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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 12:04:32 2020

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