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Iodine in PDB 5moz: Oxa-10 Avibactam Complex with Bound Iodide

Enzymatic activity of Oxa-10 Avibactam Complex with Bound Iodide

All present enzymatic activity of Oxa-10 Avibactam Complex with Bound Iodide:
3.5.2.6;

Protein crystallography data

The structure of Oxa-10 Avibactam Complex with Bound Iodide, PDB code: 5moz was solved by J.Brem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.29 / 1.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.841, 101.658, 126.727, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 18.5

Other elements in 5moz:

The structure of Oxa-10 Avibactam Complex with Bound Iodide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Oxa-10 Avibactam Complex with Bound Iodide (pdb code 5moz). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Oxa-10 Avibactam Complex with Bound Iodide, PDB code: 5moz:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 5moz

Go back to Iodine Binding Sites List in 5moz
Iodine binding site 1 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I712

b:15.0
occ:1.00
 NZ A:LYS70 3.4 15.8 1.0
NE1 A:TRP154 3.4 12.5 1.0
O A:HOH1029 3.5 13.6 1.0
O A:HOH1000 3.7 31.0 1.0
CE A:LYS70 3.8 13.3 1.0
CG A:LYS70 4.0 11.9 1.0
CG2 A:VAL117 4.0 14.2 1.0
CA A:VAL117 4.1 10.1 1.0
CE2 A:TRP154 4.2 11.0 1.0
CB A:PHE120 4.2 10.6 1.0
CZ2 A:TRP154 4.3 12.6 1.0
OG A:SER67 4.3 12.5 1.0
CA A:SER67 4.4 10.6 1.0
CD2 A:LEU155 4.4 17.3 1.0
CB A:VAL117 4.4 12.6 1.0
CG1 A:VAL117 4.4 13.1 1.0
CD1 A:TRP154 4.5 11.7 1.0
CD A:LYS70 4.5 10.9 1.0
O A:VAL117 4.7 11.5 1.0
CB A:SER67 4.8 10.6 1.0
O A:ALA66 4.9 10.9 1.0
N A:VAL117 4.9 11.9 1.0
CG A:PHE120 5.0 11.7 1.0

Iodine binding site 2 out of 9 in 5moz

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Iodine binding site 2 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I713

b:15.1
occ:1.00
 N A:ALA98 3.6 13.6 1.0
CG A:PRO118 3.9 13.5 1.0
CD A:PRO118 3.9 13.2 1.0
CA A:ARG97 4.0 12.2 1.0
CZ3 A:TRP102 4.1 12.8 1.0
CB A:PRO118 4.1 13.3 1.0
CB A:ARG97 4.1 12.2 1.0
CB A:ALA98 4.1 16.1 1.0
CE3 A:TRP102 4.3 12.5 1.0
CG A:ARG97 4.3 12.7 1.0
C A:ARG97 4.3 13.7 1.0
CA A:ALA98 4.5 13.7 1.0
N A:PRO118 4.9 11.2 1.0
CA A:PRO118 5.0 11.7 1.0

Iodine binding site 3 out of 9 in 5moz

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Iodine binding site 3 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I714

b:24.3
occ:0.90
 O A:HOH1106 3.4 48.0 1.0
NE A:ARG250 3.6 15.0 1.0
NH1 A:ARG250 3.7 18.1 1.0
O A:HOH1115 3.8 41.8 1.0
CA A:PRO248 3.9 18.4 1.0
CZ A:ARG250 4.1 15.8 1.0
CD A:LYS251 4.2 25.6 1.0
CG A:LYS251 4.2 22.4 1.0
CE A:LYS251 4.2 34.9 1.0
O A:LEU247 4.5 17.9 1.0
CG A:ARG250 4.5 15.0 1.0
CB A:PRO248 4.6 22.9 1.0
N A:PRO248 4.6 16.0 1.0
CD A:ARG250 4.6 16.3 1.0
CB A:LYS251 4.6 19.5 1.0
O A:HOH914 4.7 24.1 1.0
NZ A:LYS251 4.7 38.8 1.0
O A:PRO248 4.7 19.9 1.0
C A:LEU247 4.8 16.7 1.0
C A:PRO248 4.8 18.8 1.0
CG A:PRO248 4.9 20.0 1.0

Iodine binding site 4 out of 9 in 5moz

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Iodine binding site 4 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I715

b:17.7
occ:0.30
 O A:HOH1038 1.4 18.8 0.7
O A:HOH900 3.4 19.1 1.0
O A:HOH1062 3.5 26.6 1.0
O A:HOH968 3.5 23.7 1.0
CB A:LEU155 4.0 14.7 1.0
O A:NXL701 4.4 25.4 1.0
CD1 A:LEU155 4.4 17.0 1.0
O A:HOH848 4.5 19.3 1.0
CD2 A:LEU155 4.6 17.3 1.0
CG A:LEU155 4.6 14.2 1.0
O A:HOH1055 4.7 20.9 1.0
O A:LEU155 4.7 14.4 1.0
C A:LEU155 5.0 12.1 1.0
O A:SER209 5.0 16.7 1.0
CA A:LEU155 5.0 12.5 1.0

Iodine binding site 5 out of 9 in 5moz

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Iodine binding site 5 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I304

b:41.7
occ:0.80
 NE B:ARG250 3.6 35.0 1.0
NH1 B:ARG250 3.8 40.5 1.0
CA B:PRO248 3.9 38.7 1.0
CD B:LYS251 4.0 44.1 1.0
CZ B:ARG250 4.1 36.9 1.0
CG B:LYS251 4.2 35.2 1.0
CE B:LYS251 4.3 47.8 1.0
O B:LEU247 4.4 40.2 1.0
CG B:ARG250 4.5 35.9 1.0
CB B:PRO248 4.5 43.3 1.0
N B:PRO248 4.5 39.5 1.0
CD B:ARG250 4.6 35.2 1.0
O B:PRO248 4.7 38.3 1.0
C B:LEU247 4.7 40.7 1.0
NZ B:LYS251 4.7 49.1 1.0
C B:PRO248 4.7 40.5 1.0
CB B:LYS251 4.7 37.9 1.0
O B:HOH524 4.9 42.8 1.0
CG B:PRO248 5.0 43.4 1.0

Iodine binding site 6 out of 9 in 5moz

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Iodine binding site 6 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I305

b:33.6
occ:0.70
 I B:IOD305 0.0 33.6 0.7
I B:IOD305 3.3 43.6 0.3
O B:HOH571 3.4 38.3 1.0
CAN B:NXL308 3.4 34.6 1.0
OG B:SER67 3.5 33.7 1.0
NE1 B:TRP154 3.5 37.1 1.0
N B:SER67 3.6 30.7 1.0
O B:NXL308 3.6 45.3 1.0
N B:NXL308 3.7 37.5 1.0
C B:ALA66 3.8 30.2 1.0
CA B:SER67 3.8 30.6 1.0
CD1 B:TRP154 3.8 34.0 1.0
OAC B:NXL308 3.9 33.7 1.0
O B:ALA66 4.1 29.6 1.0
CA B:ALA66 4.1 30.9 1.0
CD2 B:LEU155 4.2 43.5 1.0
CD1 B:LEU155 4.2 43.5 1.0
CB B:SER67 4.3 31.6 1.0
CAJ B:NXL308 4.3 40.5 1.0
CB B:LEU155 4.4 37.5 1.0
O B:HOH517 4.4 25.7 0.5
C B:NXL308 4.5 47.2 1.0
CG B:LEU155 4.5 38.5 1.0
CA B:NXL308 4.6 38.5 1.0
CG2 B:VAL117 4.6 38.9 1.0
CB B:ALA66 4.6 31.6 1.0
CE2 B:TRP154 4.8 36.1 1.0
NZ B:LYS70 4.8 35.3 1.0

Iodine binding site 7 out of 9 in 5moz

Go back to Iodine Binding Sites List in 5moz
Iodine binding site 7 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I305

b:43.6
occ:0.30
 I B:IOD305 0.0 43.6 0.3
O B:HOH517 2.4 25.7 0.5
NZ B:LYS70 2.9 35.3 1.0
O B:HOH562 3.1 31.1 1.0
CE B:LYS70 3.3 39.4 1.0
I B:IOD305 3.3 33.6 0.7
CG B:LYS70 3.6 29.9 1.0
NE1 B:TRP154 3.6 37.1 1.0
O B:HOH571 3.9 38.3 1.0
CB B:PHE120 4.0 31.0 1.0
CD B:LYS70 4.0 33.1 1.0
CE2 B:TRP154 4.4 36.1 1.0
OG B:SER67 4.4 33.7 1.0
CA B:VAL117 4.4 38.9 1.0
CZ2 B:TRP154 4.5 34.3 1.0
CA B:SER67 4.5 30.6 1.0
CD1 B:TRP154 4.6 34.0 1.0
CG2 B:VAL117 4.6 38.9 1.0
CG B:PHE120 4.6 29.9 1.0
O B:VAL117 4.7 35.9 1.0
CB B:LYS70 4.9 27.8 1.0
CB B:VAL117 5.0 37.4 1.0
CB B:SER67 5.0 31.6 1.0

Iodine binding site 8 out of 9 in 5moz

Go back to Iodine Binding Sites List in 5moz
Iodine binding site 8 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I306

b:43.9
occ:0.60
 N B:ALA98 3.5 52.6 1.0
CG B:PRO118 3.8 43.4 1.0
CD B:PRO118 3.9 39.7 1.0
CA B:ARG97 3.9 53.4 1.0
CB B:ARG97 4.0 50.8 1.0
CB B:PRO118 4.1 42.2 1.0
CB B:ALA98 4.2 53.5 1.0
CG B:ARG97 4.2 50.3 1.0
C B:ARG97 4.3 54.1 1.0
CZ3 B:TRP102 4.3 45.7 1.0
CE3 B:TRP102 4.4 45.0 1.0
CA B:ALA98 4.5 54.8 1.0
N B:PRO118 4.8 38.4 1.0
CD B:ARG97 5.0 47.9 1.0

Iodine binding site 9 out of 9 in 5moz

Go back to Iodine Binding Sites List in 5moz
Iodine binding site 9 out of 9 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I307

b:27.3
occ:0.50
 O B:HOH451 3.1 49.4 1.0
N B:GLY20 3.8 35.6 1.0
CA B:MET19 3.8 42.7 1.0
CB B:CYS44 3.8 20.8 1.0
O B:LYS45 3.9 23.5 1.0
CA B:LYS49 3.9 23.8 1.0
CB B:MET19 4.0 50.6 1.0
N B:SER50 4.1 21.8 1.0
C B:LYS49 4.1 26.3 1.0
CD B:LYS49 4.2 39.3 1.0
SG B:CYS51 4.2 24.2 1.0
C B:MET19 4.3 46.5 1.0
CA B:SER46 4.3 24.2 1.0
C B:LYS45 4.4 21.4 1.0
O B:HOH403 4.5 45.7 1.0
OE2 B:GLU171 4.5 32.2 1.0
SG B:CYS44 4.6 23.5 1.0
N B:SER46 4.6 21.3 1.0
N B:LYS45 4.7 19.8 1.0
O B:SER50 4.7 22.3 1.0
N B:LYS49 4.7 22.5 1.0
CA B:CYS44 4.8 20.1 1.0
C B:CYS44 4.8 22.7 1.0
O B:LYS49 4.8 25.0 1.0
O B:SER46 4.8 23.8 1.0
CA B:GLY20 4.8 27.9 1.0
CB B:LYS49 4.8 32.4 1.0
C B:SER50 4.9 24.8 1.0
CD2 B:PHE234 4.9 24.3 1.0
N B:MET19 5.0 47.7 1.0

Reference:

C.T.Lohans, D.Y.Wang, C.Jorgensen, S.T.Cahill, I.J.Clifton, M.A.Mcdonough, H.P.Oswin, J.Spencer, C.Domene, T.D.W.Claridge, J.Brem, C.J.Schofield. (13)C-Carbamylation As A Mechanistic Probe For the Inhibition of Class D Beta-Lactamases By Avibactam and Halide Ions. Org. Biomol. Chem. V. 15 6024 2017.
ISSN: ESSN 1477-0539
PubMed: 28678295
DOI: 10.1039/C7OB01514C
Page generated: Sun Dec 13 19:40:22 2020

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