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Zinc in PDB 5ni0: Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding

Protein crystallography data

The structure of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5ni0 was solved by S.Skagseth, S.Akhter, M.H.Paulsen, O.Samuelsen, Z.Muhammad, H.-K.S.Leiros, A.Bayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.77 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.716, 91.070, 122.912, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding (pdb code 5ni0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5ni0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ni0

Go back to Zinc Binding Sites List in 5ni0
Zinc binding site 1 out of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:22.4
occ:1.00
O A:HOH527 1.8 30.1 1.0
ND1 A:HIS118 2.0 19.2 1.0
NE2 A:HIS196 2.1 21.5 1.0
NE2 A:HIS116 2.1 17.0 1.0
HB2 A:HIS118 2.8 22.8 1.0
HAE A:8XW403 2.9 65.2 1.0
CE1 A:HIS118 3.0 19.8 1.0
CG A:HIS118 3.0 19.8 1.0
CD2 A:HIS196 3.0 18.5 1.0
CE1 A:HIS116 3.0 20.0 1.0
CD2 A:HIS116 3.1 20.3 1.0
CE1 A:HIS196 3.1 25.3 1.0
HD2 A:HIS196 3.2 22.2 1.0
HE1 A:HIS118 3.2 23.7 1.0
HE1 A:HIS116 3.2 24.0 1.0
SAD A:8XW403 3.3 52.0 1.0
HAA A:8XW403 3.3 55.9 1.0
HD2 A:HIS116 3.3 24.4 1.0
HE1 A:HIS196 3.3 30.4 1.0
CB A:HIS118 3.3 19.0 1.0
CAE A:8XW403 3.5 54.4 1.0
HB3 A:HIS118 3.6 22.8 1.0
O A:HOH513 3.9 45.3 1.0
HAF A:8XW403 3.9 65.2 1.0
NE2 A:HIS118 4.1 25.9 1.0
CD2 A:HIS118 4.1 26.9 1.0
OD1 A:ASP120 4.1 22.6 1.0
ND1 A:HIS116 4.1 16.6 1.0
ND1 A:HIS196 4.2 20.8 1.0
CG A:HIS196 4.2 18.3 1.0
CG A:HIS116 4.2 18.0 1.0
CAA A:8XW403 4.2 46.6 1.0
HB2 A:CYS221 4.2 27.1 1.0
CAB A:8XW403 4.2 53.5 0.8
HB3 A:CYS221 4.4 27.1 1.0
H A:HIS118 4.4 21.6 1.0
ZN A:ZN402 4.6 29.9 0.7
HB3 A:SER197 4.6 18.9 1.0
CB A:CYS221 4.6 22.6 1.0
SG A:CYS221 4.6 23.6 1.0
CA A:HIS118 4.7 21.7 1.0
HD22 A:ASN233 4.7 63.4 1.0
OAT A:8XW403 4.8 76.6 1.0
HAB A:8XW403 4.8 55.9 1.0
CAF A:8XW403 4.8 68.2 0.9
O A:HOH541 4.9 27.6 1.0
OD2 A:ASP120 4.9 25.6 1.0
HAC A:8XW403 4.9 55.9 1.0
CG A:ASP120 4.9 30.6 1.0
HD2 A:HIS118 5.0 32.2 1.0
HAG A:8XW403 5.0 81.8 0.9
N A:HIS118 5.0 18.0 1.0

Zinc binding site 2 out of 4 in 5ni0

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Zinc binding site 2 out of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:29.9
occ:0.66
HAA A:8XW403 1.6 55.9 1.0
HAC A:8XW403 1.7 55.9 1.0
CAA A:8XW403 1.9 46.6 1.0
OD2 A:ASP120 2.1 25.6 1.0
SG A:CYS221 2.2 23.6 1.0
NE2 A:HIS263 2.2 43.9 1.0
HAB A:8XW403 2.2 55.9 1.0
HH21 A:ARG121 2.7 32.9 1.0
HAF A:8XW403 2.8 65.2 1.0
O A:HOH527 3.0 30.1 1.0
CE1 A:HIS263 3.0 28.6 1.0
HE1 A:HIS263 3.1 34.2 1.0
CG A:ASP120 3.2 30.6 1.0
CD2 A:HIS263 3.2 30.9 1.0
CAB A:8XW403 3.3 53.5 0.8
HE A:ARG121 3.3 27.7 1.0
HB3 A:CYS221 3.4 27.1 1.0
HD2 A:HIS263 3.5 37.0 1.0
CB A:CYS221 3.5 22.6 1.0
NH2 A:ARG121 3.6 27.4 1.0
HAJ A:8XW403 3.6 64.7 1.0
HE1 A:HIS116 3.7 24.0 1.0
CAE A:8XW403 3.7 54.4 1.0
OD1 A:ASP120 3.7 22.6 1.0
HAE A:8XW403 4.0 65.2 1.0
SAD A:8XW403 4.0 52.0 1.0
NE A:ARG121 4.0 23.1 1.0
HB2 A:CYS221 4.1 27.1 1.0
HH22 A:ARG121 4.1 32.9 1.0
ND1 A:HIS263 4.2 20.4 1.0
OAC A:8XW403 4.2 53.9 1.0
CZ A:ARG121 4.3 29.6 1.0
HA A:CYS221 4.3 16.5 1.0
CG A:HIS263 4.3 26.0 1.0
O A:HOH644 4.3 26.1 1.0
HB2 A:ASP120 4.4 27.4 1.0
CB A:ASP120 4.4 22.8 1.0
HAI A:8XW403 4.4 75.3 0.8
HA3 A:GLY262 4.4 20.8 1.0
CE1 A:HIS116 4.5 20.0 1.0
CA A:CYS221 4.5 13.8 1.0
ZN A:ZN401 4.6 22.4 1.0
HB3 A:ASP120 4.6 27.4 1.0
CAH A:8XW403 4.6 54.0 1.0
HAM A:8XW403 4.8 62.9 1.0
HG2 A:ARG121 4.8 20.1 1.0
CAG A:8XW403 4.9 62.7 0.8
CAF A:8XW403 4.9 68.2 0.9
HG A:SER69 4.9 19.9 1.0
NE2 A:HIS196 4.9 21.5 1.0
NE2 A:HIS116 5.0 17.0 1.0

Zinc binding site 3 out of 4 in 5ni0

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Zinc binding site 3 out of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:25.3
occ:1.00
ND1 E:HIS118 2.0 26.2 1.0
NE2 E:HIS196 2.0 25.3 1.0
NE2 E:HIS116 2.1 20.0 1.0
O E:HOH507 2.7 45.1 1.0
HB2 E:HIS118 2.9 23.6 1.0
SAD E:8XW403 2.9 40.0 0.9
HAF E:8XW403 2.9 60.4 1.0
CD2 E:HIS196 3.0 26.1 1.0
CE1 E:HIS196 3.0 30.3 1.0
CE1 E:HIS116 3.0 19.6 1.0
CE1 E:HIS118 3.0 25.8 1.0
CG E:HIS118 3.0 25.8 1.0
CD2 E:HIS116 3.1 18.8 1.0
HD2 E:HIS196 3.2 31.3 1.0
HE1 E:HIS116 3.2 23.6 1.0
HE1 E:HIS118 3.2 30.9 1.0
HE1 E:HIS196 3.2 36.4 1.0
HD2 E:HIS116 3.3 22.6 1.0
CB E:HIS118 3.3 19.7 1.0
CAE E:8XW403 3.4 50.3 1.0
HB3 E:HIS118 3.6 23.6 1.0
HAE E:8XW403 4.0 60.4 1.0
CAB E:8XW403 4.1 49.0 0.7
OD1 E:ASP120 4.1 19.7 1.0
ND1 E:HIS196 4.1 21.2 1.0
ND1 E:HIS116 4.1 15.8 1.0
NE2 E:HIS118 4.1 27.1 1.0
CG E:HIS196 4.1 25.8 1.0
CD2 E:HIS118 4.2 27.8 1.0
HB2 E:CYS221 4.2 31.0 1.0
CG E:HIS116 4.2 15.8 1.0
HD22 E:ASN233 4.3 62.4 1.0
HAA E:8XW403 4.3 53.9 1.0
ZN E:ZN402 4.4 27.2 0.5
HB3 E:CYS221 4.4 31.0 1.0
H E:HIS118 4.4 25.1 1.0
OAT E:8XW403 4.5 74.8 1.0
OAR E:8XW403 4.5 79.6 0.8
CB E:CYS221 4.6 25.9 1.0
SG E:CYS221 4.6 27.6 1.0
HB3 E:SER197 4.6 28.3 1.0
CAF E:8XW403 4.6 58.2 0.6
OAC E:8XW403 4.7 36.9 1.0
CA E:HIS118 4.7 19.2 1.0
PAQ E:8XW403 4.8 74.1 1.0
CAA E:8XW403 4.8 44.9 1.0
OD2 E:ASP120 4.8 26.6 1.0
CG E:ASP120 4.9 24.0 1.0
HB3 E:ASN233 4.9 56.5 1.0
HAI E:8XW403 5.0 66.9 1.0
ND2 E:ASN233 5.0 52.0 1.0
N E:HIS118 5.0 20.9 1.0

Zinc binding site 4 out of 4 in 5ni0

Go back to Zinc Binding Sites List in 5ni0
Zinc binding site 4 out of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:27.2
occ:0.51
O E:HOH507 1.8 45.1 1.0
OD2 E:ASP120 2.1 26.6 1.0
SG E:CYS221 2.1 27.6 1.0
NE2 E:HIS263 2.2 30.5 1.0
OAC E:8XW403 2.2 36.9 1.0
HH21 E:ARG121 2.5 39.2 1.0
SAD E:8XW403 2.8 40.0 0.9
CAB E:8XW403 2.8 49.0 0.7
CE1 E:HIS263 3.0 25.1 1.0
HE1 E:HIS263 3.0 30.1 1.0
HE E:ARG121 3.2 26.0 1.0
CG E:ASP120 3.2 24.0 1.0
NH2 E:ARG121 3.3 32.7 1.0
CD2 E:HIS263 3.4 27.0 1.0
HB3 E:CYS221 3.5 31.0 1.0
CB E:CYS221 3.5 25.9 1.0
HE1 E:HIS116 3.5 23.6 1.0
HD2 E:HIS263 3.6 32.4 1.0
HAK E:8XW403 3.7 68.3 0.7
OD1 E:ASP120 3.7 19.7 1.0
HAI E:8XW403 3.7 66.9 1.0
NE E:ARG121 3.9 21.7 1.0
HH22 E:ARG121 3.9 39.2 1.0
HB2 E:CYS221 4.0 31.0 1.0
CZ E:ARG121 4.1 26.9 1.0
ND1 E:HIS263 4.2 25.6 1.0
CAA E:8XW403 4.3 44.9 1.0
ZN E:ZN401 4.4 25.3 1.0
CE1 E:HIS116 4.4 19.6 1.0
HB2 E:ASP120 4.4 21.1 1.0
O E:HOH527 4.4 30.6 1.0
HA E:CYS221 4.4 21.4 1.0
CB E:ASP120 4.4 17.6 1.0
CG E:HIS263 4.4 21.6 1.0
CAE E:8XW403 4.5 50.3 1.0
CAH E:8XW403 4.5 56.9 0.7
CAG E:8XW403 4.5 55.8 1.0
CA E:CYS221 4.6 17.8 1.0
HA3 E:GLY262 4.6 26.0 1.0
HB3 E:ASP120 4.6 21.1 1.0
HAJ E:8XW403 4.8 68.3 0.7
HAC E:8XW403 4.8 53.9 1.0
NE2 E:HIS116 4.8 20.0 1.0
HAB E:8XW403 4.8 53.9 1.0
HG2 E:ARG121 4.9 20.8 1.0
HAA E:8XW403 4.9 53.9 1.0
HG E:SER69 4.9 23.4 1.0
NE2 E:HIS196 5.0 25.3 1.0
HE1 E:HIS196 5.0 36.4 1.0

Reference:

S.Skagseth, S.Akhter, M.H.Paulsen, Z.Muhammad, S.Lauksund, H.S.Leiros, A.Bayer. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding. Eur J Med Chem V. 135 159 2017.
ISSN: ISSN 1768-3254
PubMed: 28445786
DOI: 10.1016/J.EJMECH.2017.04.035
Page generated: Wed Dec 16 06:35:28 2020

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