Atomistry » Cobalt » PDB 5zt7-6eg9 » 6cgy
Atomistry »
  Cobalt »
    PDB 5zt7-6eg9 »
      6cgy »

Cobalt in PDB 6cgy: Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion

Protein crystallography data

The structure of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion, PDB code: 6cgy was solved by C.Bergonzi, M.Schwab, T.Naik, D.Daude, E.Chabriere, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.720, 114.740, 79.970, 90.00, 109.78, 90.00
R / Rfree (%) 17 / 19.7

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion (pdb code 6cgy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion, PDB code: 6cgy:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 6cgy

Go back to Cobalt Binding Sites List in 6cgy
Cobalt binding site 1 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co302

b:17.0
occ:1.00
O1 A:PO4305 2.1 19.3 0.8
NE2 A:HIS266 2.1 17.5 1.0
OD2 A:ASP220 2.1 19.2 1.0
NE2 A:HIS123 2.1 18.2 1.0
OD2 A:ASP122 2.2 18.9 1.0
O2 A:PO4305 2.3 19.3 0.8
P A:PO4305 2.7 43.6 0.8
CG A:ASP220 2.9 17.2 1.0
OD1 A:ASP220 3.0 19.9 1.0
CD2 A:HIS123 3.0 15.4 1.0
CD2 A:HIS266 3.1 18.6 1.0
CE1 A:HIS266 3.1 18.6 1.0
CG A:ASP122 3.1 18.8 1.0
CE1 A:HIS123 3.2 20.7 1.0
OD1 A:ASP122 3.3 18.9 1.0
CO A:CO303 3.5 17.4 1.0
O3 A:PO4305 3.7 18.7 0.8
O4 A:PO4305 3.8 22.4 0.8
CG A:HIS123 4.2 17.6 1.0
ND1 A:HIS266 4.2 19.1 1.0
CG A:HIS266 4.2 16.8 1.0
ND1 A:HIS123 4.3 20.4 1.0
CB A:ASP220 4.3 16.0 1.0
NE2 A:HIS118 4.4 16.9 1.0
CE1 A:TYR223 4.5 20.1 1.0
CB A:ASP122 4.5 19.3 1.0
CE1 A:HIS118 4.5 18.0 1.0

Cobalt binding site 2 out of 6 in 6cgy

Go back to Cobalt Binding Sites List in 6cgy
Cobalt binding site 2 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co303

b:17.4
occ:1.00
NE2 A:HIS198 2.1 16.1 1.0
O2 A:PO4305 2.2 19.3 0.8
ND1 A:HIS120 2.2 18.4 1.0
NE2 A:HIS118 2.2 16.9 1.0
OD2 A:ASP220 2.2 19.2 1.0
O3 A:PO4305 2.2 18.7 0.8
P A:PO4305 2.7 43.6 0.8
CE1 A:HIS120 3.0 21.3 1.0
CE1 A:HIS198 3.1 19.4 1.0
CD2 A:HIS118 3.1 13.5 1.0
CD2 A:HIS198 3.2 18.3 1.0
CE1 A:HIS118 3.2 18.0 1.0
CG A:HIS120 3.2 15.8 1.0
CG A:ASP220 3.3 17.2 1.0
CO A:CO302 3.5 17.0 1.0
CB A:ASP220 3.6 16.0 1.0
CB A:HIS120 3.6 16.1 1.0
O1 A:PO4305 3.6 19.3 0.8
O4 A:PO4305 3.9 22.4 0.8
ND1 A:HIS198 4.2 20.5 1.0
NE2 A:HIS120 4.2 22.3 1.0
NE2 A:HIS123 4.2 18.2 1.0
CD2 A:HIS123 4.2 15.4 1.0
CG A:HIS198 4.3 19.0 1.0
CG A:HIS118 4.3 15.1 1.0
ND1 A:HIS118 4.3 15.8 1.0
CD2 A:HIS120 4.3 20.6 1.0
OD1 A:ASP220 4.4 19.9 1.0
OD1 A:ASP122 4.5 18.9 1.0
OH A:TYR223 4.6 22.7 1.0
CE1 A:TYR223 4.8 20.1 1.0

Cobalt binding site 3 out of 6 in 6cgy

Go back to Cobalt Binding Sites List in 6cgy
Cobalt binding site 3 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Co302

b:18.9
occ:1.00
NE2 H:HIS123 2.1 19.0 1.0
NE2 H:HIS266 2.1 18.8 1.0
O3 H:PO4306 2.1 18.9 0.7
OD2 H:ASP220 2.2 19.8 1.0
OD2 H:ASP122 2.2 21.7 1.0
O2 H:PO4306 2.3 18.0 0.7
P H:PO4306 2.7 36.4 0.7
CG H:ASP220 2.9 17.5 1.0
OD1 H:ASP220 3.0 20.1 1.0
CD2 H:HIS123 3.0 17.4 1.0
CE1 H:HIS266 3.1 20.6 1.0
CD2 H:HIS266 3.1 18.6 1.0
CG H:ASP122 3.1 21.7 1.0
CE1 H:HIS123 3.1 17.8 1.0
OD1 H:ASP122 3.4 21.4 1.0
CO H:CO303 3.6 18.8 1.0
O1 H:PO4306 3.7 18.1 0.7
O4 H:PO4306 3.9 22.6 0.7
CG H:HIS123 4.2 16.8 1.0
ND1 H:HIS266 4.2 19.1 1.0
ND1 H:HIS123 4.2 20.4 1.0
CG H:HIS266 4.2 19.6 1.0
CB H:ASP220 4.4 18.3 1.0
NE2 H:HIS118 4.4 17.0 1.0
CE1 H:TYR223 4.4 19.6 1.0
CE1 H:HIS118 4.5 16.4 1.0
CB H:ASP122 4.5 21.3 1.0

Cobalt binding site 4 out of 6 in 6cgy

Go back to Cobalt Binding Sites List in 6cgy
Cobalt binding site 4 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Co303

b:18.8
occ:1.00
NE2 H:HIS198 2.1 17.5 1.0
ND1 H:HIS120 2.2 19.2 1.0
O2 H:PO4306 2.2 18.0 0.7
OD2 H:ASP220 2.2 19.8 1.0
NE2 H:HIS118 2.2 17.0 1.0
O1 H:PO4306 2.2 18.1 0.7
P H:PO4306 2.7 36.4 0.7
CE1 H:HIS120 3.0 21.2 1.0
CD2 H:HIS118 3.1 17.1 1.0
CE1 H:HIS198 3.1 19.8 1.0
CD2 H:HIS198 3.1 19.3 1.0
CG H:ASP220 3.2 17.5 1.0
CG H:HIS120 3.2 16.9 1.0
CE1 H:HIS118 3.2 16.4 1.0
CO H:CO302 3.6 18.9 1.0
CB H:ASP220 3.6 18.3 1.0
CB H:HIS120 3.6 17.0 1.0
O3 H:PO4306 3.7 18.9 0.7
O4 H:PO4306 3.9 22.6 0.7
NE2 H:HIS123 4.1 19.0 1.0
NE2 H:HIS120 4.2 20.9 1.0
ND1 H:HIS198 4.2 21.7 1.0
CD2 H:HIS123 4.2 17.4 1.0
CG H:HIS118 4.3 17.7 1.0
CG H:HIS198 4.3 18.5 1.0
CD2 H:HIS120 4.3 20.5 1.0
ND1 H:HIS118 4.3 17.7 1.0
OD1 H:ASP220 4.4 20.1 1.0
OD1 H:ASP122 4.5 21.4 1.0
OH H:TYR223 4.5 24.0 1.0
CE1 H:TYR223 4.8 19.6 1.0

Cobalt binding site 5 out of 6 in 6cgy

Go back to Cobalt Binding Sites List in 6cgy
Cobalt binding site 5 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co301

b:20.2
occ:1.00
O1 L:PO4304 1.9 22.0 0.8
NE2 L:HIS123 2.1 21.1 1.0
NE2 L:HIS266 2.1 20.6 1.0
OD2 L:ASP220 2.2 20.1 1.0
OD2 L:ASP122 2.2 23.6 1.0
O3 L:PO4304 2.2 19.8 0.8
P L:PO4304 2.7 46.7 0.8
CG L:ASP220 2.9 19.8 1.0
OD1 L:ASP220 2.9 20.2 1.0
CD2 L:HIS123 3.0 21.1 1.0
CE1 L:HIS266 3.0 24.7 1.0
CE1 L:HIS123 3.1 18.1 1.0
CG L:ASP122 3.1 29.5 1.0
CD2 L:HIS266 3.1 22.2 1.0
OD1 L:ASP122 3.3 22.8 1.0
CO L:CO302 3.5 19.5 1.0
O2 L:PO4304 3.7 23.4 0.8
O4 L:PO4304 3.8 25.4 0.8
CG L:HIS123 4.2 18.9 1.0
ND1 L:HIS123 4.2 22.6 1.0
ND1 L:HIS266 4.2 21.6 1.0
CG L:HIS266 4.3 22.0 1.0
CB L:ASP220 4.3 18.5 1.0
CE1 L:TYR223 4.4 18.8 1.0
NE2 L:HIS118 4.4 21.5 1.0
CE1 L:HIS118 4.5 19.6 1.0
CB L:ASP122 4.5 22.8 1.0

Cobalt binding site 6 out of 6 in 6cgy

Go back to Cobalt Binding Sites List in 6cgy
Cobalt binding site 6 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co302

b:19.5
occ:1.00
OD2 L:ASP220 2.2 20.1 1.0
ND1 L:HIS120 2.2 20.2 1.0
NE2 L:HIS118 2.2 21.5 1.0
NE2 L:HIS198 2.2 17.9 1.0
O2 L:PO4304 2.2 23.4 0.8
O3 L:PO4304 2.2 19.8 0.8
P L:PO4304 2.7 46.7 0.8
CE1 L:HIS120 3.0 20.4 1.0
CD2 L:HIS118 3.1 18.2 1.0
CD2 L:HIS198 3.1 22.2 1.0
CE1 L:HIS198 3.2 22.8 1.0
CE1 L:HIS118 3.2 19.6 1.0
CG L:ASP220 3.2 19.8 1.0
CG L:HIS120 3.2 20.2 1.0
CO L:CO301 3.5 20.2 1.0
O1 L:PO4304 3.6 22.0 0.8
CB L:ASP220 3.6 18.5 1.0
CB L:HIS120 3.6 20.4 1.0
O4 L:PO4304 4.0 25.4 0.8
NE2 L:HIS123 4.1 21.1 1.0
NE2 L:HIS120 4.2 22.8 1.0
CD2 L:HIS123 4.2 21.1 1.0
ND1 L:HIS198 4.3 20.4 1.0
CG L:HIS198 4.3 19.9 1.0
CG L:HIS118 4.3 17.9 1.0
ND1 L:HIS118 4.3 19.7 1.0
CD2 L:HIS120 4.3 23.0 1.0
OD1 L:ASP220 4.3 20.2 1.0
OD1 L:ASP122 4.5 22.8 1.0
OH L:TYR223 4.5 23.3 1.0
CE1 L:TYR223 4.7 18.8 1.0
O L:HOH470 4.9 43.6 1.0

Reference:

C.Bergonzi, M.Schwab, T.Naik, D.Daude, E.Chabriere, M.Elias. Structural and Biochemical Characterization of Aal, A Quorum Quenching Lactonase with Unusual Kinetic Properties. Sci Rep V. 8 11262 2018.
ISSN: ESSN 2045-2322
PubMed: 30050039
DOI: 10.1038/S41598-018-28988-5
Page generated: Sun Dec 13 10:49:46 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy