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Sodium 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
Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide 1B, PDB code: 6kw1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6kw1

Go back to Sodium Binding Sites List in 6kw1
Sodium 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 Sodium with other atoms in the Na 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:Na405

b:59.4
occ:1.00
HB3 A:ASP281 2.2 28.5 1.0
OD2 A:ASP281 2.4 55.6 1.0
HB2 A:ASP281 2.7 28.5 1.0
CB A:ASP281 2.7 23.7 1.0
CG A:ASP281 2.9 36.1 1.0
O A:HOH503 3.7 21.1 1.0
O A:HOH626 3.8 42.0 1.0
OD1 A:ASP281 4.1 42.4 1.0
CA A:ASP281 4.2 17.8 1.0
HA A:ASP281 4.4 21.3 1.0
H A:ASP281 4.4 22.9 1.0
O A:HOH631 4.4 39.7 1.0
N A:ASP281 4.8 19.1 1.0

Sodium binding site 2 out of 4 in 6kw1

Go back to Sodium Binding Sites List in 6kw1
Sodium 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 Sodium with other atoms in the Na 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:Na409

b:43.9
occ:1.00
HH21 A:ARG111 2.2 40.7 1.0
OD2 A:ASP76 2.3 36.6 1.0
HB3 A:ASP76 2.4 40.6 1.0
O A:HOH561 2.7 19.1 1.0
CB A:ASP76 3.0 33.8 1.0
CG A:ASP76 3.0 30.8 1.0
NH2 A:ARG111 3.0 33.9 1.0
HB2 A:ASP76 3.1 40.6 1.0
HG3 A:GLU79 3.3 53.2 1.0
HE A:ARG111 3.4 26.8 1.0
OE1 A:GLU79 3.4 47.2 1.0
HH22 A:ARG111 3.4 40.7 1.0
HD3 A:PRO186 3.5 26.5 1.0
HB2 A:LEU81 3.8 16.6 1.0
O A:HOH510 3.9 39.0 1.0
CZ A:ARG111 3.9 30.9 1.0
NE A:ARG111 3.9 22.4 1.0
CG A:GLU79 4.1 44.3 1.0
HA3 A:GLY185 4.1 27.1 1.0
CD A:GLU79 4.1 41.3 1.0
OD1 A:ASP76 4.2 40.1 1.0
HG1 A:THR110 4.3 24.4 1.0
CD A:PRO186 4.3 22.1 1.0
HD2 A:PRO186 4.3 26.5 1.0
HG2 A:GLU79 4.4 53.2 1.0
CA A:ASP76 4.4 25.1 1.0
O A:ASP76 4.4 28.3 1.0
OG1 A:THR110 4.5 20.4 1.0
HG3 A:PRO186 4.7 20.8 1.0
CB A:LEU81 4.7 13.9 1.0
C A:ASP76 4.9 28.8 1.0
HB2 A:ARG111 4.9 14.9 1.0
H A:ASP76 5.0 27.0 1.0
HD13 A:LEU81 5.0 20.3 1.0
HA A:ASP76 5.0 30.1 1.0

Sodium binding site 3 out of 4 in 6kw1

Go back to Sodium Binding Sites List in 6kw1
Sodium 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 Sodium with other atoms in the Na 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
A:Na412

b:53.8
occ:1.00
O A:HOH656 2.6 42.0 1.0
OE1 A:GLU225 3.0 17.3 1.0
HB2 A:SER227 3.0 23.3 1.0
OG A:SER227 3.3 22.0 1.0
O A:HOH526 3.3 28.8 1.0
HA2 B:GLY63 3.4 56.2 1.0
CB A:SER227 3.5 19.4 1.0
HB3 A:SER227 3.5 23.3 1.0
HD13 A:LEU265 3.5 45.9 1.0
CD A:GLU225 3.6 14.3 1.0
HG A:SER227 3.6 26.4 1.0
OE2 A:GLU225 3.6 17.5 1.0
O A:HOH644 4.0 25.7 1.0
O B:HOH571 4.0 43.4 1.0
HD22 A:LEU265 4.1 40.4 1.0
O A:HOH533 4.1 16.4 1.0
HB2 A:LEU265 4.3 22.0 1.0
CA B:GLY63 4.4 46.9 1.0
H A:LEU265 4.4 17.5 1.0
CD1 A:LEU265 4.5 38.3 1.0
HA3 B:GLY63 4.6 56.2 1.0
H B:GLY63 4.7 44.8 1.0
H A:SER227 4.8 20.1 1.0
HD11 A:LEU265 4.8 45.9 1.0
CD2 A:LEU265 4.9 33.6 1.0
HG3 A:GLU225 4.9 17.4 1.0
CA A:SER227 4.9 17.9 1.0
CG A:GLU225 4.9 14.5 1.0
HA3 A:GLY264 4.9 13.9 1.0
HG22 A:THR33 5.0 60.2 1.0
N B:GLY63 5.0 37.3 1.0

Sodium binding site 4 out of 4 in 6kw1

Go back to Sodium Binding Sites List in 6kw1
Sodium 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 Sodium with other atoms in the Na 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:Na407

b:45.2
occ:1.00
OD2 B:ASP76 2.2 40.8 1.0
HH21 B:ARG111 2.2 38.9 1.0
HB3 B:ASP76 2.5 43.4 1.0
O B:HOH535 2.6 20.0 1.0
CG B:ASP76 3.0 31.5 1.0
CB B:ASP76 3.0 36.2 1.0
NH2 B:ARG111 3.0 32.4 1.0
HB2 B:ASP76 3.1 43.4 1.0
HG3 B:GLU79 3.3 48.9 1.0
HE B:ARG111 3.3 30.6 1.0
HH22 B:ARG111 3.5 38.9 1.0
HD3 B:PRO186 3.6 25.7 1.0
HB2 B:LEU81 3.8 17.5 1.0
NE B:ARG111 3.9 25.5 1.0
CZ B:ARG111 3.9 32.7 1.0
HG1 B:THR110 3.9 26.2 1.0
O B:HOH504 4.0 39.4 1.0
CG B:GLU79 4.1 40.7 1.0
OE1 B:GLU79 4.1 33.8 1.0
OD1 B:ASP76 4.2 38.4 1.0
HA3 B:GLY185 4.2 26.1 1.0
OG1 B:THR110 4.4 21.9 1.0
CD B:PRO186 4.4 21.4 1.0
O B:ASP76 4.4 25.6 1.0
CA B:ASP76 4.4 25.3 1.0
CD B:GLU79 4.4 40.7 1.0
HD2 B:PRO186 4.5 25.7 1.0
HG2 B:GLU79 4.5 48.9 1.0
HG3 B:PRO186 4.7 21.6 1.0
CB B:LEU81 4.8 14.6 1.0
C B:ASP76 4.9 31.6 1.0
HB2 B:ARG111 4.9 16.1 1.0
HD13 B:LEU81 4.9 23.8 1.0
H B:ASP76 5.0 26.7 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: Tue Dec 15 12:29:53 2020

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