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Potassium in PDB 6mz2: Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9

Enzymatic activity of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9

All present enzymatic activity of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9:
3.5.2.6;

Protein crystallography data

The structure of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9, PDB code: 6mz2 was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.17 / 0.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.161, 106.842, 47.913, 90.00, 101.82, 90.00
R / Rfree (%) 11.6 / 12.7

Other elements in 6mz2:

The structure of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Potassium atom in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 (pdb code 6mz2). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 13 binding sites of Potassium where determined in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9, PDB code: 6mz2:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 13 in 6mz2

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Potassium binding site 1 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K304

b:14.8
occ:1.00
 OE2 A:GLU110 2.7 12.6 1.0
O B:HOH556 2.7 14.3 1.0
O A:PRO107 2.7 9.9 1.0
O A:HOH769 2.8 15.1 1.0
HG3 A:GLU110 3.0 12.1 1.0
HG2 A:GLU110 3.1 12.1 1.0
HG3 A:LYS111 3.1 13.0 1.0
HA A:PRO107 3.3 9.0 1.0
CG A:GLU110 3.3 10.1 1.0
CD A:GLU110 3.4 11.9 1.0
HD3 A:LYS111 3.4 14.1 1.0
HG2 A:LYS111 3.5 13.0 1.0
CG A:LYS111 3.7 10.8 1.0
C A:PRO107 3.7 7.3 1.0
CA A:PRO107 3.9 7.5 1.0
CD A:LYS111 4.0 11.8 1.0
O A:HOH448 4.0 18.4 1.0
HE2 A:LYS111 4.1 14.9 1.0
HB2 A:PRO107 4.2 10.4 1.0
O A:HOH818 4.3 35.0 1.0
O A:HOH447 4.3 36.2 1.0
CB A:PRO107 4.4 8.7 1.0
HB3 A:PRO107 4.4 10.4 1.0
O B:HOH718 4.5 39.0 1.0
O A:HOH563 4.5 15.2 1.0
CE A:LYS111 4.5 12.4 1.0
OE1 A:GLU110 4.6 13.2 1.0
H A:LYS111 4.6 7.7 1.0
HZ3 A:LYS111 4.8 15.1 1.0
OG1 B:THR230 4.8 14.6 1.0
CB A:GLU110 4.8 8.8 1.0
HD2 A:LYS111 4.8 14.1 1.0
K B:K307 4.9 17.6 0.2
N A:ILE108 4.9 5.6 1.0
N A:LYS111 4.9 6.4 1.0
HA A:ILE108 4.9 6.5 1.0

Potassium binding site 2 out of 13 in 6mz2

Go back to Potassium Binding Sites List in 6mz2
Potassium binding site 2 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K305

b:16.6
occ:0.24
 O A:TRP229 2.6 15.9 1.0
O A:HOH578 2.8 15.1 1.0
O A:HOH416 2.8 17.4 1.0
O A:HOH579 2.8 17.0 1.0
HG3 A:ARG222 2.9 14.0 1.0
HG23 A:VAL231 3.0 11.0 1.0
HD2 A:ARG222 3.2 17.4 1.0
NE A:ARG222 3.2 16.7 1.0
HE A:ARG222 3.3 20.0 1.0
CZ A:ARG222 3.4 18.3 1.0
HA A:THR230 3.5 12.5 1.0
CD A:ARG222 3.5 14.5 1.0
CG A:ARG222 3.7 11.7 1.0
HB A:VAL231 3.7 9.6 1.0
H A:VAL231 3.7 9.0 1.0
CG2 A:VAL231 3.8 9.2 1.0
C A:TRP229 3.8 13.6 1.0
O A:HOH598 3.8 35.5 1.0
NH1 A:ARG222 3.9 18.7 1.0
NH2 A:ARG222 3.9 18.9 1.0
HG21 A:VAL231 3.9 11.0 1.0
HH11 A:ARG222 4.0 22.4 1.0
HH21 A:ARG222 4.0 22.7 1.0
N A:VAL231 4.1 7.5 1.0
O A:THR227 4.2 16.3 1.0
HG2 A:ARG222 4.2 14.0 1.0
CA A:THR230 4.2 10.4 1.0
CB A:VAL231 4.2 8.0 1.0
O B:HOH547 4.3 19.2 1.0
HH12 A:ARG222 4.4 22.4 1.0
HH22 A:ARG222 4.4 22.7 1.0
HD3 A:ARG222 4.4 17.4 1.0
C A:THR230 4.4 8.9 1.0
N A:THR230 4.5 11.2 1.0
HA A:THR227 4.6 20.8 1.0
HG22 A:VAL231 4.6 11.0 1.0
HB2 A:ARG222 4.7 10.4 1.0
HB2 A:TRP229 4.7 16.7 1.0
OH B:TYR105 4.7 8.3 0.7
CB A:ARG222 4.8 8.6 1.0
O A:HOH500 4.8 13.3 1.0
O A:PRO226 4.8 12.2 1.0
CA A:VAL231 4.8 7.0 1.0
O A:HOH441 4.8 8.1 1.0
HA A:ARG222 4.9 7.9 1.0
H A:TRP229 4.9 17.1 1.0
OH B:TYR105 4.9 11.2 0.3
CA A:TRP229 4.9 14.0 1.0
C A:THR227 5.0 16.6 1.0

Potassium binding site 3 out of 13 in 6mz2

Go back to Potassium Binding Sites List in 6mz2
Potassium binding site 3 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K306

b:8.8
occ:0.23
 O A:HOH427 2.6 9.1 1.0
O B:HOH818 2.7 11.1 1.0
O A:HOH512 2.7 7.0 1.0
OE1 A:GLN128 2.8 6.8 1.0
CD A:GLN128 3.6 5.1 1.0
HE22 A:GLN128 3.7 6.1 1.0
O A:HOH535 3.8 11.1 1.0
HE1 A:TYR129 3.8 8.0 1.0
NE2 A:GLN128 4.0 5.0 1.0
O B:HOH586 4.1 9.4 1.0
HA3 B:GLY213 4.2 5.2 1.0
O A:HOH819 4.3 15.2 1.0
HB3 A:GLN128 4.3 5.6 1.0
OH A:TYR129 4.4 9.2 1.0
O A:GLY213 4.5 4.5 1.0
CE1 A:TYR129 4.5 6.7 1.0
HE22 B:GLN128 4.5 5.8 1.0
HA2 B:GLY213 4.5 5.2 1.0
O A:HOH816 4.6 16.0 1.0
O A:HOH589 4.6 16.2 1.0
HB2 A:GLN128 4.6 5.6 1.0
HA3 A:GLY213 4.7 5.1 1.0
CB A:GLN128 4.8 4.6 1.0
CA B:GLY213 4.8 4.3 1.0
CZ A:TYR129 4.8 7.4 1.0
HE21 A:GLN128 4.8 6.1 1.0
CG A:GLN128 4.8 5.0 1.0
O B:GLY213 4.9 4.6 1.0
O B:HOH787 4.9 26.6 1.0
HG23 A:THR215 5.0 6.0 1.0

Potassium binding site 4 out of 13 in 6mz2

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Potassium binding site 4 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K307

b:10.7
occ:0.34
 O A:HOH825 2.7 12.6 1.0
O A:HOH719 2.7 13.2 1.0
O A:GLY147 2.7 6.6 1.0
O A:HOH755 2.8 12.1 1.0
HB3 A:ALA150 2.8 7.3 1.0
HA2 A:GLY147 3.3 6.5 1.0
H A:PHE151 3.4 6.1 1.0
HB2 A:PHE151 3.5 6.5 1.0
O A:HOH634 3.5 39.3 1.0
C A:GLY147 3.6 5.5 1.0
CB A:ALA150 3.6 6.0 1.0
HB1 A:ALA150 3.7 7.3 1.0
N A:PHE151 3.7 5.1 1.0
CA A:GLY147 3.8 5.4 1.0
HA3 A:GLY147 3.9 6.5 1.0
O A:HOH864 4.0 42.5 1.0
HD22 A:LEU142 4.1 8.2 1.0
HA A:PHE151 4.2 6.2 1.0
CB A:PHE151 4.2 5.4 1.0
C A:ALA150 4.2 5.0 1.0
CA A:PHE151 4.3 5.1 1.0
HB2 A:ALA150 4.3 7.3 1.0
HB3 A:LEU142 4.4 7.1 1.0
CA A:ALA150 4.5 5.2 1.0
O A:HOH604 4.5 14.5 1.0
O A:HOH877 4.5 23.2 1.0
HB3 A:PHE151 4.5 6.5 1.0
H A:ALA150 4.7 5.9 1.0
O A:HOH773 4.7 23.7 1.0
HB1 A:ALA79 4.8 6.0 1.0
O A:LEU142 4.8 6.9 1.0
O A:HOH684 4.9 21.7 1.0
N A:VAL148 4.9 5.1 1.0
N A:ALA150 4.9 4.9 1.0
O A:HOH525 5.0 22.8 1.0
O A:ALA150 5.0 5.4 1.0

Potassium binding site 5 out of 13 in 6mz2

Go back to Potassium Binding Sites List in 6mz2
Potassium binding site 5 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K308

b:12.2
occ:0.24
 O A:HOH792 2.6 15.0 1.0
O A:GLY156 2.7 8.8 1.0
O A:HOH644 2.7 13.2 1.0
HA3 A:GLY156 3.2 9.0 1.0
C A:GLY156 3.5 7.1 1.0
HG2 A:GLN188 3.7 9.3 1.0
CA A:GLY156 3.8 7.5 1.0
O A:HOH766 4.0 26.1 1.0
O A:HOH580 4.1 15.9 1.0
O A:HOH588 4.1 26.2 1.0
HA2 A:GLY156 4.1 9.0 1.0
HE21 A:GLN188 4.2 11.4 1.0
HG3 A:GLN188 4.3 9.3 1.0
O A:HOH648 4.4 17.9 1.0
CG A:GLN188 4.4 7.7 1.0
HA A:ASP157 4.6 6.8 1.0
N A:ASP157 4.6 6.1 1.0
O A:HOH678 4.8 21.0 1.0
NE2 A:GLN188 4.8 9.5 1.0
O A:ILE155 4.8 8.9 1.0

Potassium binding site 6 out of 13 in 6mz2

Go back to Potassium Binding Sites List in 6mz2
Potassium binding site 6 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K309

b:10.2
occ:0.21
 O A:HOH434 2.6 13.8 1.0
O A:PRO268 2.8 8.2 1.0
O A:HOH609 2.9 16.8 1.0
HE2 A:TYR241 3.1 8.2 1.0
HA A:GLN269 3.2 10.1 1.0
HG2 A:GLN269 3.7 17.0 1.0
C A:PRO268 4.0 6.7 1.0
CE2 A:TYR241 4.0 6.8 1.0
CA A:GLN269 4.1 8.4 1.0
H A:GLN270 4.2 8.8 1.0
N A:GLN269 4.5 7.3 1.0
CG A:GLN269 4.6 14.2 1.0
OH A:TYR241 4.7 8.9 1.0
HD2 A:TYR241 4.7 7.2 1.0
N A:GLN270 4.7 7.4 1.0
HG2 A:PRO174 4.8 8.6 1.0
CB A:GLN269 4.8 11.3 1.0
CZ A:TYR241 4.9 7.5 1.0
CD2 A:TYR241 4.9 6.0 1.0
HB3 A:GLN269 4.9 13.6 1.0
C A:GLN269 5.0 7.2 1.0
HG3 A:GLN269 5.0 17.0 1.0

Potassium binding site 7 out of 13 in 6mz2

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Potassium binding site 7 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K310

b:11.7
occ:0.28
 O A:HOH411 2.4 12.9 1.0
O B:HOH659 2.6 12.9 1.0
O B:HOH755 2.7 15.7 1.0
OG1 A:THR215 2.7 5.1 1.0
HG22 A:THR216 2.9 7.3 1.0
HH11 B:ARG222 3.3 19.0 1.0
HH12 B:ARG222 3.4 19.0 1.0
HD2 A:TYR129 3.4 7.8 1.0
HA A:TYR129 3.6 5.5 1.0
HG23 A:THR216 3.6 7.3 1.0
CG2 A:THR216 3.6 6.1 1.0
NH1 B:ARG222 3.7 15.8 1.0
HB A:THR215 3.7 5.5 1.0
CB A:THR215 3.8 4.6 1.0
O B:HOH630 3.9 16.8 1.0
HG21 A:THR216 4.1 7.3 1.0
CD2 A:TYR129 4.1 6.5 1.0
OH A:TYR105 4.4 9.0 0.7
HA A:THR216 4.5 5.6 1.0
CA A:TYR129 4.5 4.6 1.0
O B:HOH519 4.5 16.6 1.0
O A:HOH757 4.5 34.6 1.0
HG21 A:THR215 4.6 6.0 1.0
OH A:TYR105 4.6 10.0 0.3
C A:THR215 4.6 4.3 1.0
HE2 A:TYR129 4.6 8.7 1.0
O A:TYR129 4.6 6.1 1.0
O A:THR215 4.6 5.0 1.0
HB3 A:TYR129 4.6 6.0 1.0
NA A:NA312 4.6 18.7 0.3
O A:HOH467 4.7 18.7 1.0
O A:GLN128 4.7 4.8 1.0
O A:HOH688 4.7 19.8 1.0
CE2 A:TYR129 4.7 7.3 1.0
OAD A:NXL301 4.7 8.5 0.2
O B:HOH505 4.8 6.3 1.0
CG2 A:THR215 4.8 5.0 1.0
NA A:NA311 4.8 17.2 0.6
CB A:THR216 4.8 4.8 1.0
N A:THR216 4.8 4.1 1.0
CA A:THR215 4.9 4.3 1.0
CG A:TYR129 4.9 5.3 1.0
CB A:TYR129 4.9 5.0 1.0
HD3 B:ARG222 4.9 16.8 1.0
CA A:THR216 4.9 4.6 1.0
C A:TYR129 5.0 4.8 1.0

Potassium binding site 8 out of 13 in 6mz2

Go back to Potassium Binding Sites List in 6mz2
Potassium binding site 8 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K304

b:16.4
occ:1.00
 O B:ALA154 2.7 10.3 1.0
O B:HOH777 3.2 32.0 1.0
HA B:ALA154 3.4 7.5 1.0
C B:ALA154 3.7 7.1 1.0
CA B:ALA154 4.0 6.3 1.0
HB1 B:ALA154 4.1 8.2 1.0
O B:HOH622 4.2 9.3 1.0
CB B:ALA154 4.6 6.8 1.0
HA B:ILE155 4.6 8.0 1.0
N B:ILE155 4.8 6.3 1.0
O B:HOH742 4.8 23.2 1.0
O B:ARG153 4.9 6.2 1.0

Potassium binding site 9 out of 13 in 6mz2

Go back to Potassium Binding Sites List in 6mz2
Potassium binding site 9 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K305

b:15.0
occ:0.36
 O B:HOH740 2.7 16.1 1.0
OD2 B:ASP53 2.8 14.3 1.0
HB3 B:ASP53 2.8 15.1 1.0
CG B:ASP53 3.5 13.0 1.0
CB B:ASP53 3.5 12.5 1.0
O B:HOH445 3.7 42.1 1.0
HB2 B:ASP53 3.8 15.1 1.0
HB1 B:ALA52 4.3 13.9 1.0
HB3 B:ALA52 4.4 13.9 1.0
OD1 B:ASP53 4.7 12.2 1.0
O B:HOH465 4.7 12.5 1.0
CA B:ASP53 4.8 12.3 1.0
CB B:ALA52 4.9 11.6 1.0

Potassium binding site 10 out of 13 in 6mz2

Go back to Potassium Binding Sites List in 6mz2
Potassium binding site 10 out of 13 in the Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Ctx-M-14 Class A Beta-Lactamase in Complex with Avibactam at pH 7.9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K306

b:9.5
occ:0.22
 O B:ARG222 2.7 8.2 1.0
O B:LEU225 2.8 10.3 1.0
HG22 B:THR227 2.9 25.7 1.0
HA B:THR227 3.0 21.3 1.0
HG23 B:THR227 3.5 25.7 1.0
O B:HOH425 3.6 38.0 1.0
CG2 B:THR227 3.6 21.4 1.0
HA B:ALA223 3.6 9.2 1.0
H B:LEU225 3.8 10.2 1.0
C B:ARG222 3.8 7.8 1.0
CA B:THR227 3.8 17.8 1.0
O A:HOH577 3.9 22.1 1.0
C B:LEU225 3.9 9.9 1.0
O A:HOH711 4.0 40.0 1.0
N B:THR227 4.0 15.2 1.0
HB2 B:LEU225 4.1 12.2 1.0
C B:PRO226 4.1 12.5 1.0
O B:PRO226 4.2 11.3 1.0
HB2 B:ARG222 4.2 13.6 1.0
CB B:THR227 4.3 20.5 1.0
HG21 B:THR227 4.3 25.7 1.0
CA B:ALA223 4.3 7.6 1.0
H B:THR227 4.4 18.2 1.0
N B:LEU225 4.4 8.5 1.0
HG3 B:ARG222 4.5 15.6 1.0
O A:HOH467 4.5 18.7 1.0
N B:ALA223 4.5 7.3 1.0
C B:ALA223 4.6 7.8 1.0
HH22 A:ARG276 4.6 14.4 0.6
O B:ALA223 4.6 9.4 1.0
CA B:LEU225 4.6 9.5 1.0
HB B:THR227 4.7 24.6 1.0
O B:HOH533 4.7 18.8 1.0
HA B:ARG222 4.8 10.1 1.0
CA B:ARG222 4.8 8.4 1.0
N B:PRO226 4.8 10.5 1.0
CB B:LEU225 4.8 10.2 1.0
CB B:ARG222 4.9 11.3 1.0
CA B:PRO226 4.9 11.3 1.0
HA B:PRO226 4.9 13.6 1.0
HH12 A:ARG276 4.9 14.1 0.6

Reference:

O.A.Pemberton, R.Sanishvili, M.T.Kemp, F.L.Kearns, H.L.Woodcock, Y.Chen. Mechanism of Proton Transfer in Class A Beta-Lactamase Catalysis and Inhibition By Avibactam To Be Published.
Page generated: Mon Aug 12 16:54:42 2024

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