Atomistry » Zinc » PDB 5h6b-5ho1 » 5hh4
Atomistry »
  Zinc »
    PDB 5h6b-5ho1 »
      5hh4 »

Zinc in PDB 5hh4: Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor, PDB code: 5hh4 was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.16 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.943, 78.309, 260.545, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.6

Other elements in 5hh4:

The structure of Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor (pdb code 5hh4). 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 A Phosphonate-Based Inhibitor, PDB code: 5hh4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 1 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:24.2
occ:1.00
 ND1 A:HIS79 1.9 15.3 1.0
NE2 A:HIS139 2.0 20.9 1.0
O A:HOH422 2.1 27.2 1.0
NE2 A:HIS77 2.2 17.1 1.0
CE1 A:HIS79 2.9 22.6 1.0
CG A:HIS79 2.9 18.4 1.0
CD2 A:HIS139 3.0 22.1 1.0
CE1 A:HIS139 3.0 24.9 1.0
CD2 A:HIS77 3.1 19.8 1.0
O A:HOH433 3.2 34.3 1.0
CB A:HIS79 3.3 19.1 1.0
CE1 A:HIS77 3.3 22.8 1.0
ZN A:ZN302 3.5 31.4 1.0
OD1 A:ASP81 3.8 27.3 1.0
O01 A:60M303 3.8 33.8 1.0
SG A:CYS158 3.8 22.5 1.0
O09 A:60M303 3.9 60.1 1.0
CB A:CYS158 3.9 25.5 1.0
NE2 A:HIS79 4.0 22.2 1.0
CD2 A:HIS79 4.1 20.7 1.0
ND1 A:HIS139 4.1 21.5 1.0
CG A:HIS139 4.1 22.7 1.0
CG A:HIS77 4.3 21.0 1.0
ND1 A:HIS77 4.4 16.8 1.0
CG2 A:THR140 4.5 18.2 1.0
N05 A:60M303 4.5 44.0 1.0
C02 A:60M303 4.6 39.9 1.0
OD2 A:ASP81 4.6 28.2 1.0
CG A:ASP81 4.6 30.6 1.0
CA A:HIS79 4.8 19.4 1.0

Zinc binding site 2 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 2 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:31.4
occ:1.00
 OD2 A:ASP81 2.2 28.2 1.0
NE2 A:HIS197 2.2 24.2 1.0
O A:HOH422 2.2 27.2 1.0
O01 A:60M303 2.3 33.8 1.0
SG A:CYS158 2.4 22.5 1.0
N05 A:60M303 2.7 44.0 1.0
CD2 A:HIS197 3.1 23.9 1.0
CG A:ASP81 3.2 30.6 1.0
CE1 A:HIS197 3.2 21.6 1.0
C02 A:60M303 3.2 39.9 1.0
C04 A:60M303 3.4 44.6 1.0
OD1 A:ASP81 3.5 27.3 1.0
CB A:CYS158 3.5 25.5 1.0
ZN A:ZN301 3.5 24.2 1.0
C06 A:60M303 3.7 39.3 1.0
C07 A:60M303 3.9 37.1 1.0
O A:HOH433 4.2 34.3 1.0
ND1 A:HIS197 4.3 22.6 1.0
CG A:HIS197 4.3 26.9 1.0
NE2 A:HIS139 4.3 20.9 1.0
O09 A:60M303 4.3 60.1 1.0
O03 A:60M303 4.4 39.3 1.0
CB A:ASP81 4.5 24.3 1.0
CB A:SER196 4.5 26.3 1.0
NE2 A:HIS77 4.6 17.1 1.0
CE1 A:HIS139 4.6 24.9 1.0
CA A:CYS158 4.6 27.4 1.0
CE1 A:HIS77 4.7 22.8 1.0
C14 A:60M303 4.7 41.0 1.0
OG A:SER196 4.8 26.6 1.0
P08 A:60M303 4.9 58.4 1.0
C12 A:60M303 4.9 40.2 1.0

Zinc binding site 3 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 3 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:37.9
occ:1.00
 O B:HOH479 2.1 29.9 1.0
NE2 B:HIS197 2.1 24.1 1.0
O03 B:60M303 2.2 40.3 1.0
OD2 B:ASP81 2.3 27.9 1.0
SG B:CYS158 2.5 29.1 1.0
N05 B:60M303 2.7 44.5 1.0
CE1 B:HIS197 3.1 23.8 1.0
C02 B:60M303 3.1 47.7 1.0
CD2 B:HIS197 3.2 24.8 1.0
CG B:ASP81 3.3 29.7 1.0
C04 B:60M303 3.4 46.0 1.0
ZN B:ZN302 3.4 25.8 1.0
CB B:CYS158 3.5 20.5 1.0
OD1 B:ASP81 3.6 26.3 1.0
C06 B:60M303 3.7 42.9 1.0
C07 B:60M303 4.0 44.2 1.0
O B:HOH499 4.2 37.5 1.0
NE2 B:HIS139 4.2 26.8 1.0
ND1 B:HIS197 4.2 26.1 1.0
CG B:HIS197 4.3 25.0 1.0
O01 B:60M303 4.3 47.0 1.0
NE2 B:HIS77 4.4 21.5 1.0
O09 B:60M303 4.4 87.9 1.0
CE1 B:HIS139 4.5 28.2 1.0
CB B:SER196 4.5 25.3 1.0
CB B:ASP81 4.6 19.3 1.0
CE1 B:HIS77 4.6 19.6 1.0
CA B:CYS158 4.7 23.8 1.0
C14 B:60M303 4.7 43.6 1.0
OG B:SER196 4.8 31.2 1.0
CD B:LYS33 5.0 20.2 1.0
ND1 B:HIS79 5.0 18.8 1.0

Zinc binding site 4 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 4 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:25.8
occ:1.00
 ND1 B:HIS79 1.9 18.8 1.0
O B:HOH479 2.0 29.9 1.0
NE2 B:HIS139 2.0 26.8 1.0
NE2 B:HIS77 2.2 21.5 1.0
CE1 B:HIS79 2.8 31.6 1.0
CG B:HIS79 2.9 18.6 1.0
CE1 B:HIS139 2.9 28.2 1.0
CD2 B:HIS77 3.0 18.1 1.0
CD2 B:HIS139 3.0 26.2 1.0
O B:HOH499 3.2 37.5 1.0
CE1 B:HIS77 3.3 19.6 1.0
CB B:HIS79 3.3 15.4 1.0
ZN B:ZN301 3.4 37.9 1.0
O03 B:60M303 3.8 40.3 1.0
OD1 B:ASP81 3.9 26.3 1.0
SG B:CYS158 3.9 29.1 1.0
NE2 B:HIS79 3.9 25.2 1.0
O09 B:60M303 3.9 87.9 1.0
CD2 B:HIS79 4.0 18.4 1.0
CB B:CYS158 4.0 20.5 1.0
ND1 B:HIS139 4.0 29.8 1.0
CG B:HIS139 4.1 29.9 1.0
CG B:HIS77 4.2 20.0 1.0
ND1 B:HIS77 4.3 22.9 1.0
OD2 B:ASP81 4.5 27.9 1.0
C02 B:60M303 4.5 47.7 1.0
N05 B:60M303 4.5 44.5 1.0
CG2 B:THR140 4.6 25.6 1.0
CG B:ASP81 4.6 29.7 1.0
CA B:HIS79 4.8 17.0 1.0

Zinc binding site 5 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 5 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:21.1
occ:0.94
 ND1 C:HIS79 2.0 15.2 1.0
NE2 C:HIS139 2.1 21.2 1.0
O C:HOH524 2.2 25.8 1.0
NE2 C:HIS77 2.2 20.6 1.0
CD2 C:HIS77 3.0 13.7 1.0
CE1 C:HIS79 3.0 27.7 1.0
CG C:HIS79 3.0 19.0 1.0
CD2 C:HIS139 3.1 16.5 1.0
CE1 C:HIS139 3.2 14.5 1.0
CE1 C:HIS77 3.3 24.3 1.0
CB C:HIS79 3.4 17.3 1.0
ZN C:ZN302 3.4 27.0 0.9
O C:HOH563 3.8 31.3 1.0
SG C:CYS158 3.9 24.8 1.0
OD1 C:ASP81 3.9 32.2 1.0
CB C:CYS158 3.9 18.4 1.0
O C:HOH465 4.1 22.5 1.0
NE2 C:HIS79 4.1 25.9 1.0
CD2 C:HIS79 4.2 21.1 1.0
CG C:HIS77 4.2 17.2 1.0
CG C:HIS139 4.2 18.9 1.0
ND1 C:HIS139 4.2 16.9 1.0
ND1 C:HIS77 4.3 23.9 1.0
OD2 C:ASP81 4.3 27.5 1.0
CG2 C:THR140 4.5 13.2 1.0
CG C:ASP81 4.6 32.6 1.0
O C:HOH535 4.7 49.0 1.0
CA C:HIS79 4.8 16.2 1.0

Zinc binding site 6 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 6 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:27.0
occ:0.87
 OD2 C:ASP81 2.0 27.5 1.0
O C:HOH524 2.1 25.8 1.0
NE2 C:HIS197 2.2 20.3 1.0
SG C:CYS158 2.3 24.8 1.0
CE1 C:HIS197 3.0 21.3 1.0
CG C:ASP81 3.1 32.6 1.0
O C:HOH465 3.1 22.5 1.0
CD2 C:HIS197 3.3 22.1 1.0
CB C:CYS158 3.4 18.4 1.0
ZN C:ZN301 3.4 21.1 0.9
OD1 C:ASP81 3.5 32.2 1.0
O C:HOH462 3.8 37.8 1.0
O C:HOH563 4.0 31.3 1.0
ND1 C:HIS197 4.2 18.5 1.0
NE2 C:HIS77 4.2 20.6 1.0
CE1 C:HIS77 4.3 24.3 1.0
CG C:HIS197 4.3 19.6 1.0
CB C:SER196 4.3 21.6 1.0
CD C:LYS33 4.4 20.6 1.0
CB C:ASP81 4.4 20.0 1.0
CE C:LYS33 4.4 23.3 1.0
NE2 C:HIS139 4.5 21.2 1.0
OG C:SER196 4.6 23.5 1.0
CA C:CYS158 4.6 19.4 1.0
CE1 C:HIS139 5.0 14.5 1.0

Zinc binding site 7 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 7 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:33.4
occ:0.51
 ND1 D:HIS79 2.1 52.4 1.0
NE2 D:HIS139 2.2 69.5 1.0
O D:HOH456 2.7 45.8 1.0
CE1 D:HIS77 2.7 65.4 1.0
CD2 D:HIS139 3.0 68.3 1.0
CE1 D:HIS79 3.0 50.8 1.0
CG D:HIS79 3.1 52.2 1.0
ND1 D:HIS77 3.1 65.0 1.0
CE1 D:HIS139 3.4 67.2 1.0
ZN D:ZN302 3.4 57.0 1.0
CB D:HIS79 3.4 56.4 1.0
NE2 D:HIS77 3.8 61.2 1.0
O D:HOH448 3.9 46.1 1.0
O D:HOH458 3.9 41.6 1.0
OD1 D:ASP81 4.0 60.8 1.0
SG D:CYS158 4.0 72.7 1.0
CG2 D:THR140 4.1 56.5 1.0
NE2 D:HIS79 4.1 47.5 1.0
CD2 D:HIS79 4.1 46.5 1.0
CB D:CYS158 4.2 44.1 1.0
CG D:HIS139 4.2 65.4 1.0
CG D:HIS77 4.3 52.9 1.0
ND1 D:HIS139 4.4 64.5 1.0
OD2 D:ASP81 4.4 41.7 1.0
CD2 D:HIS77 4.6 56.8 1.0
CG D:ASP81 4.6 49.0 1.0
CA D:HIS79 4.8 52.5 1.0
O D:HOH472 4.9 60.0 1.0

Zinc binding site 8 out of 8 in 5hh4

Go back to Zinc Binding Sites List in 5hh4
Zinc binding site 8 out of 8 in the Crystal Structure of Metallo-Beta-Lactamase Imp-1 in Complex with A Phosphonate-Based 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-Lactamase Imp-1 in Complex with A Phosphonate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:57.0
occ:1.00
 O D:HOH456 2.0 45.8 1.0
OD2 D:ASP81 2.3 41.7 1.0
O D:HOH458 2.4 41.6 1.0
NE2 D:HIS197 2.5 71.8 1.0
SG D:CYS158 2.7 72.7 1.0
CD2 D:HIS197 3.0 67.5 1.0
CG D:ASP81 3.2 49.0 1.0
ZN D:ZN301 3.4 33.4 0.5
CE1 D:HIS197 3.6 70.5 1.0
OD1 D:ASP81 3.6 60.8 1.0
CB D:CYS158 3.7 44.1 1.0
CE1 D:HIS77 4.0 65.4 1.0
NE2 D:HIS139 4.1 69.5 1.0
CG D:HIS197 4.3 65.8 1.0
NE2 D:HIS77 4.3 61.2 1.0
CB D:ASP81 4.4 50.3 1.0
ND1 D:HIS197 4.5 68.0 1.0
CE1 D:HIS139 4.5 67.2 1.0
CD2 D:HIS139 4.9 68.3 1.0
NZ D:LYS161 4.9 67.2 1.0
O D:HOH448 4.9 46.1 1.0
CA D:CYS158 5.0 38.3 1.0

Reference:

P.Hinchliffe, C.A.Tanner, A.P.Krismanich, G.Labbe, V.J.Goodfellow, L.Marrone, A.Y.Desoky, K.Calvopina, E.E.Whittle, F.Zeng, M.B.Avison, N.C.Bols, S.Siemann, J.Spencer, G.I.Dmitrienko. Structural and Kinetic Studies of the Potent Inhibition of Metallo-Beta-Lactamases By 6-Phosphonomethylpyridine-2-Carboxylates. Biochemistry V. 57 1880 2018.
ISSN: ISSN 1520-4995
PubMed: 29485857
DOI: 10.1021/ACS.BIOCHEM.7B01299
Page generated: Sun Oct 27 17:27:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy