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Sodium 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:

Iodine (I) 9 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

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

Sodium binding site 1 out of 6 in 5moz

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Sodium binding site 1 out of 6 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:22.5
occ:1.00
 O A:HOH1063 2.2 23.8 0.5
O A:HOH1082 2.8 39.2 1.0
O A:HOH976 3.0 27.2 1.0
N A:LEU64 3.2 12.6 1.0
O A:HOH1063 3.2 25.4 0.5
CA A:TYR63 3.7 11.8 1.0
CG A:LEU64 3.9 13.8 1.0
C A:TYR63 3.9 11.4 1.0
CB A:LEU64 4.0 12.2 1.0
CB A:TYR63 4.0 11.9 1.0
NE A:ARG160 4.0 17.2 1.0
CD1 A:LEU64 4.0 14.6 1.0
CD1 A:TYR63 4.1 13.8 1.0
O A:HOH1069 4.1 31.4 1.0
CA A:LEU64 4.2 12.1 1.0
CD A:ARG160 4.2 15.0 1.0
O A:HOH1019 4.5 47.2 1.0
CZ A:ARG160 4.5 14.9 1.0
CG A:TYR63 4.5 11.8 1.0
CG1 A:VAL219 4.6 14.8 1.0
O A:HOH1090 4.8 41.4 1.0
O A:GLU62 4.9 14.3 1.0
O A:HOH1009 4.9 36.9 1.0
NH1 A:ARG160 5.0 19.4 1.0
CB A:VAL219 5.0 15.1 1.0

Sodium binding site 2 out of 6 in 5moz

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Sodium binding site 2 out of 6 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:28.6
occ:1.00
 O A:HOH946 2.8 51.0 1.0
O A:HOH813 3.1 42.4 0.5
O A:LYS45 3.4 29.8 1.0
CA A:LYS49 3.6 41.3 1.0
N A:SER50 3.7 30.1 1.0
CB A:CYS44 3.7 23.8 1.0
C A:LYS49 3.8 47.5 1.0
C A:LYS45 3.9 28.1 1.0
CA A:SER46 4.0 28.8 1.0
O A:SER50 4.1 27.9 1.0
N A:LYS49 4.2 34.3 1.0
N A:SER46 4.3 27.1 1.0
O A:SER46 4.4 37.1 1.0
N A:LYS45 4.4 23.0 1.0
SG A:CYS51 4.4 28.9 1.0
C A:SER50 4.5 30.8 1.0
C A:CYS44 4.5 21.7 1.0
C A:SER46 4.6 37.8 1.0
OE2 A:GLU171 4.6 29.8 1.0
CA A:CYS44 4.6 19.0 1.0
O A:LYS49 4.7 41.0 1.0
CA A:SER50 4.7 30.1 1.0
CB A:LYS49 4.7 46.8 1.0
O A:HOH1074 4.7 55.0 1.0
SG A:CYS44 4.7 25.3 1.0
CA A:LYS45 4.8 28.1 1.0
CD2 A:PHE234 4.9 24.9 1.0
OE1 A:GLU171 5.0 35.5 1.0

Sodium binding site 3 out of 6 in 5moz

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Sodium binding site 3 out of 6 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na709

b:34.3
occ:1.00
 O A:HOH1071 2.3 49.8 1.0
O A:HOH839 3.7 31.8 1.0
OD2 A:ASP242 3.8 33.2 1.0
CG A:ASP242 3.8 22.6 1.0
O A:HOH913 3.9 21.2 1.0
CB A:ASP240 3.9 17.4 1.0
N A:ASP242 4.0 16.0 1.0
O A:HOH972 4.0 22.0 1.0
CB A:PRO217 4.0 24.4 1.0
C A:ASP240 4.1 15.1 1.0
O A:ASP240 4.1 16.8 1.0
N A:ILE241 4.1 14.7 1.0
OD1 A:ASP242 4.2 25.2 1.0
C A:ILE241 4.2 15.8 1.0
CB A:ASP242 4.2 17.6 1.0
CA A:ILE241 4.2 14.5 1.0
O A:HOH1051 4.4 41.1 1.0
CG A:PRO217 4.5 31.3 1.0
O A:HOH966 4.6 35.1 1.0
CA A:ASP242 4.7 16.3 1.0
CA A:ASP240 4.7 16.8 1.0
O A:HOH964 4.8 36.4 1.0
O A:ILE241 4.9 14.3 1.0

Sodium binding site 4 out of 6 in 5moz

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Sodium binding site 4 out of 6 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na710

b:30.6
occ:1.00
 N A:GLU199 3.4 30.2 1.0
O A:HOH847 3.4 46.0 1.0
O A:HOH1024 3.9 42.2 1.0
CA A:GLU199 3.9 27.8 1.0
CB A:ALA197 4.0 26.3 1.0
C A:GLU199 4.0 29.4 1.0
CB A:GLU199 4.0 28.5 1.0
N A:TYR200 4.1 25.4 1.0
N A:PRO198 4.1 25.6 1.0
CD A:PRO198 4.1 27.5 1.0
CB A:TYR200 4.2 27.3 1.0
C A:PRO198 4.4 31.7 1.0
O A:GLU199 4.5 28.9 1.0
CB A:PRO198 4.6 33.3 1.0
C A:ALA197 4.6 22.5 1.0
CA A:PRO198 4.6 27.1 1.0
CG A:PRO198 4.8 32.1 1.0
CA A:TYR200 4.8 23.1 1.0
CA A:ALA197 4.9 26.2 1.0
CG A:GLU199 5.0 29.8 1.0

Sodium binding site 5 out of 6 in 5moz

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Sodium binding site 5 out of 6 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na711

b:43.8
occ:1.00
 O A:HOH924 3.1 33.3 0.5
OE2 A:GLU31 3.3 55.8 1.0
CG A:GLU31 3.5 43.1 1.0
OG A:SER260 3.7 33.3 1.0
CD A:GLU31 3.9 50.0 1.0
CB A:SER260 4.1 30.5 1.0
CG1 A:ILE257 4.1 21.2 1.0
CD1 A:TRP28 4.2 29.7 1.0
CA A:ILE257 4.3 20.7 1.0
O A:LYS256 4.7 23.9 1.0
CA A:TRP28 4.7 26.2 1.0
CB A:ILE257 4.7 19.6 1.0
NE1 A:TRP28 4.8 27.6 1.0
N A:ILE257 4.8 20.4 1.0
O A:SER27 4.8 35.1 1.0
O A:HOH809 4.9 33.0 1.0
CB A:GLU31 4.9 36.4 1.0
CG A:TRP28 4.9 24.9 1.0
C A:LYS256 5.0 21.0 1.0
CG2 A:ILE257 5.0 23.3 1.0

Sodium binding site 6 out of 6 in 5moz

Go back to Sodium Binding Sites List in 5moz
Sodium binding site 6 out of 6 in the Oxa-10 Avibactam Complex with Bound Iodide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Oxa-10 Avibactam Complex with Bound Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:34.5
occ:1.00
 O B:HOH572 2.3 49.0 1.0
OG B:SER172 2.7 22.5 1.0
O B:HOH515 2.8 24.3 1.0
O B:HOH591 3.0 31.5 0.5
O B:GLU168 3.5 18.7 1.0
CB B:SER172 3.5 17.8 1.0
C B:GLU168 3.9 17.7 1.0
CA B:PHE169 4.0 18.3 1.0
O B:PHE139 4.1 22.9 1.0
N B:PHE169 4.1 18.4 1.0
O B:HOH490 4.2 25.4 1.0
O B:HOH491 4.2 26.9 1.0
O B:HOH506 4.4 47.9 1.0
CD2 B:LEU178 4.4 22.2 1.0
O B:HOH591 4.4 27.8 0.5
CB B:GLU168 4.6 19.6 1.0
CB B:PHE169 4.9 19.5 1.0
C B:PHE169 4.9 17.0 1.0
O B:PHE169 4.9 17.7 1.0
CA B:SER172 4.9 16.8 1.0
CA B:GLU168 4.9 18.3 1.0
C B:PHE139 5.0 23.7 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: Mon Oct 7 22:44:16 2024

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