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Zinc in PDB 2ves: Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor

Enzymatic activity of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor

All present enzymatic activity of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor:
3.5.1.108;

Protein crystallography data

The structure of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor, PDB code: 2ves was solved by I.Mochalkin, J.D.Knafels, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.72 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.542, 103.331, 105.284, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor (pdb code 2ves). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor, PDB code: 2ves:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2ves

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Zinc binding site 1 out of 7 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1295

b:22.4
occ:1.00
 NE2 A:HIS78 2.0 20.1 1.0
O28 A:GVR1296 2.0 17.7 1.0
NE2 A:HIS237 2.0 21.4 1.0
OD1 A:ASP241 2.1 22.3 1.0
O30 A:GVR1296 2.3 20.6 1.0
CG A:ASP241 2.8 21.6 1.0
OD2 A:ASP241 2.8 21.7 1.0
C27 A:GVR1296 2.9 19.2 1.0
CE1 A:HIS237 3.0 22.8 1.0
N29 A:GVR1296 3.0 18.4 1.0
CE1 A:HIS78 3.0 19.4 1.0
CD2 A:HIS78 3.0 19.8 1.0
CD2 A:HIS237 3.1 22.5 1.0
ND1 A:HIS237 4.1 21.9 1.0
ND1 A:HIS78 4.1 19.7 1.0
CG A:HIS237 4.2 21.7 1.0
CG A:HIS78 4.2 20.1 1.0
O A:HOH2352 4.2 21.1 1.0
OG1 A:THR190 4.2 22.7 1.0
CB A:ASP241 4.2 22.1 1.0
CB A:THR190 4.3 22.0 1.0
C26 A:GVR1296 4.3 18.7 1.0
OE2 A:GLU77 4.5 25.2 1.0
CG A:GLU77 4.5 23.1 1.0
O A:HOH2412 4.6 23.1 1.0
CE1 A:HIS264 4.8 24.4 1.0
O A:HIS237 4.8 21.4 1.0
CA A:ASP241 4.8 21.8 1.0
NE2 A:HIS264 4.9 25.3 1.0
CA A:THR190 5.0 21.9 1.0
CD2 A:LEU240 5.0 21.9 1.0

Zinc binding site 2 out of 7 in 2ves

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Zinc binding site 2 out of 7 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1297

b:17.9
occ:1.00
 OE1 B:GLU219 1.9 18.7 1.0
OD2 A:ASP159 2.0 21.6 1.0
OD1 A:ASP161 2.0 21.4 1.0
ND1 B:HIS162 2.0 20.1 1.0
CD B:GLU219 2.8 19.5 1.0
CG A:ASP161 2.8 22.1 1.0
CG A:ASP159 2.8 22.1 1.0
CE1 B:HIS162 3.0 20.6 1.0
OE2 B:GLU219 3.0 20.9 1.0
OD2 A:ASP161 3.0 23.8 1.0
CG B:HIS162 3.1 19.2 1.0
OD1 A:ASP159 3.1 22.1 1.0
CB B:HIS162 3.5 20.1 1.0
CA B:HIS162 3.7 20.4 1.0
O B:HOH2324 3.9 17.0 1.0
NE2 B:HIS162 4.1 20.2 1.0
CD2 B:HIS162 4.2 20.2 1.0
CG B:GLU219 4.2 20.8 1.0
O A:HOH2270 4.2 31.0 1.0
CB A:ASP159 4.2 22.1 1.0
CB A:ASP161 4.2 21.4 1.0
N B:HIS162 4.4 20.6 1.0
CD B:PRO163 4.5 19.9 1.0
O A:PHE160 4.6 21.1 1.0
C A:ASP159 4.6 21.9 1.0
C A:PHE160 4.6 21.6 1.0
CA A:ASP159 4.7 22.0 1.0
N A:ASP161 4.7 21.1 1.0
CA A:ASP161 4.7 21.7 1.0
O A:ASP159 4.8 21.3 1.0
N A:PHE160 4.9 21.9 1.0
NH2 B:ARG195 4.9 24.6 1.0

Zinc binding site 3 out of 7 in 2ves

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Zinc binding site 3 out of 7 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1289

b:21.3
occ:1.00
 O28 B:GVR1290 2.0 17.9 1.0
OD1 B:ASP241 2.1 20.4 1.0
NE2 B:HIS78 2.1 20.5 1.0
NE2 B:HIS237 2.2 19.7 1.0
O30 B:GVR1290 2.3 20.1 1.0
CG B:ASP241 2.7 20.5 1.0
OD2 B:ASP241 2.8 20.0 1.0
C27 B:GVR1290 2.9 18.9 1.0
N29 B:GVR1290 3.0 18.1 1.0
CD2 B:HIS78 3.1 21.1 1.0
CD2 B:HIS237 3.1 20.1 1.0
CE1 B:HIS78 3.1 22.8 1.0
CE1 B:HIS237 3.1 20.1 1.0
OG1 B:THR190 4.2 20.0 1.0
O B:HOH2354 4.2 24.4 1.0
ND1 B:HIS237 4.2 19.4 1.0
ND1 B:HIS78 4.2 21.2 1.0
CG B:HIS237 4.2 21.1 1.0
CB B:ASP241 4.2 20.6 1.0
CG B:HIS78 4.2 20.9 1.0
C26 B:GVR1290 4.3 18.4 1.0
CB B:THR190 4.3 20.0 1.0
OE2 B:GLU77 4.5 24.9 1.0
CG B:GLU77 4.5 22.2 1.0
O B:HOH2177 4.6 21.6 1.0
CE1 B:HIS264 4.8 24.4 1.0
O B:HIS237 4.8 20.2 1.0
NE2 B:HIS264 4.8 24.3 1.0
CA B:ASP241 4.8 20.4 1.0

Zinc binding site 4 out of 7 in 2ves

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Zinc binding site 4 out of 7 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1291

b:19.9
occ:1.00
 OE1 C:GLU219 1.9 22.1 1.0
OD2 B:ASP159 2.0 21.3 1.0
OD1 B:ASP161 2.0 20.8 1.0
ND1 C:HIS162 2.1 22.3 1.0
CG B:ASP161 2.7 21.9 1.0
CD C:GLU219 2.7 25.3 1.0
OD2 B:ASP161 2.8 26.6 1.0
CG B:ASP159 2.9 22.3 1.0
OE2 C:GLU219 2.9 25.2 1.0
CE1 C:HIS162 3.0 23.4 1.0
CG C:HIS162 3.1 22.0 1.0
OD1 B:ASP159 3.2 22.2 1.0
CB C:HIS162 3.5 22.0 1.0
CA C:HIS162 3.8 22.1 1.0
O C:HOH2310 3.9 21.8 1.0
CG C:GLU219 4.1 25.7 1.0
NE2 C:HIS162 4.2 23.0 1.0
CB B:ASP161 4.2 21.2 1.0
CD2 C:HIS162 4.2 22.2 1.0
CB B:ASP159 4.3 22.2 1.0
O B:HOH2266 4.4 42.7 1.0
N C:HIS162 4.5 21.6 1.0
CD C:PRO163 4.5 23.2 1.0
C B:ASP159 4.6 21.7 1.0
O B:PHE160 4.6 21.2 1.0
C B:PHE160 4.7 21.0 1.0
CA B:ASP159 4.7 22.1 1.0
N B:ASP161 4.7 20.9 1.0
CA B:ASP161 4.7 21.0 1.0
N B:PHE160 4.9 21.5 1.0
O B:ASP159 4.9 21.6 1.0

Zinc binding site 5 out of 7 in 2ves

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Zinc binding site 5 out of 7 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1300

b:20.9
occ:1.00
 OD1 C:ASP241 2.1 18.8 1.0
O28 C:GVR1301 2.1 18.0 1.0
NE2 C:HIS78 2.1 21.0 1.0
NE2 C:HIS237 2.1 20.8 1.0
O30 C:GVR1301 2.2 21.1 1.0
CG C:ASP241 2.8 20.6 1.0
OD2 C:ASP241 2.8 20.5 1.0
C27 C:GVR1301 2.9 20.5 1.0
N29 C:GVR1301 3.0 20.5 1.0
CE1 C:HIS237 3.0 22.3 1.0
CD2 C:HIS78 3.1 20.6 1.0
CE1 C:HIS78 3.1 21.0 1.0
CD2 C:HIS237 3.2 21.8 1.0
ND1 C:HIS237 4.2 20.6 1.0
OG1 C:THR190 4.2 23.9 1.0
ND1 C:HIS78 4.2 21.2 1.0
CG C:HIS78 4.2 20.4 1.0
CB C:ASP241 4.2 20.4 1.0
CG C:HIS237 4.3 21.4 1.0
O C:HOH2341 4.3 26.0 1.0
C26 C:GVR1301 4.3 21.2 1.0
CB C:THR190 4.3 23.4 1.0
OE2 C:GLU77 4.4 25.1 1.0
CG C:GLU77 4.5 21.8 1.0
CE1 C:HIS264 4.6 23.4 1.0
O C:HOH2163 4.7 36.8 1.0
NE2 C:HIS264 4.8 23.7 1.0
CA C:ASP241 4.8 20.6 1.0
O C:HIS237 4.9 20.9 1.0
CD C:GLU77 5.0 24.3 1.0

Zinc binding site 6 out of 7 in 2ves

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Zinc binding site 6 out of 7 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1302

b:18.9
occ:1.00
 OD2 C:ASP159 1.9 20.3 1.0
OE1 A:GLU219 2.0 21.9 1.0
OD1 C:ASP161 2.0 20.2 1.0
ND1 A:HIS162 2.1 19.3 1.0
CD A:GLU219 2.7 21.7 1.0
CG C:ASP159 2.8 21.4 1.0
CG C:ASP161 2.8 21.9 1.0
OE2 A:GLU219 2.9 21.6 1.0
OD2 C:ASP161 3.0 24.3 1.0
CE1 A:HIS162 3.1 21.5 1.0
OD1 C:ASP159 3.1 22.9 1.0
CG A:HIS162 3.2 21.5 1.0
CB A:HIS162 3.5 22.5 1.0
CA A:HIS162 3.8 22.4 1.0
O A:HOH2324 3.9 19.8 1.0
CG A:GLU219 4.2 22.5 1.0
NE2 A:HIS162 4.2 20.8 1.0
CB C:ASP159 4.2 21.3 1.0
CB C:ASP161 4.3 21.4 1.0
CD2 A:HIS162 4.3 21.6 1.0
O C:HOH2260 4.3 38.0 1.0
N A:HIS162 4.4 22.0 1.0
C C:ASP159 4.6 21.0 1.0
CD A:PRO163 4.6 23.6 1.0
O C:PHE160 4.6 20.2 1.0
C C:PHE160 4.6 21.1 1.0
CA C:ASP159 4.7 21.3 1.0
N C:ASP161 4.7 21.2 1.0
CA C:ASP161 4.7 21.6 1.0
O C:ASP159 4.8 21.1 1.0
N C:PHE160 4.8 20.7 1.0
O A:HOH2272 5.0 26.1 1.0

Zinc binding site 7 out of 7 in 2ves

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Zinc binding site 7 out of 7 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1303

b:45.4
occ:1.00
 OE1 A:GLN203 2.2 34.2 1.0
OE2 C:GLU134 2.3 33.6 1.0
O C:HOH2406 2.4 34.3 1.0
O C:HOH2407 2.4 38.2 1.0
OG C:SER136 2.5 27.6 1.0
O C:HOH2408 2.7 30.4 1.0
CD C:GLU134 3.1 30.8 1.0
OE1 C:GLU134 3.1 32.7 1.0
CD A:GLN203 3.1 32.8 1.0
NE2 A:GLN203 3.5 33.5 1.0
CB C:SER136 3.5 26.3 1.0
N C:SER136 3.8 26.0 1.0
CA C:SER136 4.2 26.1 1.0
O C:HOH2238 4.3 23.1 1.0
O A:HOH2312 4.3 42.8 1.0
C C:VAL135 4.4 25.8 1.0
O C:SER136 4.5 25.5 1.0
O A:HOH2307 4.5 35.8 1.0
CG A:GLN203 4.5 31.9 1.0
CG C:GLU134 4.5 28.5 1.0
C C:SER136 4.7 26.1 1.0
CA C:VAL135 4.7 26.1 1.0
CB A:GLN203 4.9 31.0 1.0

Reference:

I.Mochalkin, J.D.Knafels, S.Lightle. Crystal Structure of Lpxc From Pseudomonas Aeruginosa Complexed with the Potent Bb-78485 Inhibitor. Protein Sci. V. 17 450 2008.
ISSN: ISSN 0961-8368
PubMed: 18287278
DOI: 10.1110/PS.073324108
Page generated: Thu Oct 17 04:16:20 2024

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