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Zinc in PDB 4j3d: Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor

Protein crystallography data

The structure of Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor, PDB code: 4j3d was solved by S.Lahiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 156.88 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.762, 156.878, 49.334, 90.00, 102.40, 90.00
R / Rfree (%) 20.1 / 28.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor (pdb code 4j3d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor, PDB code: 4j3d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4j3d

Go back to Zinc Binding Sites List in 4j3d
Zinc binding site 1 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

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

b:23.5
occ:1.00
NE2 A:HIS78 2.1 26.3 1.0
O30 A:1JS303 2.1 24.2 1.0
OD1 A:ASP241 2.2 16.1 1.0
CE1 A:HIS237 2.2 20.0 1.0
O32 A:1JS303 2.4 23.2 1.0
OD2 A:ASP241 2.7 22.3 1.0
CG A:ASP241 2.8 19.7 1.0
C29 A:1JS303 2.8 25.6 1.0
N31 A:1JS303 3.0 25.8 1.0
CD2 A:HIS78 3.0 24.6 1.0
NE2 A:HIS237 3.0 18.2 1.0
CE1 A:HIS78 3.1 30.4 1.0
ND1 A:HIS237 3.2 20.8 1.0
OE2 A:GLU77 4.0 19.1 1.0
CG A:GLU77 4.1 20.3 1.0
OG1 A:THR190 4.2 19.2 1.0
CG A:HIS78 4.2 23.0 1.0
ND1 A:HIS78 4.2 28.5 1.0
CD2 A:HIS237 4.2 16.0 1.0
C18 A:1JS303 4.2 24.8 1.0
CB A:ASP241 4.2 19.7 1.0
CG A:HIS237 4.3 20.9 1.0
CB A:THR190 4.3 22.5 1.0
C20 A:1JS303 4.5 28.0 1.0
CD A:GLU77 4.6 21.6 1.0
ZN A:ZN302 4.7 34.9 1.0
O A:HIS237 4.9 20.6 1.0
CA A:ASP241 4.9 20.4 1.0
N17 A:1JS303 4.9 22.5 1.0

Zinc binding site 2 out of 4 in 4j3d

Go back to Zinc Binding Sites List in 4j3d
Zinc binding site 2 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

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

b:34.9
occ:1.00
N31 A:1JS303 1.9 25.8 1.0
NE2 A:HIS264 2.0 23.5 1.0
O A:MET62 2.2 29.6 1.0
O A:HOH402 2.3 19.5 1.0
O32 A:1JS303 2.7 23.2 1.0
CD2 A:HIS264 2.8 24.8 1.0
C29 A:1JS303 3.0 25.6 1.0
CE1 A:HIS264 3.1 23.0 1.0
C A:MET62 3.1 30.3 1.0
C18 A:1JS303 3.3 24.8 1.0
C20 A:1JS303 3.8 28.0 1.0
OE2 A:GLU77 3.9 19.1 1.0
N A:SER63 3.9 28.8 1.0
CG A:HIS264 4.0 23.1 1.0
CA A:MET62 4.0 32.2 1.0
CA A:SER63 4.0 28.0 1.0
O30 A:1JS303 4.1 24.2 1.0
ND1 A:HIS264 4.1 22.8 1.0
O A:HOH429 4.2 22.0 1.0
NZ A:LYS238 4.3 33.2 1.0
OD2 A:ASP241 4.3 22.3 1.0
N17 A:1JS303 4.7 22.5 1.0
ZN A:ZN301 4.7 23.5 1.0
CB A:MET62 4.8 32.3 1.0
CD A:GLU77 4.8 21.6 1.0
CG A:ASP241 4.8 19.7 1.0
O16 A:1JS303 4.8 27.9 1.0
CB A:SER63 4.9 28.6 1.0

Zinc binding site 3 out of 4 in 4j3d

Go back to Zinc Binding Sites List in 4j3d
Zinc binding site 3 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:30.4
occ:1.00
OD1 B:ASP241 2.0 21.0 1.0
O30 B:1JS303 2.1 29.1 1.0
NE2 B:HIS78 2.1 24.2 1.0
NE2 B:HIS237 2.2 25.2 1.0
O32 B:1JS303 2.4 29.9 1.0
CG B:ASP241 2.7 24.5 1.0
OD2 B:ASP241 2.7 28.5 1.0
C29 B:1JS303 2.8 32.3 1.0
N31 B:1JS303 2.9 31.3 1.0
CD2 B:HIS237 3.0 24.3 1.0
CD2 B:HIS78 3.1 24.9 1.0
CE1 B:HIS78 3.1 26.1 1.0
CE1 B:HIS237 3.2 24.3 1.0
OG1 B:THR190 4.1 25.7 1.0
C18 B:1JS303 4.2 32.3 1.0
CB B:ASP241 4.2 23.4 1.0
CG B:HIS237 4.2 25.5 1.0
OE2 B:GLU77 4.2 25.8 1.0
CG B:GLU77 4.2 23.0 1.0
ND1 B:HIS78 4.2 27.2 1.0
ND1 B:HIS237 4.2 23.4 1.0
CG B:HIS78 4.2 25.0 1.0
C20 B:1JS303 4.4 35.8 1.0
CB B:THR190 4.5 26.5 1.0
ZN B:ZN302 4.7 40.5 1.0
CD B:GLU77 4.7 22.4 1.0
CA B:ASP241 4.8 23.5 1.0
N17 B:1JS303 4.9 31.0 1.0
O B:HIS237 5.0 26.7 1.0

Zinc binding site 4 out of 4 in 4j3d

Go back to Zinc Binding Sites List in 4j3d
Zinc binding site 4 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:40.5
occ:1.00
N31 B:1JS303 1.9 31.3 1.0
NE2 B:HIS264 2.2 26.8 1.0
O B:MET62 2.3 38.6 1.0
O B:HOH402 2.3 18.9 1.0
O32 B:1JS303 2.8 29.9 1.0
CD2 B:HIS264 2.8 28.7 1.0
C29 B:1JS303 2.9 32.3 1.0
C B:MET62 3.2 39.0 1.0
C18 B:1JS303 3.3 32.3 1.0
CE1 B:HIS264 3.3 27.6 1.0
C20 B:1JS303 3.9 35.8 1.0
CA B:MET62 3.9 40.4 1.0
O30 B:1JS303 4.0 29.1 1.0
OE2 B:GLU77 4.0 25.8 1.0
N B:SER63 4.1 37.0 1.0
OD2 B:ASP241 4.1 28.5 1.0
CG B:HIS264 4.1 28.3 1.0
CA B:SER63 4.2 35.6 1.0
NZ B:LYS238 4.3 28.3 1.0
ND1 B:HIS264 4.3 29.5 1.0
O B:HOH439 4.3 29.3 1.0
O B:HOH447 4.6 50.4 1.0
N17 B:1JS303 4.6 31.0 1.0
O B:HOH528 4.7 36.4 1.0
ZN B:ZN301 4.7 30.4 1.0
CB B:MET62 4.7 41.0 1.0
O16 B:1JS303 4.7 35.0 1.0
CG B:ASP241 4.7 24.5 1.0
O B:THR61 4.9 42.6 1.0
CB B:SER63 5.0 35.9 1.0
CD B:GLU77 5.0 22.4 1.0

Reference:

M.R.Hale, P.Hill, S.Lahiri, M.D.Miller, P.Ross, R.Alm, N.Gao, A.Kutschke, M.Johnstone, B.Prince, J.Thresher, W.Yang. Exploring the Udp Pocket of Lpxc Through Amino Acid Analogs. Bioorg.Med.Chem.Lett. V. 23 2362 2013.
ISSN: ISSN 0960-894X
PubMed: 23499237
DOI: 10.1016/J.BMCL.2013.02.055
Page generated: Wed Dec 16 05:24:55 2020

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