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Zinc in PDB 7yha: Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid

Enzymatic activity of Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid

All present enzymatic activity of Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid, PDB code: 7yha was solved by G.-B.Li, Y.-H.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.80 / 2.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.915, 104.938, 103.686, 90, 94.61, 90
R / Rfree (%) 26 / 30.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid (pdb code 7yha). 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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid, PDB code: 7yha:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7yha

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Zinc binding site 1 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:25.9
occ:1.00
 OD2 A:ASP99 2.0 23.6 1.0
O03 A:ITK304 2.1 20.2 1.0
NE2 A:HIS215 2.1 22.2 1.0
O01 A:ITK303 2.3 28.9 1.0
O A:HOH451 2.4 17.4 1.0
SG A:CYS176 2.5 19.2 1.0
CE1 A:HIS215 2.9 21.4 1.0
CG A:ASP99 3.1 21.5 1.0
P02 A:ITK304 3.3 20.8 1.0
CD2 A:HIS215 3.3 19.9 1.0
P02 A:ITK303 3.5 31.3 1.0
OD1 A:ASP99 3.6 24.2 1.0
CB A:CYS176 3.6 21.7 1.0
ZN A:ZN302 3.6 23.6 1.0
O04 A:ITK304 3.7 21.7 1.0
O04 A:ITK303 3.8 25.0 1.0
C05 A:ITK304 3.8 24.8 1.0
O03 A:ITK303 3.9 31.3 1.0
ND1 A:HIS215 4.1 17.8 1.0
CB A:ASP99 4.3 21.8 1.0
CG A:HIS215 4.3 24.2 1.0
NE2 A:HIS157 4.4 18.5 1.0
O01 A:ITK304 4.5 21.6 1.0
CB A:SER214 4.7 21.4 1.0
NE2 A:HIS95 4.7 24.6 1.0
CE1 A:HIS157 4.8 18.3 1.0
CA A:CYS176 4.8 21.9 1.0
OG A:SER214 4.9 22.5 1.0
CE1 A:HIS95 4.9 18.5 1.0

Zinc binding site 2 out of 8 in 7yha

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Zinc binding site 2 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:23.6
occ:1.00
 O A:HOH451 1.6 17.4 1.0
ND1 A:HIS97 2.0 18.1 1.0
NE2 A:HIS157 2.1 18.5 1.0
NE2 A:HIS95 2.1 24.6 1.0
CG A:HIS97 3.0 22.1 1.0
CD2 A:HIS95 3.0 18.4 1.0
CE1 A:HIS97 3.1 17.6 1.0
CD2 A:HIS157 3.1 18.8 1.0
CE1 A:HIS157 3.1 18.3 1.0
CE1 A:HIS95 3.2 18.5 1.0
CB A:HIS97 3.3 20.0 1.0
ZN A:ZN301 3.6 25.9 1.0
SG A:CYS176 3.6 19.2 1.0
CB A:CYS176 3.8 21.7 1.0
O03 A:ITK304 3.8 20.2 1.0
OD1 A:ASP99 3.8 24.2 1.0
O04 A:ITK304 4.1 21.7 1.0
CD2 A:HIS97 4.1 21.4 1.0
NE2 A:HIS97 4.1 20.4 1.0
ND1 A:HIS157 4.2 20.2 1.0
CG A:HIS157 4.2 23.3 1.0
CG A:HIS95 4.2 20.8 1.0
ND1 A:HIS95 4.3 17.2 1.0
OD2 A:ASP99 4.3 23.6 1.0
CG2 A:THR158 4.4 19.7 1.0
O04 A:ITK303 4.5 25.0 1.0
CG A:ASP99 4.5 21.5 1.0
P02 A:ITK304 4.5 20.8 1.0
O03 A:ITK303 4.6 31.3 1.0
CA A:HIS97 4.7 22.2 1.0
O01 A:ITK303 4.9 28.9 1.0
P02 A:ITK303 4.9 31.3 1.0

Zinc binding site 3 out of 8 in 7yha

Go back to Zinc Binding Sites List in 7yha
Zinc binding site 3 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:23.2
occ:1.00
 NE2 B:HIS157 2.0 23.6 1.0
O B:HOH437 2.0 19.7 1.0
ND1 B:HIS97 2.0 21.2 1.0
NE2 B:HIS95 2.1 19.7 1.0
CE1 B:HIS157 2.8 19.9 1.0
CG B:HIS97 3.0 18.8 1.0
CE1 B:HIS97 3.0 20.9 1.0
CD2 B:HIS95 3.0 16.8 1.0
CD2 B:HIS157 3.1 22.1 1.0
CE1 B:HIS95 3.1 18.5 1.0
CB B:HIS97 3.3 22.9 1.0
ZN B:ZN302 3.4 25.1 1.0
SG B:CYS176 3.5 21.2 1.0
O03 B:ITK303 3.7 21.9 1.0
CB B:CYS176 3.7 19.2 1.0
OD1 B:ASP99 3.8 21.1 1.0
ND1 B:HIS157 4.0 22.0 1.0
NE2 B:HIS97 4.1 21.0 1.0
CD2 B:HIS97 4.1 23.4 1.0
O04 B:ITK303 4.1 25.7 1.0
CG B:HIS157 4.1 21.0 1.0
CG B:HIS95 4.2 18.1 1.0
ND1 B:HIS95 4.2 18.2 1.0
OD2 B:ASP99 4.3 25.1 1.0
CG2 B:THR158 4.3 20.7 1.0
O04 B:ITK304 4.4 24.1 1.0
CG B:ASP99 4.5 21.2 1.0
P02 B:ITK303 4.5 23.9 1.0
CA B:HIS97 4.7 21.8 1.0
O03 B:ITK304 4.8 31.7 1.0
O01 B:ITK304 4.8 21.0 1.0
P02 B:ITK304 4.9 26.5 1.0

Zinc binding site 4 out of 8 in 7yha

Go back to Zinc Binding Sites List in 7yha
Zinc binding site 4 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:25.1
occ:1.00
 O03 B:ITK303 2.0 21.9 1.0
OD2 B:ASP99 2.1 25.1 1.0
O B:HOH437 2.1 19.7 1.0
NE2 B:HIS215 2.1 22.4 1.0
O01 B:ITK304 2.3 21.0 1.0
SG B:CYS176 2.4 21.2 1.0
CE1 B:HIS215 3.0 18.5 1.0
CG B:ASP99 3.1 21.2 1.0
CD2 B:HIS215 3.2 20.5 1.0
P02 B:ITK303 3.2 23.9 1.0
ZN B:ZN301 3.4 23.2 1.0
P02 B:ITK304 3.5 26.5 1.0
CB B:CYS176 3.5 19.2 1.0
OD1 B:ASP99 3.6 21.1 1.0
O04 B:ITK303 3.7 25.7 1.0
C05 B:ITK303 3.7 25.2 1.0
O04 B:ITK304 3.8 24.1 1.0
O03 B:ITK304 3.9 31.7 1.0
ND1 B:HIS215 4.2 19.4 1.0
CG B:HIS215 4.3 21.6 1.0
NE2 B:HIS157 4.4 23.6 1.0
CB B:ASP99 4.4 22.3 1.0
O01 B:ITK303 4.5 20.7 1.0
NE2 B:HIS95 4.6 19.7 1.0
CE1 B:HIS157 4.6 19.9 1.0
CA B:CYS176 4.7 22.4 1.0
CE1 B:HIS95 4.7 18.5 1.0
CB B:SER214 4.8 21.4 1.0
ND1 B:HIS97 4.9 21.2 1.0

Zinc binding site 5 out of 8 in 7yha

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Zinc binding site 5 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:25.0
occ:1.00
 ND1 C:HIS97 2.0 25.2 1.0
NE2 C:HIS95 2.1 27.4 1.0
O C:HOH421 2.1 24.6 1.0
NE2 C:HIS157 2.2 24.1 1.0
CD2 C:HIS157 3.0 23.9 1.0
CG C:HIS97 3.0 25.7 1.0
CE1 C:HIS97 3.0 22.1 1.0
CD2 C:HIS95 3.1 21.0 1.0
CE1 C:HIS95 3.1 21.7 1.0
CE1 C:HIS157 3.3 19.9 1.0
CB C:HIS97 3.3 24.4 1.0
SG C:CYS176 3.5 18.2 1.0
ZN C:ZN302 3.6 25.3 1.0
CB C:CYS176 3.7 25.7 1.0
O04 C:ITK304 3.7 22.4 1.0
OD1 C:ASP99 3.8 21.6 1.0
NE2 C:HIS97 4.1 25.6 1.0
O01 C:ITK304 4.1 25.6 1.0
CD2 C:HIS97 4.1 22.7 1.0
CG C:HIS157 4.2 24.3 1.0
CG C:HIS95 4.2 24.3 1.0
ND1 C:HIS95 4.2 22.4 1.0
O03 C:ITK303 4.3 29.7 1.0
ND1 C:HIS157 4.3 21.6 1.0
OD2 C:ASP99 4.4 25.3 1.0
CG2 C:THR158 4.4 20.8 1.0
P02 C:ITK304 4.5 23.5 1.0
CG C:ASP99 4.5 21.9 1.0
CA C:HIS97 4.7 24.3 1.0
O04 C:ITK303 4.9 29.1 1.0

Zinc binding site 6 out of 8 in 7yha

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Zinc binding site 6 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:25.3
occ:1.00
 NE2 C:HIS215 2.1 22.2 1.0
OD2 C:ASP99 2.1 25.3 1.0
O04 C:ITK304 2.1 22.4 1.0
O C:HOH421 2.2 24.6 1.0
O04 C:ITK303 2.3 29.1 1.0
SG C:CYS176 2.5 18.2 1.0
CE1 C:HIS215 2.7 25.9 1.0
CG C:ASP99 3.1 21.9 1.0
P02 C:ITK304 3.2 23.5 1.0
CD2 C:HIS215 3.3 22.2 1.0
P02 C:ITK303 3.5 33.6 1.0
OD1 C:ASP99 3.5 21.6 1.0
ZN C:ZN301 3.6 25.0 1.0
CB C:CYS176 3.6 25.7 1.0
O03 C:ITK303 3.7 29.7 1.0
O01 C:ITK304 3.7 25.6 1.0
C05 C:ITK304 3.7 24.6 1.0
ND1 C:HIS215 4.0 21.5 1.0
O01 C:ITK303 4.1 29.9 1.0
CG C:HIS215 4.2 23.2 1.0
CB C:ASP99 4.3 21.2 1.0
NE2 C:HIS157 4.4 24.1 1.0
O03 C:ITK304 4.5 25.3 1.0
CB C:SER214 4.7 22.1 1.0
NE2 C:HIS95 4.8 27.4 1.0
CA C:CYS176 4.8 25.7 1.0
CD C:LYS51 4.9 22.0 1.0
CE1 C:HIS157 4.9 19.9 1.0
CE1 C:HIS95 5.0 21.7 1.0

Zinc binding site 7 out of 8 in 7yha

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Zinc binding site 7 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:23.3
occ:1.00
 O D:HOH420 1.9 20.5 1.0
NE2 D:HIS157 2.0 21.7 1.0
ND1 D:HIS97 2.0 19.5 1.0
NE2 D:HIS95 2.2 19.0 1.0
CG D:HIS97 3.0 19.5 1.0
CD2 D:HIS157 3.0 20.9 1.0
CE1 D:HIS97 3.0 20.6 1.0
CE1 D:HIS157 3.0 22.5 1.0
CD2 D:HIS95 3.1 19.6 1.0
CE1 D:HIS95 3.2 17.9 1.0
CB D:HIS97 3.3 18.1 1.0
ZN D:ZN302 3.5 27.9 1.0
SG D:CYS176 3.6 21.5 1.0
O03 D:ITK303 3.7 24.3 1.0
CB D:CYS176 3.7 22.0 1.0
OD1 D:ASP99 3.8 22.8 1.0
O04 D:ITK303 4.0 19.4 1.0
NE2 D:HIS97 4.1 20.1 1.0
CD2 D:HIS97 4.1 18.9 1.0
ND1 D:HIS157 4.1 22.6 1.0
CG D:HIS157 4.1 20.4 1.0
CG D:HIS95 4.3 17.4 1.0
ND1 D:HIS95 4.3 17.9 1.0
OD2 D:ASP99 4.5 23.4 1.0
P02 D:ITK303 4.5 21.4 1.0
CG2 D:THR158 4.5 19.4 1.0
O03 D:ITK304 4.5 28.8 1.0
O04 D:ITK304 4.6 23.8 1.0
CG D:ASP99 4.6 20.4 1.0
O01 D:ITK304 4.6 23.3 1.0
CA D:HIS97 4.7 19.3 1.0
P02 D:ITK304 4.8 28.2 1.0

Zinc binding site 8 out of 8 in 7yha

Go back to Zinc Binding Sites List in 7yha
Zinc binding site 8 out of 8 in the Crystal Structure of Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid


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 Imp-1 Mbl in Complex with (3-(4-(P-Tolyl)-1H-1,2, 3-Triazol-1-Yl)Benzyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:27.9
occ:1.00
 NE2 D:HIS215 2.1 20.2 1.0
OD2 D:ASP99 2.1 23.4 1.0
O D:HOH420 2.1 20.5 1.0
O03 D:ITK303 2.2 24.3 1.0
O01 D:ITK304 2.2 23.3 1.0
SG D:CYS176 2.5 21.5 1.0
CD2 D:HIS215 3.0 23.2 1.0
CE1 D:HIS215 3.1 16.2 1.0
CG D:ASP99 3.1 20.4 1.0
P02 D:ITK303 3.2 21.4 1.0
P02 D:ITK304 3.4 28.2 1.0
OD1 D:ASP99 3.4 22.8 1.0
ZN D:ZN301 3.5 23.3 1.0
CB D:CYS176 3.5 22.0 1.0
C05 D:ITK303 3.6 22.7 1.0
O04 D:ITK303 3.7 19.4 1.0
O03 D:ITK304 3.7 28.8 1.0
O04 D:ITK304 3.9 23.8 1.0
ND1 D:HIS215 4.2 20.5 1.0
CG D:HIS215 4.2 23.8 1.0
NE2 D:HIS157 4.4 21.7 1.0
CB D:ASP99 4.4 18.8 1.0
O01 D:ITK303 4.5 23.2 1.0
CB D:SER214 4.7 20.2 1.0
NE2 D:HIS95 4.7 19.0 1.0
CE1 D:HIS157 4.7 22.5 1.0
CA D:CYS176 4.8 19.8 1.0
CE1 D:HIS95 4.9 17.9 1.0
C05 D:ITK304 4.9 26.7 1.0
CD D:LYS51 5.0 19.8 1.0
ND1 D:HIS97 5.0 19.5 1.0
C06 D:ITK303 5.0 24.4 1.0

Reference:

Y.H.Yan, H.S.Ding, K.R.Zhu, B.S.Mu, Y.Zheng, M.Y.Huang, C.Zhou, W.F.Li, Z.Wang, Y.Wu, G.B.Li. Metal Binding Pharmacophore Click-Derived Discovery of New Broad-Spectrum Metallo-Beta-Lactamase Inhibitors. Eur.J.Med.Chem. V. 257 15473 2023.
ISSN: ISSN 0223-5234
PubMed: 37209449
DOI: 10.1016/J.EJMECH.2023.115473
Page generated: Wed Oct 30 15:50:12 2024

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