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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

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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

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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

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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

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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

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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

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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

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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

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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

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