Atomistry » Zinc » PDB 7doy-7dws » 7dtm
Atomistry »
  Zinc »
    PDB 7doy-7dws »
      7dtm »

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

Go back to Zinc Binding Sites List in 7dtm
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

Go back to Zinc Binding Sites List in 7dtm
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

Go back to Zinc Binding Sites List in 7dtm
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

Go back to Zinc Binding Sites List in 7dtm
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

Go back to Zinc Binding Sites List in 7dtm
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

Go back to Zinc Binding Sites List in 7dtm
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

Go back to Zinc Binding Sites List in 7dtm
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

Last articles

Mg in 5M1T
Mg in 5M2T
Mg in 5M3F
Mg in 5LZQ
Mg in 5M2A
Mg in 5M1R
Mg in 5M1M
Mg in 5M0I
Mg in 5M1K
Mg in 5M16
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy