Atomistry » Zinc » PDB 6jev-6jss » 6jka
Atomistry »
  Zinc »
    PDB 6jev-6jss »
      6jka »

Zinc in PDB 6jka: Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor, PDB code: 6jka was solved by T.Kamo, K.Kuroda, S.Kondo, U.Hayashi, S.Fudo, M.Nukaga, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.68 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.477, 77.764, 261.527, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor (pdb code 6jka). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor, PDB code: 6jka:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 1 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing 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 Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:22.3
occ:1.00
O A:HOH444 1.8 27.2 1.0
NE2 A:HIS143 2.0 25.0 1.0
ND1 A:HIS83 2.0 22.3 1.0
NE2 A:HIS81 2.1 21.8 1.0
CE1 A:HIS143 2.8 22.3 1.0
CE1 A:HIS83 3.0 27.3 1.0
CG A:HIS83 3.0 26.5 1.0
CD2 A:HIS81 3.0 19.2 1.0
CD2 A:HIS143 3.1 25.6 1.0
CE1 A:HIS81 3.1 23.4 1.0
CAO A:BS0303 3.2 40.7 1.0
ZN A:ZN302 3.3 25.6 1.0
CB A:HIS83 3.3 21.8 1.0
O A:HOH461 3.5 32.8 1.0
CAL A:BS0303 3.6 50.0 1.0
SG A:CYS162 3.8 25.6 1.0
CAN A:BS0303 3.8 42.9 1.0
OD1 A:ASP85 3.8 23.5 1.0
CAQ A:BS0303 3.9 46.1 1.0
CAK A:BS0303 3.9 49.0 1.0
CB A:CYS162 3.9 23.2 1.0
ND1 A:HIS143 4.0 25.0 1.0
NE2 A:HIS83 4.1 26.8 1.0
CG A:HIS143 4.1 24.9 1.0
CD2 A:HIS83 4.1 28.5 1.0
CG A:HIS81 4.2 21.6 1.0
ND1 A:HIS81 4.2 21.0 1.0
OD2 A:ASP85 4.4 20.3 1.0
CG A:ASP85 4.5 24.7 1.0
SAJ A:BS0303 4.8 52.6 1.0
CA A:HIS83 4.8 20.1 1.0
CAP A:BS0303 4.9 48.0 1.0
NAM A:BS0303 4.9 43.0 1.0
CG2 A:THR144 4.9 21.3 1.0

Zinc binding site 2 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 2 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing 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 Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:25.6
occ:1.00
O A:HOH444 2.0 27.2 1.0
NE2 A:HIS201 2.1 27.1 1.0
OD2 A:ASP85 2.2 20.3 1.0
O A:HOH461 2.2 32.8 1.0
SG A:CYS162 2.3 25.6 1.0
CE1 A:HIS201 2.9 21.3 1.0
CG A:ASP85 3.2 24.7 1.0
CD2 A:HIS201 3.2 24.0 1.0
ZN A:ZN301 3.3 22.3 1.0
CB A:CYS162 3.4 23.2 1.0
OD1 A:ASP85 3.5 23.5 1.0
CAK A:BS0303 3.5 49.0 1.0
NAM A:BS0303 3.5 43.0 1.0
CAN A:BS0303 3.8 42.9 1.0
CAL A:BS0303 3.9 50.0 1.0
CAI A:BS0303 4.0 43.4 1.0
ND1 A:HIS201 4.1 24.1 1.0
NE2 A:HIS143 4.2 25.0 1.0
CG A:HIS201 4.2 24.7 1.0
NE2 A:HIS81 4.3 21.8 1.0
CAP A:BS0303 4.3 48.0 1.0
CE1 A:HIS81 4.3 23.4 1.0
CAO A:BS0303 4.3 40.7 1.0
SAJ A:BS0303 4.4 52.6 1.0
CB A:SER200 4.4 21.4 1.0
CE1 A:HIS143 4.5 22.3 1.0
CB A:ASP85 4.5 18.6 1.0
CA A:CYS162 4.6 23.1 1.0
OG A:SER200 4.6 23.6 1.0
CD A:LYS37 4.8 18.0 1.0
CAH A:BS0303 4.9 51.1 1.0

Zinc binding site 3 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 3 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing 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 Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:32.1
occ:1.00
OD2 B:ASP85 2.0 28.0 1.0
NE2 B:HIS201 2.2 26.6 1.0
SG B:CYS162 2.3 31.2 1.0
CAW B:BQU303 2.5 46.7 1.0
OAY B:BQU303 2.6 53.1 1.0
OAX B:BQU303 2.8 29.7 1.0
CG B:ASP85 3.0 31.4 1.0
CD2 B:HIS201 3.1 31.1 1.0
CE1 B:HIS201 3.1 28.7 1.0
CB B:CYS162 3.3 26.0 1.0
CAV B:BQU303 3.3 47.6 1.0
OD1 B:ASP85 3.4 27.9 1.0
ZN B:ZN302 3.5 28.0 1.0
NE2 B:HIS81 4.2 20.3 1.0
CG B:HIS201 4.2 31.6 1.0
ND1 B:HIS201 4.2 26.9 1.0
CE1 B:HIS81 4.2 26.6 1.0
NE2 B:HIS143 4.2 32.6 1.0
CB B:SER200 4.3 25.4 1.0
CB B:ASP85 4.3 25.4 1.0
CAR B:BQU303 4.4 58.0 1.0
CAQ B:BQU303 4.5 56.5 1.0
CAU B:BQU303 4.5 58.4 1.0
CA B:CYS162 4.5 28.1 1.0
OG B:SER200 4.5 28.1 1.0
NAT B:BQU303 4.6 45.2 1.0
CD B:LYS37 4.7 23.7 1.0
CAS B:BQU303 4.8 57.1 1.0
CE1 B:HIS143 4.8 30.9 1.0
CE B:LYS37 4.8 24.1 1.0
CAP B:BQU303 5.0 55.1 1.0

Zinc binding site 4 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 4 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing 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 Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:28.0
occ:1.00
OAX B:BQU303 1.6 29.7 1.0
NE2 B:HIS81 2.0 20.3 1.0
NE2 B:HIS143 2.0 32.6 1.0
ND1 B:HIS83 2.1 25.8 1.0
CAW B:BQU303 2.6 46.7 1.0
CD2 B:HIS81 2.8 20.4 1.0
OAY B:BQU303 2.9 53.1 1.0
CD2 B:HIS143 2.9 31.3 1.0
CG B:HIS83 3.1 25.0 1.0
CE1 B:HIS143 3.1 30.9 1.0
CE1 B:HIS83 3.1 26.4 1.0
CE1 B:HIS81 3.1 26.6 1.0
CB B:HIS83 3.4 23.1 1.0
NAT B:BQU303 3.4 45.2 1.0
ZN B:ZN301 3.5 32.1 1.0
CAV B:BQU303 3.9 47.6 1.0
SG B:CYS162 3.9 31.2 1.0
CB B:CYS162 3.9 26.0 1.0
OD1 B:ASP85 3.9 27.9 1.0
CG B:HIS81 4.0 23.1 1.0
CG B:HIS143 4.1 32.1 1.0
ND1 B:HIS81 4.1 23.4 1.0
ND1 B:HIS143 4.1 31.1 1.0
NE2 B:HIS83 4.1 27.4 1.0
CD2 B:HIS83 4.2 23.1 1.0
CAQ B:BQU303 4.3 56.5 1.0
CG2 B:THR144 4.3 27.4 1.0
OD2 B:ASP85 4.6 28.0 1.0
CG B:ASP85 4.7 31.4 1.0
CA B:HIS83 4.8 25.1 1.0
CAU B:BQU303 5.0 58.4 1.0
N B:HIS83 5.0 22.6 1.0
CAR B:BQU303 5.0 58.0 1.0

Zinc binding site 5 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 5 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing 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 Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:26.5
occ:1.00
O C:HOH478 1.9 23.3 1.0
OD2 C:ASP85 2.0 27.3 1.0
NE2 C:HIS201 2.1 25.5 1.0
SG C:CYS162 2.3 23.3 1.0
O C:HOH469 2.8 30.1 1.0
CG C:ASP85 3.0 29.2 1.0
CD2 C:HIS201 3.1 24.1 1.0
CE1 C:HIS201 3.1 24.4 1.0
OD1 C:ASP85 3.2 23.2 1.0
ZN C:ZN302 3.4 22.1 1.0
CB C:CYS162 3.4 23.5 1.0
O C:HOH494 3.8 39.4 1.0
NE2 C:HIS81 3.9 23.6 1.0
CE1 C:HIS81 4.0 24.6 1.0
ND1 C:HIS201 4.2 26.6 1.0
CG C:HIS201 4.2 27.4 1.0
NE2 C:HIS143 4.3 22.8 1.0
CB C:ASP85 4.4 26.0 1.0
CB C:SER200 4.4 21.7 1.0
CE C:LYS37 4.4 22.1 1.0
O C:HOH496 4.4 37.6 1.0
CD C:LYS37 4.5 20.1 1.0
CA C:CYS162 4.6 21.4 1.0
OG C:SER200 4.6 26.6 1.0
O C:HOH493 4.7 37.8 1.0
CE1 C:HIS143 4.8 20.3 1.0
NZ C:LYS165 5.0 28.3 1.0

Zinc binding site 6 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 6 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing 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 Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:22.1
occ:1.00
ND1 C:HIS83 2.0 19.3 1.0
NE2 C:HIS143 2.0 22.8 1.0
NE2 C:HIS81 2.1 23.6 1.0
O C:HOH478 2.2 23.3 1.0
CD2 C:HIS81 2.8 20.1 1.0
CG C:HIS83 3.0 20.5 1.0
CD2 C:HIS143 3.0 20.5 1.0
CE1 C:HIS83 3.0 21.7 1.0
CE1 C:HIS143 3.0 20.3 1.0
CB C:HIS83 3.3 17.8 1.0
CE1 C:HIS81 3.3 24.6 1.0
ZN C:ZN301 3.4 26.5 1.0
O C:HOH496 3.5 37.6 1.0
OD1 C:ASP85 3.8 23.2 1.0
SG C:CYS162 3.8 23.3 1.0
O C:HOH469 3.9 30.1 1.0
O C:HOH494 4.0 39.4 1.0
CB C:CYS162 4.0 23.5 1.0
CG C:HIS81 4.0 19.4 1.0
NE2 C:HIS83 4.1 22.2 1.0
CD2 C:HIS83 4.1 21.7 1.0
ND1 C:HIS143 4.1 19.8 1.0
CG C:HIS143 4.2 24.0 1.0
ND1 C:HIS81 4.2 21.8 1.0
OD2 C:ASP85 4.5 27.3 1.0
CG C:ASP85 4.6 29.2 1.0
CG2 C:THR144 4.6 18.9 1.0
CA C:HIS83 4.7 21.3 1.0

Zinc binding site 7 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 7 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing 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 Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:42.8
occ:1.00
O D:HOH428 1.8 38.1 1.0
OD2 D:ASP85 2.0 32.3 1.0
SG D:CYS162 2.2 38.5 1.0
NE2 D:HIS201 2.5 38.6 1.0
O D:HOH420 2.9 41.6 1.0
CG D:ASP85 2.9 37.7 1.0
ZN D:ZN302 3.1 37.1 1.0
OD1 D:ASP85 3.3 35.6 1.0
CB D:CYS162 3.3 33.2 1.0
CD2 D:HIS201 3.4 41.4 1.0
CE1 D:HIS201 3.4 34.2 1.0
NE2 D:HIS143 4.0 35.1 1.0
NE2 D:HIS81 4.1 37.4 1.0
CE1 D:HIS81 4.2 36.2 1.0
CB D:ASP85 4.3 37.0 1.0
ND1 D:HIS201 4.4 41.0 1.0
CG D:HIS201 4.4 42.6 1.0
CE1 D:HIS143 4.4 41.9 1.0
CA D:CYS162 4.5 33.7 1.0
CD D:LYS37 4.6 34.3 1.0
CB D:SER200 4.6 35.4 1.0
CE D:LYS37 4.7 31.4 1.0
ND1 D:HIS83 4.8 32.6 1.0
CD2 D:HIS143 4.9 38.1 1.0
OG D:SER200 5.0 33.1 1.0

Zinc binding site 8 out of 8 in 6jka

Go back to Zinc Binding Sites List in 6jka
Zinc binding site 8 out of 8 in the Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Metallo-Beta-Lactamse, Imp-1, in Complex with A Thiazole-Bearing Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:37.1
occ:1.00
NE2 D:HIS143 1.9 35.1 1.0
NE2 D:HIS81 2.0 37.4 1.0
ND1 D:HIS83 2.0 32.6 1.0
O D:HOH428 2.3 38.1 1.0
CE1 D:HIS143 2.9 41.9 1.0
CD2 D:HIS81 2.9 26.9 1.0
CD2 D:HIS143 3.0 38.1 1.0
CG D:HIS83 3.0 32.3 1.0
CE1 D:HIS83 3.0 37.2 1.0
CE1 D:HIS81 3.0 36.2 1.0
ZN D:ZN301 3.1 42.8 1.0
CB D:HIS83 3.3 25.9 1.0
OD1 D:ASP85 3.6 35.6 1.0
SG D:CYS162 3.8 38.5 1.0
CB D:CYS162 3.8 33.2 1.0
O D:HOH420 3.9 41.6 1.0
ND1 D:HIS143 4.0 36.8 1.0
CG D:HIS143 4.1 36.0 1.0
CG D:HIS81 4.1 34.9 1.0
ND1 D:HIS81 4.1 32.8 1.0
NE2 D:HIS83 4.1 34.6 1.0
CD2 D:HIS83 4.1 30.5 1.0
OD2 D:ASP85 4.2 32.3 1.0
CG D:ASP85 4.3 37.7 1.0
CA D:HIS83 4.8 33.6 1.0
CG2 D:THR144 4.9 34.6 1.0

Reference:

T.Kamo, K.Kuroda, S.Kondo, U.Hayashi, S.Fudo, M.Nukaga, T.Hoshino. Identification of the Inhibitory Compounds For Metallo-Beta-Lactamases To Be Published.
Page generated: Thu Aug 21 16:23:47 2025

Last articles

Zn in 6S0H
Zn in 6S0I
Zn in 6S0K
Zn in 6S1M
Zn in 6RZS
Zn in 6RZR
Zn in 6S03
Zn in 6RZX
Zn in 6RYU
Zn in 6RXF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy