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Zinc in PDB 7dtn: Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) in Complex with Citrate.

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) in Complex with Citrate.

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) in Complex with Citrate.:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) in Complex with Citrate., PDB code: 7dtn 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) 30.00 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.709, 72.862, 82.188, 84.78, 75.58, 73.69
R / Rfree (%) 16.4 / 19.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) in Complex with Citrate. (pdb code 7dtn). 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 Mutant (D120E) in Complex with Citrate., PDB code: 7dtn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7dtn

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Zinc binding site 1 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.9
occ:1.00
 OE2 A:GLU81 2.0 19.6 1.0
OB1 A:FLC303 2.1 18.7 1.0
ND1 A:HIS79 2.1 14.4 1.0
NE2 A:HIS139 2.1 13.2 1.0
NE2 A:HIS77 2.2 12.7 1.0
OD2 A:OCS158 2.6 26.5 1.0
CE1 A:HIS79 3.0 14.7 1.0
CD2 A:HIS139 3.1 12.6 1.0
CD2 A:HIS77 3.1 12.2 1.0
CBC A:FLC303 3.1 20.6 1.0
CE1 A:HIS139 3.2 12.4 1.0
CG A:HIS79 3.2 13.6 1.0
CD A:GLU81 3.2 16.7 1.0
CE1 A:HIS77 3.2 12.4 1.0
OB2 A:FLC303 3.4 20.0 1.0
CB A:HIS79 3.5 13.5 1.0
SG A:OCS158 3.6 20.2 1.0
ZN A:ZN302 3.7 17.5 1.0
OE1 A:GLU81 3.9 15.3 1.0
CB A:OCS158 3.9 17.9 1.0
NE2 A:HIS79 4.2 14.3 1.0
ND1 A:HIS139 4.2 12.3 1.0
CG A:HIS139 4.2 12.4 1.0
CD2 A:HIS79 4.2 14.5 1.0
CG A:GLU81 4.3 15.0 1.0
CG A:HIS77 4.3 12.1 1.0
OD1 A:OCS158 4.3 23.9 1.0
ND1 A:HIS77 4.3 12.0 1.0
CB A:FLC303 4.4 23.1 1.0
OHB A:FLC303 4.5 20.7 1.0
OA1 A:FLC303 4.5 21.4 1.0
OD3 A:OCS158 4.7 29.7 1.0
CG2 A:THR140 4.8 15.1 1.0
OG1 A:FLC303 4.9 33.2 1.0
CA A:HIS79 5.0 13.3 1.0

Zinc binding site 2 out of 8 in 7dtn

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Zinc binding site 2 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:17.5
occ:1.00
 OD2 A:OCS158 1.7 26.5 1.0
OHB A:FLC303 1.9 20.7 1.0
NE2 A:HIS197 2.1 14.3 1.0
OA1 A:FLC303 2.1 21.4 1.0
OE1 A:GLU81 2.2 15.3 1.0
OB1 A:FLC303 2.3 18.7 1.0
OD3 A:OCS158 2.6 29.7 1.0
SG A:OCS158 2.7 20.2 1.0
CB A:FLC303 2.9 23.1 1.0
CBC A:FLC303 2.9 20.6 1.0
CD A:GLU81 3.0 16.7 1.0
CD2 A:HIS197 3.0 14.9 1.0
CE1 A:HIS197 3.1 14.5 1.0
CAC A:FLC303 3.1 21.7 1.0
OE2 A:GLU81 3.1 19.6 1.0
CA A:FLC303 3.5 21.8 1.0
ZN A:ZN301 3.7 14.9 1.0
OD1 A:OCS158 3.7 23.9 1.0
CB A:OCS158 4.0 17.9 1.0
OB2 A:FLC303 4.1 20.0 1.0
ND1 A:HIS197 4.2 15.1 1.0
CG A:HIS197 4.2 14.8 1.0
OA2 A:FLC303 4.2 22.6 1.0
OG1 A:FLC303 4.2 33.2 1.0
CG A:FLC303 4.2 25.3 1.0
NE2 A:HIS139 4.4 13.2 1.0
CG A:GLU81 4.4 15.0 1.0
CE1 A:HIS139 4.5 12.4 1.0
CGC A:FLC303 4.7 28.8 1.0
CB A:SER196 4.8 12.6 1.0
NZ A:LYS161 4.8 18.7 1.0

Zinc binding site 3 out of 8 in 7dtn

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Zinc binding site 3 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:14.0
occ:1.00
 OE2 B:GLU81 2.0 16.5 1.0
OB2 B:FLC303 2.1 20.1 1.0
ND1 B:HIS79 2.1 12.7 1.0
NE2 B:HIS139 2.2 11.6 1.0
NE2 B:HIS77 2.2 12.3 1.0
OD1 B:OCS158 2.3 27.1 1.0
CE1 B:HIS79 3.0 13.0 1.0
CD2 B:HIS77 3.0 11.5 1.0
CBC B:FLC303 3.1 21.9 1.0
CE1 B:HIS139 3.1 11.1 1.0
CD2 B:HIS139 3.1 11.1 1.0
CG B:HIS79 3.1 12.2 1.0
CD B:GLU81 3.2 14.8 1.0
CE1 B:HIS77 3.2 11.8 1.0
OB1 B:FLC303 3.4 21.1 1.0
CB B:HIS79 3.5 11.8 1.0
SG B:OCS158 3.6 22.1 1.0
ZN B:ZN302 3.7 18.2 1.0
OE1 B:GLU81 3.9 13.8 1.0
CB B:OCS158 4.0 18.6 1.0
NE2 B:HIS79 4.1 12.5 1.0
CG B:GLU81 4.2 13.7 1.0
CG B:HIS77 4.2 11.4 1.0
CD2 B:HIS79 4.2 12.9 1.0
ND1 B:HIS139 4.2 11.4 1.0
CG B:HIS139 4.3 11.4 1.0
ND1 B:HIS77 4.3 11.4 1.0
OHB B:FLC303 4.4 22.1 1.0
OD3 B:OCS158 4.4 29.0 1.0
CB B:FLC303 4.4 24.1 1.0
OD2 B:OCS158 4.4 23.0 1.0
OA2 B:FLC303 4.5 22.1 1.0
O B:HOH428 4.6 29.7 1.0
CG2 B:THR140 4.7 14.1 1.0
OG2 B:FLC303 4.9 35.0 1.0
CA B:HIS79 5.0 11.6 1.0

Zinc binding site 4 out of 8 in 7dtn

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Zinc binding site 4 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:18.2
occ:1.00
 OHB B:FLC303 1.9 22.1 1.0
NE2 B:HIS197 2.1 15.1 1.0
OD3 B:OCS158 2.1 29.0 1.0
OD1 B:OCS158 2.2 27.1 1.0
OA2 B:FLC303 2.2 22.1 1.0
OE1 B:GLU81 2.2 13.8 1.0
OB2 B:FLC303 2.3 20.1 1.0
SG B:OCS158 2.7 22.1 1.0
CB B:FLC303 2.9 24.1 1.0
CD B:GLU81 3.0 14.8 1.0
CBC B:FLC303 3.0 21.9 1.0
OE2 B:GLU81 3.0 16.5 1.0
CD2 B:HIS197 3.0 15.5 1.0
CE1 B:HIS197 3.0 15.0 1.0
CAC B:FLC303 3.2 23.2 1.0
CA B:FLC303 3.5 23.1 1.0
OD2 B:OCS158 3.6 23.0 1.0
ZN B:ZN301 3.7 14.0 1.0
CB B:OCS158 4.0 18.6 1.0
ND1 B:HIS197 4.2 14.9 1.0
CG B:HIS197 4.2 14.7 1.0
OB1 B:FLC303 4.2 21.1 1.0
CG B:FLC303 4.3 27.1 1.0
OG2 B:FLC303 4.3 35.0 1.0
OA1 B:FLC303 4.3 23.6 1.0
CG B:GLU81 4.4 13.7 1.0
NE2 B:HIS139 4.4 11.6 1.0
CE1 B:HIS139 4.5 11.1 1.0
CB B:SER196 4.7 12.8 1.0
CGC B:FLC303 4.7 31.8 1.0
NZ B:LYS161 4.9 22.1 1.0
NE2 B:HIS77 4.9 12.3 1.0

Zinc binding site 5 out of 8 in 7dtn

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Zinc binding site 5 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:13.1
occ:1.00
 OB1 C:FLC303 2.0 15.8 1.0
OE2 C:GLU81 2.0 15.9 1.0
ND1 C:HIS79 2.1 12.4 1.0
NE2 C:HIS139 2.1 10.9 1.0
NE2 C:HIS77 2.2 10.1 1.0
OD1 C:OCS158 2.7 23.4 1.0
CE1 C:HIS79 3.0 12.6 1.0
CBC C:FLC303 3.0 18.6 1.0
CD2 C:HIS77 3.1 10.0 1.0
CE1 C:HIS139 3.1 11.0 1.0
CD2 C:HIS139 3.1 10.8 1.0
CG C:HIS79 3.1 11.9 1.0
CE1 C:HIS77 3.2 10.3 1.0
CD C:GLU81 3.2 14.6 1.0
OB2 C:FLC303 3.4 19.6 1.0
CB C:HIS79 3.5 11.3 1.0
ZN C:ZN302 3.6 16.7 1.0
SG C:OCS158 3.7 18.4 1.0
OE1 C:GLU81 3.9 13.5 1.0
CB C:OCS158 3.9 16.3 1.0
NE2 C:HIS79 4.1 13.4 1.0
ND1 C:HIS139 4.2 10.9 1.0
CD2 C:HIS79 4.2 12.3 1.0
CG C:HIS139 4.3 10.6 1.0
CG C:HIS77 4.3 9.7 1.0
ND1 C:HIS77 4.3 10.0 1.0
CG C:GLU81 4.3 12.7 1.0
OD3 C:OCS158 4.3 22.9 1.0
O C:HOH441 4.3 33.2 1.0
CB C:FLC303 4.4 20.5 1.0
OA1 C:FLC303 4.4 18.4 1.0
OHB C:FLC303 4.4 19.1 1.0
OD2 C:OCS158 4.8 25.2 1.0
CG2 C:THR140 4.8 10.8 1.0
OG1 C:FLC303 4.9 29.7 1.0
CAC C:FLC303 5.0 18.4 1.0
CA C:HIS79 5.0 11.0 1.0

Zinc binding site 6 out of 8 in 7dtn

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Zinc binding site 6 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:16.7
occ:1.00
 OD1 C:OCS158 1.7 23.4 1.0
OHB C:FLC303 2.0 19.1 1.0
OA1 C:FLC303 2.1 18.4 1.0
NE2 C:HIS197 2.1 13.9 1.0
OE1 C:GLU81 2.2 13.5 1.0
OB1 C:FLC303 2.3 15.8 1.0
OD2 C:OCS158 2.8 25.2 1.0
SG C:OCS158 2.8 18.4 1.0
CB C:FLC303 2.9 20.5 1.0
CD C:GLU81 2.9 14.6 1.0
CBC C:FLC303 2.9 18.6 1.0
OE2 C:GLU81 3.0 15.9 1.0
CE1 C:HIS197 3.1 14.2 1.0
CAC C:FLC303 3.1 18.4 1.0
CD2 C:HIS197 3.2 14.4 1.0
CA C:FLC303 3.5 18.9 1.0
ZN C:ZN301 3.6 13.1 1.0
OD3 C:OCS158 3.8 22.9 1.0
CB C:OCS158 4.1 16.3 1.0
OB2 C:FLC303 4.1 19.6 1.0
OG1 C:FLC303 4.2 29.7 1.0
OA2 C:FLC303 4.2 17.4 1.0
ND1 C:HIS197 4.2 14.3 1.0
CG C:HIS197 4.3 14.1 1.0
CG C:FLC303 4.3 22.9 1.0
CG C:GLU81 4.4 12.7 1.0
NE2 C:HIS139 4.4 10.9 1.0
CE1 C:HIS139 4.5 11.0 1.0
CGC C:FLC303 4.7 26.1 1.0
CB C:SER196 4.8 13.2 1.0
NZ C:LYS161 4.8 19.6 1.0

Zinc binding site 7 out of 8 in 7dtn

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Zinc binding site 7 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:15.2
occ:1.00
 OE2 D:GLU81 2.1 16.6 1.0
OB2 D:FLC303 2.1 21.1 1.0
ND1 D:HIS79 2.1 14.2 1.0
NE2 D:HIS139 2.1 12.6 1.0
NE2 D:HIS77 2.2 12.4 1.0
OD1 D:OCS158 2.2 27.8 1.0
CE1 D:HIS79 3.0 14.6 1.0
CD2 D:HIS139 3.1 12.4 1.0
CE1 D:HIS139 3.1 12.3 1.0
CG D:HIS79 3.1 13.6 1.0
CBC D:FLC303 3.1 23.7 1.0
CD2 D:HIS77 3.1 11.8 1.0
CD D:GLU81 3.2 16.2 1.0
CE1 D:HIS77 3.2 12.2 1.0
OB1 D:FLC303 3.5 24.0 1.0
CB D:HIS79 3.5 12.9 1.0
SG D:OCS158 3.6 18.9 1.0
ZN D:ZN302 3.6 19.1 1.0
OE1 D:GLU81 3.9 15.5 1.0
CB D:OCS158 4.0 17.1 1.0
OD2 D:OCS158 4.0 24.2 1.0
NE2 D:HIS79 4.1 15.2 1.0
ND1 D:HIS139 4.2 12.7 1.0
CD2 D:HIS79 4.2 14.2 1.0
CG D:HIS139 4.2 12.4 1.0
CG D:GLU81 4.3 14.7 1.0
CG D:HIS77 4.3 11.5 1.0
ND1 D:HIS77 4.3 11.7 1.0
CB D:FLC303 4.4 25.3 1.0
OHB D:FLC303 4.5 23.3 1.0
OD3 D:OCS158 4.5 22.4 1.0
OA2 D:FLC303 4.5 22.0 1.0
CG2 D:THR140 4.7 12.3 1.0
OG2 D:FLC303 4.8 34.5 1.0
CA D:HIS79 5.0 12.6 1.0

Zinc binding site 8 out of 8 in 7dtn

Go back to Zinc Binding Sites List in 7dtn
Zinc binding site 8 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 Mutant (D120E) 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 Mutant (D120E) in Complex with Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:19.1
occ:1.00
 OD2 D:OCS158 1.8 24.2 1.0
OHB D:FLC303 2.0 23.3 1.0
NE2 D:HIS197 2.1 17.9 1.0
OA2 D:FLC303 2.2 22.0 1.0
OE1 D:GLU81 2.3 15.5 1.0
OB2 D:FLC303 2.3 21.1 1.0
OD1 D:OCS158 2.5 27.8 1.0
SG D:OCS158 2.7 18.9 1.0
CB D:FLC303 2.9 25.3 1.0
CBC D:FLC303 3.0 23.7 1.0
CD D:GLU81 3.0 16.2 1.0
CE1 D:HIS197 3.0 17.7 1.0
CD2 D:HIS197 3.1 18.2 1.0
OE2 D:GLU81 3.1 16.6 1.0
CAC D:FLC303 3.2 24.1 1.0
CA D:FLC303 3.5 23.8 1.0
ZN D:ZN301 3.6 15.2 1.0
OD3 D:OCS158 3.8 22.4 1.0
CB D:OCS158 4.0 17.1 1.0
ND1 D:HIS197 4.2 16.7 1.0
OB1 D:FLC303 4.2 24.0 1.0
CG D:HIS197 4.2 17.5 1.0
OG2 D:FLC303 4.2 34.5 1.0
OA1 D:FLC303 4.3 24.3 1.0
CG D:FLC303 4.3 28.5 1.0
NE2 D:HIS139 4.3 12.6 1.0
CG D:GLU81 4.4 14.7 1.0
CE1 D:HIS139 4.4 12.3 1.0
CGC D:FLC303 4.7 32.1 1.0
CB D:SER196 4.7 13.6 1.0
NZ D:LYS161 4.9 22.5 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 19:15:57 2024

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