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Zinc in PDB 7dtm: Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate., PDB code: 7dtm was solved by Y.Yamaguchi, H.Kurosaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.53 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.944, 75.675, 82.264, 83.53, 75.44, 74.13
R / Rfree (%) 21.2 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate. (pdb code 7dtm). 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-Lactamase Imp-1 in Complex with Citrate., PDB code: 7dtm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7dtm

Go back to Zinc Binding Sites List in 7dtm
Zinc binding site 1 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:23.9
occ:1.00
 OB2 A:FLC303 2.1 31.2 1.0
NE2 A:HIS77 2.1 18.7 1.0
ND1 A:HIS79 2.2 24.0 1.0
NE2 A:HIS139 2.2 26.2 1.0
CBC A:FLC303 2.8 34.4 1.0
CD2 A:HIS77 2.9 19.1 1.0
OB1 A:FLC303 2.9 29.9 1.0
CD2 A:HIS139 3.0 25.1 1.0
CG A:HIS79 3.1 23.7 1.0
CE1 A:HIS79 3.2 24.5 1.0
CE1 A:HIS77 3.3 20.7 1.0
CE1 A:HIS139 3.4 24.9 1.0
CB A:HIS79 3.4 22.8 1.0
ZN A:ZN302 3.7 31.2 1.0
OD1 A:ASP81 3.9 28.4 1.0
SG A:CYS158 3.9 25.3 1.0
CB A:CYS158 3.9 24.3 1.0
CG A:HIS77 4.1 19.4 1.0
OA2 A:FLC303 4.1 35.0 1.0
CG A:HIS139 4.2 24.5 1.0
NE2 A:HIS79 4.3 24.2 1.0
CD2 A:HIS79 4.3 23.9 1.0
ND1 A:HIS77 4.3 19.8 1.0
CB A:FLC303 4.3 37.5 1.0
OD2 A:ASP81 4.3 27.0 1.0
ND1 A:HIS139 4.4 24.6 1.0
CG A:ASP81 4.5 27.1 1.0
CG2 A:THR140 4.5 22.5 1.0
OHB A:FLC303 4.6 39.2 1.0
CAC A:FLC303 4.7 37.4 1.0
CA A:HIS79 4.8 23.0 1.0

Zinc binding site 2 out of 8 in 7dtm

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Zinc binding site 2 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:31.2
occ:1.00
 OD2 A:ASP81 2.0 27.0 1.0
NE2 A:HIS197 2.2 31.3 1.0
OB2 A:FLC303 2.2 31.2 1.0
OHB A:FLC303 2.3 39.2 1.0
OA2 A:FLC303 2.3 35.0 1.0
SG A:CYS158 2.4 25.3 1.0
CBC A:FLC303 2.9 34.4 1.0
CB A:FLC303 3.1 37.5 1.0
CE1 A:HIS197 3.1 28.8 1.0
CG A:ASP81 3.2 27.1 1.0
CD2 A:HIS197 3.2 30.0 1.0
CAC A:FLC303 3.3 37.4 1.0
CA A:FLC303 3.6 37.8 1.0
CB A:CYS158 3.6 24.3 1.0
OD1 A:ASP81 3.6 28.4 1.0
ZN A:ZN301 3.7 23.9 1.0
OB1 A:FLC303 4.1 29.9 1.0
ND1 A:HIS197 4.2 29.0 1.0
CG A:HIS197 4.3 29.9 1.0
OG2 A:FLC303 4.3 45.9 1.0
CB A:ASP81 4.4 25.4 1.0
OA1 A:FLC303 4.4 38.2 1.0
NE2 A:HIS77 4.4 18.7 1.0
CG A:FLC303 4.5 39.3 1.0
CB A:SER196 4.5 26.7 1.0
NE2 A:HIS139 4.5 26.2 1.0
CE1 A:HIS77 4.6 20.7 1.0
CA A:CYS158 4.7 23.4 1.0
CD A:LYS33 4.7 23.8 1.0
OG A:SER196 4.8 26.5 1.0
CE A:LYS33 4.8 23.7 1.0
CGC A:FLC303 4.8 42.5 1.0

Zinc binding site 3 out of 8 in 7dtm

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Zinc binding site 3 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:31.9
occ:1.00
 OD2 B:ASP81 2.0 29.1 1.0
NE2 B:HIS197 2.2 33.2 1.0
OB1 B:FLC303 2.3 27.7 1.0
OHB B:FLC303 2.4 35.3 1.0
SG B:CYS158 2.4 29.3 1.0
OA1 B:FLC303 2.6 37.2 1.0
CD2 B:HIS197 3.0 32.6 1.0
CBC B:FLC303 3.1 33.1 1.0
CG B:ASP81 3.1 27.9 1.0
CB B:FLC303 3.2 36.2 1.0
CE1 B:HIS197 3.2 31.5 1.0
CAC B:FLC303 3.5 37.7 1.0
CB B:CYS158 3.6 26.0 1.0
OD1 B:ASP81 3.6 28.0 1.0
ZN B:ZN302 3.7 26.1 1.0
CA B:FLC303 3.7 37.5 1.0
CG B:HIS197 4.2 31.8 1.0
OB2 B:FLC303 4.2 32.5 1.0
ND1 B:HIS197 4.3 32.0 1.0
CB B:ASP81 4.4 26.2 1.0
CB B:SER196 4.4 24.9 1.0
OG1 B:FLC303 4.5 40.5 1.0
NE2 B:HIS139 4.5 26.7 1.0
CG B:FLC303 4.6 37.0 1.0
OG B:SER196 4.6 24.8 1.0
NE2 B:HIS77 4.6 20.2 1.0
CE1 B:HIS77 4.6 20.9 1.0
OA2 B:FLC303 4.6 40.6 1.0
CD B:LYS33 4.7 24.3 1.0
CE B:LYS33 4.7 24.4 1.0
CA B:CYS158 4.7 24.2 1.0
CGC B:FLC303 5.0 39.2 1.0
CE1 B:HIS139 5.0 26.2 1.0

Zinc binding site 4 out of 8 in 7dtm

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Zinc binding site 4 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:26.1
occ:1.00
 OB1 B:FLC303 2.1 27.7 1.0
NE2 B:HIS139 2.2 26.7 1.0
ND1 B:HIS79 2.2 24.3 1.0
NE2 B:HIS77 2.2 20.2 1.0
CBC B:FLC303 3.0 33.1 1.0
CD2 B:HIS139 3.0 26.3 1.0
CD2 B:HIS77 3.1 19.5 1.0
OB2 B:FLC303 3.1 32.5 1.0
CG B:HIS79 3.1 24.1 1.0
CE1 B:HIS79 3.1 25.1 1.0
CE1 B:HIS77 3.2 20.9 1.0
CE1 B:HIS139 3.3 26.2 1.0
CB B:HIS79 3.4 23.8 1.0
ZN B:ZN301 3.7 31.9 1.0
OD1 B:ASP81 3.8 28.0 1.0
SG B:CYS158 3.9 29.3 1.0
CB B:CYS158 3.9 26.0 1.0
OA1 B:FLC303 4.2 37.2 1.0
CG B:HIS139 4.2 26.7 1.0
NE2 B:HIS79 4.2 24.2 1.0
CG B:HIS77 4.2 19.4 1.0
CD2 B:HIS79 4.3 23.9 1.0
ND1 B:HIS139 4.3 27.0 1.0
ND1 B:HIS77 4.3 20.5 1.0
CB B:FLC303 4.4 36.2 1.0
OD2 B:ASP81 4.4 29.1 1.0
CG B:ASP81 4.5 27.9 1.0
CG2 B:THR140 4.6 21.4 1.0
OHB B:FLC303 4.6 35.3 1.0
CAC B:FLC303 4.7 37.7 1.0
CA B:HIS79 4.8 23.8 1.0

Zinc binding site 5 out of 8 in 7dtm

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Zinc binding site 5 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:27.0
occ:1.00
 OB1 C:FLC303 2.0 29.0 1.0
ND1 C:HIS79 2.1 27.3 1.0
NE2 C:HIS77 2.2 20.0 1.0
NE2 C:HIS139 2.2 28.3 1.0
CD2 C:HIS77 2.8 20.9 1.0
CBC C:FLC303 2.9 34.3 1.0
CD2 C:HIS139 3.0 27.0 1.0
CE1 C:HIS79 3.1 26.9 1.0
CG C:HIS79 3.1 26.3 1.0
OB2 C:FLC303 3.1 35.5 1.0
CE1 C:HIS139 3.4 29.7 1.0
CE1 C:HIS77 3.4 22.7 1.0
CB C:HIS79 3.4 25.7 1.0
ZN C:ZN302 3.6 32.2 1.0
SG C:CYS158 3.8 28.4 1.0
OD1 C:ASP81 3.9 28.4 1.0
CB C:CYS158 3.9 24.7 1.0
CG C:HIS77 4.1 21.0 1.0
NE2 C:HIS79 4.2 27.1 1.0
OA1 C:FLC303 4.2 32.4 1.0
CD2 C:HIS79 4.2 26.9 1.0
CG C:HIS139 4.2 27.4 1.0
CB C:FLC303 4.3 35.6 1.0
ND1 C:HIS77 4.3 21.2 1.0
ND1 C:HIS139 4.4 28.0 1.0
CG2 C:THR140 4.4 24.8 1.0
OHB C:FLC303 4.5 38.4 1.0
OD2 C:ASP81 4.5 32.6 1.0
CG C:ASP81 4.6 29.4 1.0
CAC C:FLC303 4.6 35.1 1.0
CA C:HIS79 4.9 25.4 1.0

Zinc binding site 6 out of 8 in 7dtm

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Zinc binding site 6 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:32.2
occ:1.00
 OHB C:FLC303 2.1 38.4 1.0
OD2 C:ASP81 2.1 32.6 1.0
SG C:CYS158 2.3 28.4 1.0
OA1 C:FLC303 2.3 32.4 1.0
NE2 C:HIS197 2.3 34.6 1.0
OB1 C:FLC303 2.4 29.0 1.0
CB C:FLC303 3.1 35.6 1.0
CBC C:FLC303 3.1 34.3 1.0
CD2 C:HIS197 3.1 34.2 1.0
CG C:ASP81 3.2 29.4 1.0
CAC C:FLC303 3.3 35.1 1.0
CE1 C:HIS197 3.4 34.2 1.0
CB C:CYS158 3.5 24.7 1.0
OD1 C:ASP81 3.6 28.4 1.0
ZN C:ZN301 3.6 27.0 1.0
CA C:FLC303 3.6 35.3 1.0
OG1 C:FLC303 4.3 41.9 1.0
OB2 C:FLC303 4.3 35.5 1.0
NE2 C:HIS77 4.3 20.0 1.0
CG C:HIS197 4.3 34.3 1.0
NE2 C:HIS139 4.4 28.3 1.0
CG C:FLC303 4.4 37.2 1.0
CB C:SER196 4.4 28.8 1.0
CB C:ASP81 4.4 27.9 1.0
OA2 C:FLC303 4.4 36.1 1.0
ND1 C:HIS197 4.4 33.9 1.0
CE1 C:HIS77 4.5 22.7 1.0
OG C:SER196 4.7 27.8 1.0
CA C:CYS158 4.7 25.4 1.0
CGC C:FLC303 4.7 39.4 1.0
CD C:LYS33 4.8 21.6 1.0
CE C:LYS33 4.9 20.9 1.0

Zinc binding site 7 out of 8 in 7dtm

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Zinc binding site 7 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:26.3
occ:1.00
 OB2 D:FLC303 2.0 30.3 1.0
ND1 D:HIS79 2.2 25.0 1.0
NE2 D:HIS77 2.2 22.5 1.0
NE2 D:HIS139 2.2 24.9 1.0
CBC D:FLC303 2.9 36.2 1.0
CD2 D:HIS77 2.9 21.9 1.0
CD2 D:HIS139 3.0 24.5 1.0
CG D:HIS79 3.1 25.2 1.0
CE1 D:HIS79 3.1 26.3 1.0
OB1 D:FLC303 3.2 35.2 1.0
CE1 D:HIS139 3.3 25.6 1.0
CE1 D:HIS77 3.3 23.3 1.0
CB D:HIS79 3.4 24.3 1.0
ZN D:ZN302 3.6 31.1 1.0
OD1 D:ASP81 3.8 26.7 1.0
SG D:CYS158 3.9 26.3 1.0
CB D:CYS158 3.9 23.1 1.0
OA2 D:FLC303 4.1 32.7 1.0
CG D:HIS77 4.2 21.0 1.0
NE2 D:HIS79 4.2 26.3 1.0
CD2 D:HIS79 4.2 27.2 1.0
CG D:HIS139 4.2 25.1 1.0
CB D:FLC303 4.3 37.8 1.0
OD2 D:ASP81 4.3 27.6 1.0
ND1 D:HIS77 4.3 21.8 1.0
ND1 D:HIS139 4.3 24.7 1.0
CG D:ASP81 4.4 26.3 1.0
OHB D:FLC303 4.5 38.9 1.0
CG2 D:THR140 4.5 22.4 1.0
CAC D:FLC303 4.6 34.4 1.0
CA D:HIS79 4.8 23.4 1.0

Zinc binding site 8 out of 8 in 7dtm

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Zinc binding site 8 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with Citrate.


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-Lactamase Imp-1 in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:31.1
occ:1.00
 OD2 D:ASP81 2.0 27.6 1.0
OHB D:FLC303 2.2 38.9 1.0
NE2 D:HIS197 2.2 27.1 1.0
OB2 D:FLC303 2.3 30.3 1.0
SG D:CYS158 2.3 26.3 1.0
OA2 D:FLC303 2.4 32.7 1.0
CBC D:FLC303 3.0 36.2 1.0
CB D:FLC303 3.0 37.8 1.0
CD2 D:HIS197 3.0 27.6 1.0
CG D:ASP81 3.1 26.3 1.0
CAC D:FLC303 3.3 34.4 1.0
CE1 D:HIS197 3.3 26.8 1.0
CB D:CYS158 3.5 23.1 1.0
CA D:FLC303 3.5 35.6 1.0
OD1 D:ASP81 3.6 26.7 1.0
ZN D:ZN301 3.6 26.3 1.0
OB1 D:FLC303 4.2 35.2 1.0
CG D:HIS197 4.3 28.1 1.0
OG2 D:FLC303 4.3 46.2 1.0
ND1 D:HIS197 4.3 27.4 1.0
CB D:ASP81 4.4 24.8 1.0
CG D:FLC303 4.4 40.5 1.0
OA1 D:FLC303 4.4 35.7 1.0
CB D:SER196 4.4 26.3 1.0
NE2 D:HIS139 4.5 24.9 1.0
NE2 D:HIS77 4.5 22.5 1.0
CE1 D:HIS77 4.6 23.3 1.0
OG D:SER196 4.7 27.2 1.0
CA D:CYS158 4.7 22.1 1.0
CGC D:FLC303 4.8 42.9 1.0
CE D:LYS33 4.9 24.9 1.0
CD D:LYS33 4.9 25.7 1.0
CE1 D:HIS139 5.0 25.6 1.0

Reference:

Y.Yamaguchi, K.Kato, Y.Ichimaru, W.Jin, M.Sakai, M.Abe, J.I.Wachino, Y.Arakawa, Y.Miyagi, M.Imai, N.Fukuishi, Y.Yamagata, M.Otsuka, M.Fujita, H.Kurosaki. Crystal Structures of Metallo-Beta-Lactamase (Imp-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester. J.Med.Chem. V. 64 10019 2021.
ISSN: ISSN 0022-2623
PubMed: 34242022
DOI: 10.1021/ACS.JMEDCHEM.1C00308
Page generated: Tue Oct 29 19:15:55 2024

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