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Zinc in PDB 3qg6: Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody

Protein crystallography data

The structure of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody, PDB code: 3qg6 was solved by R.N.Kirchdoerfer, J.D.Janda, G.F.Kaufmann, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.360, 98.498, 73.670, 90.00, 114.03, 90.00
R / Rfree (%) 18.4 / 23.9

Other elements in 3qg6:

The structure of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody (pdb code 3qg6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody, PDB code: 3qg6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3qg6

Go back to Zinc Binding Sites List in 3qg6
Zinc binding site 1 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn214

b:36.5
occ:1.00
O A:ASP1 2.2 36.0 1.0
N A:ASP1 2.2 35.0 1.0
OXT L:GLU213 2.8 48.7 1.0
O A:HOH247 3.0 11.7 1.0
C A:ASP1 3.0 34.6 1.0
CA A:ASP1 3.1 34.0 1.0
C L:GLU213 3.6 41.1 1.0
O L:GLU213 3.8 42.5 1.0
CB A:ASP1 4.0 33.8 1.0
O L:ASN212 4.2 41.1 1.0
N A:VAL2 4.3 32.6 1.0
CG A:ASP1 4.9 39.1 1.0
CA L:GLU213 4.9 34.4 1.0
NE2 A:GLN27 4.9 43.6 1.0
CG2 A:VAL3 4.9 33.6 1.0
O A:HOH264 5.0 19.0 1.0
CA A:VAL2 5.0 32.0 1.0

Zinc binding site 2 out of 9 in 3qg6

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Zinc binding site 2 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn216

b:23.5
occ:1.00
NE2 A:HIS189 2.0 27.9 1.0
OE2 H:GLU85 2.1 37.0 1.0
OE2 A:GLU185 2.2 24.0 1.0
OE1 H:GLU85 2.5 29.1 1.0
CD H:GLU85 2.7 30.2 1.0
CE1 A:HIS189 2.8 27.7 1.0
O H:HOH292 2.9 2.0 1.0
CD2 A:HIS189 3.1 27.3 1.0
CD A:GLU185 3.3 33.4 1.0
CG A:GLU185 3.9 29.8 1.0
ND1 A:HIS189 4.0 27.0 1.0
CG H:GLU85 4.1 24.9 1.0
CG A:HIS189 4.2 26.2 1.0
OE1 A:GLU185 4.3 33.2 1.0
NH1 A:ARG155 4.6 32.6 1.0
CB A:GLU185 4.8 26.1 1.0
O A:HOH223 4.9 17.8 1.0
O A:GLU185 4.9 23.8 1.0

Zinc binding site 3 out of 9 in 3qg6

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Zinc binding site 3 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn217

b:73.8
occ:1.00
ND1 A:HIS93 2.2 34.5 1.0
O A:HOH271 2.4 29.5 1.0
CG A:HIS93 3.1 31.3 1.0
CE1 A:HIS93 3.2 35.7 1.0
CB A:HIS93 3.4 28.3 1.0
CA A:HIS93 3.9 27.5 1.0
NE2 A:HIS93 4.3 34.8 1.0
CD2 A:HIS93 4.3 33.2 1.0
N A:VAL94 4.8 26.6 1.0
C A:HIS93 4.9 27.9 1.0
N A:HIS93 4.9 27.2 1.0

Zinc binding site 4 out of 9 in 3qg6

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Zinc binding site 4 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn229

b:77.1
occ:1.00
OD1 B:ASP72 2.0 37.2 1.0
OG B:SER74 2.6 33.8 1.0
CG B:ASP72 2.9 33.8 1.0
OD2 B:ASP72 3.2 42.4 1.0
CB B:SER74 3.4 29.0 1.0
N B:SER74 4.1 26.9 1.0
CA B:SER74 4.3 27.5 1.0
CB B:ASP72 4.3 27.0 1.0
CA B:ASP72 4.6 25.8 1.0
N B:LYS75 4.6 27.3 1.0
C B:ASP72 4.8 26.1 1.0
C B:SER74 4.8 28.3 1.0
N B:THR73 5.0 25.6 1.0

Zinc binding site 5 out of 9 in 3qg6

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Zinc binding site 5 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn229

b:52.3
occ:1.00
NE2 H:HIS82A 2.4 39.0 1.0
CD2 H:HIS82A 3.3 36.3 1.0
CE1 H:HIS82A 3.4 40.1 1.0
NH1 H:ARG66 3.9 74.4 1.0
CG H:HIS82A 4.4 32.6 1.0
ND1 H:HIS82A 4.5 37.1 1.0
CB H:SER82B 4.5 31.4 1.0
OG H:SER82B 5.0 37.1 1.0

Zinc binding site 6 out of 9 in 3qg6

Go back to Zinc Binding Sites List in 3qg6
Zinc binding site 6 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn215

b:30.4
occ:1.00
OE2 B:GLU85 2.1 41.6 1.0
NE2 L:HIS189 2.1 30.4 1.0
OE2 L:GLU185 2.2 31.4 1.0
OE1 B:GLU85 2.5 33.5 1.0
CD B:GLU85 2.6 34.8 1.0
O B:HOH291 3.0 2.0 1.0
CE1 L:HIS189 3.0 30.2 1.0
CD2 L:HIS189 3.2 29.7 1.0
CD L:GLU185 3.3 37.8 1.0
CG L:GLU185 3.9 33.5 1.0
O L:HOH287 3.9 22.4 1.0
CG B:GLU85 4.1 29.2 1.0
ND1 L:HIS189 4.2 30.2 1.0
O B:HOH292 4.2 28.3 1.0
OE1 L:GLU185 4.3 40.3 1.0
CG L:HIS189 4.3 28.7 1.0
NH1 L:ARG155 4.6 34.8 1.0
CB L:GLU185 4.7 30.0 1.0

Zinc binding site 7 out of 9 in 3qg6

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Zinc binding site 7 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn216

b:62.6
occ:1.00
ND1 L:HIS93 2.1 30.7 1.0
O L:HOH278 2.8 37.2 1.0
O L:HOH279 2.8 26.1 1.0
O L:HOH232 2.9 10.3 1.0
CE1 L:HIS93 3.0 32.4 1.0
CG L:HIS93 3.2 27.4 1.0
CB L:HIS93 3.7 23.6 1.0
CA L:HIS93 4.1 22.7 1.0
NE2 L:HIS93 4.2 31.8 1.0
CD2 L:HIS93 4.3 30.3 1.0
O L:HOH295 4.5 14.4 1.0

Zinc binding site 8 out of 9 in 3qg6

Go back to Zinc Binding Sites List in 3qg6
Zinc binding site 8 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn217

b:64.1
occ:1.00
O L:HOH251 2.9 13.1 1.0
OD2 L:ASP60 3.6 64.8 1.0
CG L:ASP60 4.1 56.3 1.0
OD1 L:ASP60 4.4 60.9 1.0
CB L:ASP60 4.9 46.5 1.0

Zinc binding site 9 out of 9 in 3qg6

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Zinc binding site 9 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn218

b:34.2
occ:1.00
N L:ASP1 2.0 25.0 1.0
O L:ASP1 2.3 24.2 1.0
O L:HOH277 3.0 11.2 1.0
C L:ASP1 3.0 23.2 1.0
CA L:ASP1 3.0 23.9 1.0
OXT A:GLU213 3.0 41.5 1.0
C A:GLU213 3.8 31.0 1.0
O A:GLU213 3.9 31.5 1.0
CB L:ASP1 4.0 24.2 1.0
O A:ASN212 4.2 33.0 1.0
N L:VAL2 4.3 19.6 1.0
NE2 L:GLN27 4.7 41.6 1.0
CG L:ASP1 4.8 26.6 1.0
OD1 L:ASP1 4.9 27.5 1.0

Reference:

R.N.Kirchdoerfer, A.L.Garner, C.E.Flack, J.M.Mee, A.R.Horswill, K.D.Janda, G.F.Kaufmann, I.A.Wilson. Structural Basis For Ligand Recognition and Discrimination of A Quorum-Quenching Antibody. J.Biol.Chem. V. 286 17351 2011.
ISSN: ISSN 0021-9258
PubMed: 21454495
DOI: 10.1074/JBC.M111.231258
Page generated: Wed Dec 16 04:45:09 2020

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