.4 43.4 1.0
CD2 K:HIS53 3.2 42.3 1.0
CE1 K:HIS53 3.4 40.4 1.0
O M:HOH174 3.7 58.7 1.0
CG2 M:THR64 3.8 41.0 1.0
OG1 M:THR64 4.1 44.0 1.0
OE1 K:GLN49 4.4 61.3 1.0
CG K:HIS53 4.4 41.5 1.0
ND1 K:HIS53 4.5 41.3 1.0
CB M:THR64 4.6 39.2 1.0
SD K:MET32 4.7 59.1 1.0
CD K:GLN49 4.7 56.4 1.0
NE2 K:GLN49 4.8 55.4 1.0
CD K:LYS51 4.9 56.5 1.0
CE2 M:PHE25 4.9 50.1 1.0

Reference:

N.Horstmann, J.Orans, P.Valentin-Hansen, S.A.Shelburne, R.G.Brennan. Structural Mechanism of Staphylococcus Aureus Hfq Binding to An Rna A-Tract. Nucleic Acids Res. V. 40 11023 2012.
ISSN: ISSN 0305-1048
PubMed: 22965117
DOI: 10.1093/NAR/GKS809
Page generated: Wed Dec 16 04:45:56 2020

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