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Zinc in PDB 4oze: A.Aolicus Lpxc in Complex with Native Product

Protein crystallography data

The structure of A.Aolicus Lpxc in Complex with Native Product, PDB code: 4oze was solved by N.B.Olivier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.76 / 1.61
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 101.332, 101.332, 123.553, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18.5

Other elements in 4oze:

The structure of A.Aolicus Lpxc in Complex with Native Product also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the A.Aolicus Lpxc in Complex with Native Product (pdb code 4oze). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the A.Aolicus Lpxc in Complex with Native Product, PDB code: 4oze:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4oze

Go back to Zinc Binding Sites List in 4oze
Zinc binding site 1 out of 7 in the A.Aolicus Lpxc in Complex with Native Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A.Aolicus Lpxc in Complex with Native Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.9
occ:1.00
O A:HOH713 1.9 21.3 1.0
OD1 A:ASP230 2.0 18.0 1.0
NE2 A:HIS226 2.0 16.1 1.0
NE2 A:HIS74 2.0 19.2 1.0
CG A:ASP230 2.7 17.9 1.0
OD2 A:ASP230 2.8 18.5 1.0
CE1 A:HIS226 2.9 16.2 1.0
CD2 A:HIS74 3.0 19.4 1.0
CD2 A:HIS226 3.0 16.4 1.0
CE1 A:HIS74 3.1 19.6 1.0
ZN A:ZN304 3.5 20.4 1.0
O A:HOH712 3.9 30.9 1.0
CG A:GLU73 4.1 18.1 1.0
ND1 A:HIS226 4.1 16.2 1.0
CG A:HIS226 4.1 15.7 1.0
CG A:HIS74 4.2 19.0 1.0
ND1 A:HIS74 4.2 20.2 1.0
CB A:ASP230 4.2 15.6 1.0
OG1 A:THR179 4.3 25.6 1.0
CB A:THR179 4.3 23.4 1.0
OE2 A:GLU73 4.5 19.6 1.0
C3 A:24G306 4.6 28.4 1.0
NE2 A:HIS253 4.6 18.2 1.0
CE1 A:HIS253 4.8 18.1 1.0
CA A:ASP230 4.8 13.9 1.0
CD A:GLU73 4.8 23.0 1.0
O A:HIS226 4.8 17.1 1.0
N11 A:24G306 4.8 17.5 1.0
CA A:THR179 4.8 17.8 1.0
C4 A:24G306 4.9 32.0 1.0
CD2 A:PHE229 5.0 17.6 1.0

Zinc binding site 2 out of 7 in 4oze

Go back to Zinc Binding Sites List in 4oze
Zinc binding site 2 out of 7 in the A.Aolicus Lpxc in Complex with Native Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A.Aolicus Lpxc in Complex with Native Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:26.2
occ:1.00
NE2 A:HIS58 2.1 23.7 1.0
NE2 A:HIS188 2.1 24.2 1.0
O A:HOH462 2.1 25.9 1.0
CL A:CL305 2.2 27.4 1.0
CD2 A:HIS188 3.0 24.6 1.0
CD2 A:HIS58 3.0 25.2 1.0
CE1 A:HIS58 3.1 23.3 1.0
CE1 A:HIS188 3.1 24.9 1.0
CG A:HIS188 4.1 23.5 1.0
CG A:HIS58 4.2 23.3 1.0
ND1 A:HIS58 4.2 24.1 1.0
ND1 A:HIS188 4.2 25.4 1.0
CG2 A:VAL192 4.4 21.3 1.0
CB A:ASN57 4.4 17.5 0.6
OD1 A:ASN57 4.7 32.6 0.6
CG1 A:VAL192 4.7 21.7 1.0
CB A:ASN57 4.8 25.0 0.5
CG A:ASN57 5.0 34.9 0.6
O A:HOH701 5.0 50.5 1.0

Zinc binding site 3 out of 7 in 4oze

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Zinc binding site 3 out of 7 in the A.Aolicus Lpxc in Complex with Native Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A.Aolicus Lpxc in Complex with Native Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:21.2
occ:1.00
OE1 A:GLU120 1.9 21.6 1.0
N A:GLY2 2.1 18.7 1.0
CD A:GLU120 2.6 24.1 1.0
OE2 A:GLU120 2.7 22.6 1.0
CA A:GLY2 3.0 18.8 1.0
C A:GLY2 3.3 21.3 1.0
O A:GLY2 3.4 22.3 1.0
CG A:GLU120 4.1 25.3 1.0
N A:LEU3 4.2 18.6 1.0
O A:HOH445 4.6 33.1 1.0
CD2 A:LEU3 4.7 22.4 1.0
CB A:GLU120 4.8 21.1 1.0

Zinc binding site 4 out of 7 in 4oze

Go back to Zinc Binding Sites List in 4oze
Zinc binding site 4 out of 7 in the A.Aolicus Lpxc in Complex with Native Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A.Aolicus Lpxc in Complex with Native Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:20.4
occ:1.00
NE2 A:HIS253 2.0 18.2 1.0
O A:HOH713 2.0 21.3 1.0
OE2 A:GLU73 2.0 19.6 1.0
N11 A:24G306 2.1 17.5 1.0
C3 A:24G306 2.8 28.4 1.0
CE1 A:HIS253 2.9 18.1 1.0
CD A:GLU73 3.0 23.0 1.0
CD2 A:HIS253 3.0 18.6 1.0
C4 A:24G306 3.3 32.0 1.0
CG A:GLU73 3.4 18.1 1.0
ZN A:ZN301 3.5 17.9 1.0
O A:HOH711 3.7 35.0 1.0
O A:HOH712 3.8 30.9 1.0
O12 A:24G306 3.9 31.2 1.0
OD2 A:ASP230 3.9 18.5 1.0
OD1 A:ASP230 4.0 18.0 1.0
OE1 A:GLU73 4.0 18.7 1.0
ND1 A:HIS253 4.1 18.0 1.0
CG A:HIS253 4.1 17.1 1.0
CA A:SER59 4.1 16.7 1.0
CG A:ASP230 4.1 17.9 1.0
C2 A:24G306 4.3 30.5 1.0
O A:HIS58 4.3 20.4 1.0
O5 A:24G306 4.5 34.0 1.0
NE2 A:HIS74 4.5 19.2 1.0
CB A:GLU73 4.5 16.5 1.0
O10 A:24G306 4.6 31.5 1.0
N A:SER59 4.7 17.8 1.0
C A:HIS58 4.7 20.6 1.0
CB A:SER59 4.8 21.1 1.0
C A:SER59 5.0 21.5 1.0
O A:HOH714 5.0 21.5 1.0

Zinc binding site 5 out of 7 in 4oze

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Zinc binding site 5 out of 7 in the A.Aolicus Lpxc in Complex with Native Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A.Aolicus Lpxc in Complex with Native Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:17.9
occ:1.00
O B:HOH667 1.9 19.9 1.0
OD1 B:ASP230 2.0 17.4 1.0
NE2 B:HIS74 2.0 18.5 1.0
NE2 B:HIS226 2.0 15.8 1.0
CG B:ASP230 2.8 17.9 1.0
OD2 B:ASP230 2.8 18.4 1.0
CE1 B:HIS226 2.9 15.9 1.0
CD2 B:HIS74 3.0 18.3 1.0
CE1 B:HIS74 3.0 19.0 1.0
CD2 B:HIS226 3.1 17.1 1.0
ZN B:ZN303 3.5 20.6 1.0
O B:HOH665 3.9 30.6 1.0
CG B:GLU73 4.0 19.7 1.0
ND1 B:HIS226 4.1 16.4 1.0
CG B:HIS226 4.1 15.8 1.0
CG B:HIS74 4.2 17.6 1.0
ND1 B:HIS74 4.2 19.5 1.0
CB B:ASP230 4.2 16.1 1.0
OG1 B:THR179 4.3 25.0 1.0
CB B:THR179 4.3 23.3 1.0
OE2 B:GLU73 4.4 19.6 1.0
C3 B:24G305 4.6 30.0 1.0
NE2 B:HIS253 4.6 18.3 1.0
CA B:ASP230 4.8 14.0 1.0
CE1 B:HIS253 4.8 18.6 1.0
CD B:GLU73 4.8 22.2 1.0
N11 B:24G305 4.8 19.5 1.0
CA B:THR179 4.9 17.1 1.0
O B:HIS226 4.9 16.2 1.0
C4 B:24G305 4.9 33.5 1.0
CD2 B:PHE229 5.0 17.6 1.0

Zinc binding site 6 out of 7 in 4oze

Go back to Zinc Binding Sites List in 4oze
Zinc binding site 6 out of 7 in the A.Aolicus Lpxc in Complex with Native Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A.Aolicus Lpxc in Complex with Native Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:24.9
occ:1.00
NE2 B:HIS188 2.0 24.4 1.0
NE2 B:HIS58 2.0 23.3 1.0
O B:HOH461 2.1 23.0 1.0
CL B:CL304 2.2 27.1 1.0
CD2 B:HIS188 3.0 25.1 1.0
CD2 B:HIS58 3.0 24.6 1.0
CE1 B:HIS58 3.0 23.5 1.0
CE1 B:HIS188 3.1 25.2 1.0
CG B:HIS188 4.1 23.6 1.0
CG B:HIS58 4.2 23.2 1.0
ND1 B:HIS188 4.2 25.1 1.0
ND1 B:HIS58 4.2 24.9 1.0
CG2 B:VAL192 4.4 20.8 1.0
CB B:ASN57 4.5 17.9 0.5
OD1 B:ASN57 4.7 28.1 0.5
CG1 B:VAL192 4.7 21.6 1.0
CB B:ASN57 4.7 25.3 0.5
O B:HOH594 5.0 65.3 1.0
CG B:ASN57 5.0 33.5 0.5

Zinc binding site 7 out of 7 in 4oze

Go back to Zinc Binding Sites List in 4oze
Zinc binding site 7 out of 7 in the A.Aolicus Lpxc in Complex with Native Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A.Aolicus Lpxc in Complex with Native Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:20.6
occ:1.00
O B:HOH667 1.9 19.9 1.0
NE2 B:HIS253 2.0 18.3 1.0
OE2 B:GLU73 2.0 19.6 1.0
N11 B:24G305 2.1 19.5 1.0
C3 B:24G305 2.8 30.0 1.0
CD B:GLU73 2.9 22.2 1.0
CE1 B:HIS253 3.0 18.6 1.0
CD2 B:HIS253 3.0 18.6 1.0
C4 B:24G305 3.3 33.5 1.0
CG B:GLU73 3.4 19.7 1.0
ZN B:ZN301 3.5 17.9 1.0
O B:HOH666 3.6 37.5 1.0
O B:HOH665 3.8 30.6 1.0
O12 B:24G305 3.9 33.3 1.0
OD2 B:ASP230 3.9 18.4 1.0
OD1 B:ASP230 4.0 17.4 1.0
OE1 B:GLU73 4.0 17.7 1.0
CG B:HIS253 4.1 18.0 1.0
ND1 B:HIS253 4.1 18.3 1.0
CG B:ASP230 4.1 17.9 1.0
CA B:SER59 4.2 17.4 1.0
C2 B:24G305 4.3 30.6 1.0
O B:HIS58 4.3 19.3 1.0
NE2 B:HIS74 4.5 18.5 1.0
O5 B:24G305 4.5 34.7 1.0
CB B:GLU73 4.5 17.0 1.0
O10 B:24G305 4.6 30.1 1.0
N B:SER59 4.7 18.0 1.0
C B:HIS58 4.7 20.3 1.0
CB B:SER59 4.9 19.3 1.0
C B:SER59 5.0 21.5 1.0

Reference:

M.D.Miller, N.Gao, P.Ross, N.B.Olivier. Mechanistic Insight From the Crystal Structure of A.Aolicus Lpxc in the Presence of Product To Be Published.
Page generated: Wed Dec 16 05:39:54 2020

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