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Zinc in PDB 6kw1: The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B

Protein crystallography data

The structure of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B, PDB code: 6kw1 was solved by K.W.Yang, Y.Xiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.19 / 1.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.759, 79.421, 67.981, 90.00, 130.94, 90.00
R / Rfree (%) 17.7 / 20.6

Other elements in 6kw1:

The structure of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms
Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B (pdb code 6kw1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B, PDB code: 6kw1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6kw1

Go back to Zinc Binding Sites List in 6kw1
Zinc binding site 1 out of 4 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:13.5
occ:1.00
ND1 A:HIS118 2.0 12.4 1.0
NE2 A:HIS196 2.1 8.6 1.0
NE2 A:HIS116 2.1 8.1 1.0
N09 A:9RX406 2.1 27.5 1.0
HB2 A:HIS118 2.8 12.7 1.0
CG A:HIS118 3.0 9.4 1.0
CE1 A:HIS118 3.0 13.0 1.0
CD2 A:HIS196 3.0 8.3 1.0
CD2 A:HIS116 3.1 10.2 1.0
C10 A:9RX406 3.1 32.8 1.0
N08 A:9RX406 3.1 25.8 1.0
CE1 A:HIS116 3.1 9.7 1.0
CE1 A:HIS196 3.1 9.1 1.0
HD2 A:HIS196 3.2 10.0 1.0
HD2 A:HIS116 3.2 12.2 1.0
HE1 A:HIS118 3.2 15.6 1.0
CB A:HIS118 3.3 10.6 1.0
HE1 A:HIS116 3.3 11.7 1.0
HE1 A:HIS196 3.3 10.9 1.0
HB3 A:HIS118 3.5 12.7 1.0
S12 A:9RX406 3.7 37.9 1.0
OD1 A:ASP120 3.7 15.9 1.0
ZN A:ZN402 3.9 18.3 1.0
HB2 A:CYS221 4.0 12.8 1.0
NE2 A:HIS118 4.1 14.1 1.0
CD2 A:HIS118 4.1 11.7 1.0
ND1 A:HIS116 4.2 9.7 1.0
C07 A:9RX406 4.2 29.9 1.0
N11 A:9RX406 4.2 34.3 1.0
CG A:HIS116 4.2 9.0 1.0
ND1 A:HIS196 4.2 9.1 1.0
CG A:HIS196 4.2 8.7 1.0
HB3 A:CYS221 4.2 12.8 1.0
SG A:CYS221 4.4 12.4 1.0
CB A:CYS221 4.4 10.6 1.0
OD2 A:ASP120 4.4 15.3 1.0
CG A:ASP120 4.5 17.4 1.0
H A:HIS118 4.5 13.8 1.0
O28 A:9RX406 4.6 21.5 1.0
CA A:HIS118 4.7 15.3 1.0
HG2 A:ARG121 4.7 18.7 1.0
HD22 A:ASN233 4.8 62.3 1.0
H152 A:9RX406 4.9 61.7 1.0
HE2 A:HIS118 4.9 17.0 1.0
HB3 A:SER197 4.9 11.1 1.0
HE A:ARG121 4.9 23.1 1.0
C15 A:9RX406 4.9 51.4 1.0
HD1 A:HIS116 5.0 11.7 1.0
HD2 A:HIS118 5.0 14.0 1.0
HD1 A:HIS196 5.0 10.9 1.0

Zinc binding site 2 out of 4 in 6kw1

Go back to Zinc Binding Sites List in 6kw1
Zinc binding site 2 out of 4 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:18.3
occ:1.00
N08 A:9RX406 2.0 25.8 1.0
NE2 A:HIS263 2.1 13.5 1.0
OD2 A:ASP120 2.2 15.3 1.0
SG A:CYS221 2.2 12.4 1.0
O28 A:9RX406 2.5 21.5 1.0
C07 A:9RX406 2.9 29.9 1.0
N09 A:9RX406 3.0 27.5 1.0
HH21 A:ARG121 3.1 20.4 1.0
CD2 A:HIS263 3.1 13.8 1.0
CE1 A:HIS263 3.1 11.7 1.0
HD2 A:HIS263 3.2 16.5 1.0
HB3 A:CYS221 3.2 12.8 1.0
CG A:ASP120 3.3 17.4 1.0
HE1 A:HIS263 3.4 14.1 1.0
C26 A:9RX406 3.4 26.2 1.0
C04 A:9RX406 3.4 30.1 1.0
CB A:CYS221 3.4 10.6 1.0
HE A:ARG121 3.6 23.1 1.0
C03 A:9RX406 3.6 26.7 1.0
HE1 A:HIS116 3.7 11.7 1.0
OD1 A:ASP120 3.8 15.9 1.0
NH2 A:ARG121 3.8 17.0 1.0
ZN A:ZN401 3.9 13.5 1.0
HB2 A:CYS221 3.9 12.8 1.0
N11 A:9RX406 4.0 34.3 1.0
C10 A:9RX406 4.0 32.8 1.0
HE1 A:HIS196 4.2 10.9 1.0
CG A:HIS263 4.2 11.3 1.0
ND1 A:HIS263 4.2 10.0 1.0
NE A:ARG121 4.3 19.3 1.0
NE2 A:HIS196 4.3 8.6 1.0
C05 A:9RX406 4.3 34.3 1.0
HH22 A:ARG121 4.3 20.4 1.0
CE1 A:HIS196 4.4 9.1 1.0
O A:HOH515 4.4 14.2 1.0
HA A:CYS221 4.4 10.9 1.0
CE1 A:HIS116 4.4 9.7 1.0
O27 A:9RX406 4.5 22.9 1.0
CZ A:ARG121 4.5 16.2 1.0
CB A:ASP120 4.5 18.8 1.0
CA A:CYS221 4.6 9.1 1.0
HB2 A:ASP120 4.6 22.5 1.0
H051 A:9RX406 4.6 41.1 1.0
NE2 A:HIS116 4.6 8.1 1.0
HA3 A:GLY262 4.6 15.7 1.0
C02 A:9RX406 4.6 27.3 1.0
HB3 A:ASP120 4.7 22.5 1.0

Zinc binding site 3 out of 4 in 6kw1

Go back to Zinc Binding Sites List in 6kw1
Zinc binding site 3 out of 4 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:13.2
occ:1.00
ND1 B:HIS118 2.0 14.1 1.0
NE2 B:HIS196 2.1 9.6 1.0
NE2 B:HIS116 2.1 8.7 1.0
N09 B:9RX404 2.1 32.1 1.0
HB2 B:HIS118 2.8 13.4 1.0
CG B:HIS118 3.0 10.1 1.0
CD2 B:HIS196 3.0 9.2 1.0
CD2 B:HIS116 3.0 10.2 1.0
CE1 B:HIS116 3.1 9.4 1.0
CE1 B:HIS118 3.1 12.6 1.0
N08 B:9RX404 3.1 29.8 1.0
CE1 B:HIS196 3.1 10.2 1.0
C10 B:9RX404 3.1 36.7 1.0
HD2 B:HIS196 3.2 11.1 1.0
HD2 B:HIS116 3.2 12.3 1.0
HE1 B:HIS116 3.3 11.2 1.0
CB B:HIS118 3.3 11.2 1.0
HE1 B:HIS118 3.3 15.1 1.0
HE1 B:HIS196 3.3 12.3 1.0
HB3 B:HIS118 3.4 13.4 1.0
OD1 B:ASP120 3.7 14.3 1.0
S12 B:9RX404 3.8 42.5 1.0
ZN B:ZN402 3.9 17.3 1.0
HB2 B:CYS221 4.0 14.4 1.0
ND1 B:HIS116 4.1 12.0 1.0
CD2 B:HIS118 4.1 10.8 1.0
NE2 B:HIS118 4.1 13.7 1.0
CG B:HIS116 4.2 9.6 1.0
ND1 B:HIS196 4.2 10.2 1.0
C07 B:9RX404 4.2 32.7 1.0
CG B:HIS196 4.2 9.7 1.0
N11 B:9RX404 4.2 37.0 1.0
HD22 B:ASN233 4.2 70.5 1.0
HB3 B:CYS221 4.3 14.4 1.0
SG B:CYS221 4.4 11.5 1.0
OD2 B:ASP120 4.4 14.7 1.0
CB B:CYS221 4.4 12.0 1.0
CG B:ASP120 4.5 17.2 1.0
H152 B:9RX404 4.5 63.0 1.0
H B:HIS118 4.5 12.7 1.0
O27 B:9RX404 4.6 22.0 1.0
CA B:HIS118 4.7 12.8 1.0
C15 B:9RX404 4.7 52.5 1.0
HG2 B:ARG121 4.7 19.1 1.0
HE B:ARG121 4.8 22.3 1.0
H151 B:9RX404 4.9 63.0 1.0
HB3 B:SER197 4.9 11.6 1.0
HD1 B:HIS116 4.9 14.4 1.0
ND2 B:ASN233 4.9 58.7 1.0
HE2 B:HIS118 4.9 16.4 1.0
HD1 B:HIS196 5.0 12.3 1.0
HD2 B:HIS118 5.0 12.9 1.0

Zinc binding site 4 out of 4 in 6kw1

Go back to Zinc Binding Sites List in 6kw1
Zinc binding site 4 out of 4 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:17.3
occ:1.00
N08 B:9RX404 2.1 29.8 1.0
NE2 B:HIS263 2.1 14.0 1.0
OD2 B:ASP120 2.2 14.7 1.0
SG B:CYS221 2.2 11.5 1.0
O27 B:9RX404 2.5 22.0 1.0
C07 B:9RX404 3.0 32.7 1.0
HH21 B:ARG121 3.0 21.1 1.0
N09 B:9RX404 3.0 32.1 1.0
CE1 B:HIS263 3.1 13.5 1.0
CD2 B:HIS263 3.1 14.9 1.0
HB3 B:CYS221 3.2 14.4 1.0
HE1 B:HIS263 3.3 16.2 1.0
HD2 B:HIS263 3.3 17.9 1.0
CG B:ASP120 3.3 17.2 1.0
CB B:CYS221 3.4 12.0 1.0
C26 B:9RX404 3.4 23.8 1.0
C04 B:9RX404 3.4 31.9 1.0
HE B:ARG121 3.5 22.3 1.0
C03 B:9RX404 3.6 27.7 1.0
HE1 B:HIS116 3.7 11.2 1.0
NH2 B:ARG121 3.8 17.6 1.0
OD1 B:ASP120 3.8 14.3 1.0
HB2 B:CYS221 3.9 14.4 1.0
ZN B:ZN401 3.9 13.2 1.0
N11 B:9RX404 4.0 37.0 1.0
C10 B:9RX404 4.1 36.7 1.0
HE1 B:HIS196 4.2 12.3 1.0
ND1 B:HIS263 4.2 11.4 1.0
CG B:HIS263 4.2 13.2 1.0
NE B:ARG121 4.3 18.6 1.0
HH22 B:ARG121 4.3 21.1 1.0
NE2 B:HIS196 4.3 9.6 1.0
CE1 B:HIS196 4.3 10.2 1.0
C05 B:9RX404 4.4 36.2 1.0
O B:HOH512 4.4 14.5 1.0
CE1 B:HIS116 4.4 9.4 1.0
HA B:CYS221 4.4 12.7 1.0
CZ B:ARG121 4.5 16.7 1.0
CB B:ASP120 4.5 19.2 1.0
O28 B:9RX404 4.5 22.7 1.0
CA B:CYS221 4.6 10.6 1.0
HB2 B:ASP120 4.6 23.1 1.0
HA3 B:GLY262 4.6 15.3 1.0
NE2 B:HIS116 4.6 8.7 1.0
H051 B:9RX404 4.7 43.4 1.0
C02 B:9RX404 4.7 27.6 1.0
HB3 B:ASP120 4.7 23.1 1.0
HD1 B:HIS263 5.0 13.8 1.0

Reference:

K.W.Yang, Y.Xiang. The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B To Be Published.
Page generated: Wed Dec 16 12:10:27 2020

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