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Cobalt in PDB 5fat: Oxa-48 in Complex with Fpi-1602

Enzymatic activity of Oxa-48 in Complex with Fpi-1602

All present enzymatic activity of Oxa-48 in Complex with Fpi-1602:
3.5.2.6;

Protein crystallography data

The structure of Oxa-48 in Complex with Fpi-1602, PDB code: 5fat was solved by A.M.King, D.T.King, S.French, E.Brouillette, A.Asli, A.N.Alexander, M.Vuckovic, S.N.Maiti, T.R.Parr, E.D.Brown, F.Malouin, N.C.J.Strynadka, G.D.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.18 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.110, 75.750, 106.650, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.6

Other elements in 5fat:

The structure of Oxa-48 in Complex with Fpi-1602 also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms
Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Oxa-48 in Complex with Fpi-1602 (pdb code 5fat). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Oxa-48 in Complex with Fpi-1602, PDB code: 5fat:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 5fat

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Cobalt binding site 1 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co304

b:26.9
occ:1.00
 ND1 A:HIS34 2.0 33.1 1.0
O A:HOH539 2.1 36.1 1.0
O A:HOH449 2.2 36.2 1.0
OE2 A:GLU37 2.2 33.3 1.0
OE2 A:GLU256 2.5 29.0 1.0
CE1 A:HIS34 2.5 31.4 1.0
CD A:GLU37 3.1 45.0 1.0
CD A:GLU256 3.2 29.2 1.0
CG A:HIS34 3.3 29.6 1.0
OE1 A:GLU37 3.3 39.9 1.0
CD A:CD305 3.4 29.2 1.0
OE1 A:GLU256 3.8 34.0 1.0
NE2 A:HIS34 3.8 33.7 1.0
CB A:HIS34 4.0 29.2 1.0
CG A:GLU256 4.1 28.0 1.0
CB A:GLU256 4.1 28.1 1.0
CD2 A:HIS34 4.1 32.3 1.0
CA A:HIS34 4.2 31.7 1.0
O A:HOH547 4.4 53.4 1.0
CG A:GLU37 4.5 42.1 1.0
O A:HOH452 4.8 32.9 1.0
N A:HIS34 4.9 32.3 1.0

Cobalt binding site 2 out of 8 in 5fat

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Cobalt binding site 2 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co306

b:56.8
occ:1.00
 CD2 A:HIS90 3.1 38.2 1.0
ND1 B:HIS178 3.1 35.1 1.0
NE2 A:HIS90 3.6 38.3 1.0
O B:HOH427 3.9 42.1 1.0
CG A:HIS90 3.9 37.2 1.0
CE1 B:HIS178 4.0 35.0 1.0
CG B:HIS178 4.1 32.8 1.0
CA B:HIS178 4.2 27.7 1.0
CB B:HIS178 4.3 30.5 1.0
CE1 A:HIS90 4.5 38.5 1.0
CB A:HIS90 4.6 34.2 1.0
O B:HIS178 4.6 25.3 1.0
ND1 A:HIS90 4.7 40.4 1.0
C B:HIS178 4.9 26.3 1.0

Cobalt binding site 3 out of 8 in 5fat

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Cobalt binding site 3 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co301

b:65.6
occ:1.00
 OE1 B:GLU256 1.7 78.6 1.0
ND1 B:HIS34 2.4 53.9 1.0
CD B:GLU256 2.9 58.9 1.0
CE1 B:HIS34 3.2 56.3 1.0
CG B:HIS34 3.5 52.9 1.0
OE2 B:GLU256 3.6 64.6 1.0
CB B:HIS34 4.0 55.5 1.0
CG B:GLU256 4.0 56.6 1.0
CA B:HIS34 4.1 56.2 1.0
NE2 B:HIS38 4.2 42.1 1.0
CB B:GLU256 4.2 51.2 1.0
NE2 B:HIS34 4.4 48.9 1.0
CD2 B:HIS34 4.6 49.9 1.0
CD2 B:HIS38 4.7 56.5 1.0
CB B:GLU37 4.8 73.8 1.0
N B:HIS34 4.9 55.4 1.0
CG B:GLU37 4.9 86.7 1.0
O B:HOH426 5.0 47.3 1.0

Cobalt binding site 4 out of 8 in 5fat

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Cobalt binding site 4 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co302

b:58.4
occ:1.00
 CO B:CO303 3.5 63.3 1.0
OE1 B:GLU147 4.3 35.5 1.0
CE1 B:HIS140 4.9 38.1 1.0
O B:ASN146 4.9 35.1 1.0

Cobalt binding site 5 out of 8 in 5fat

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Cobalt binding site 5 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co303

b:63.3
occ:1.00
 CE1 B:HIS140 2.4 38.1 1.0
NE2 B:HIS140 2.8 34.8 1.0
CO B:CO302 3.5 58.4 1.0
ND1 B:HIS140 3.7 35.5 1.0
CD2 B:HIS140 4.2 32.4 1.0
OE1 B:GLU147 4.3 35.5 1.0
CG B:HIS140 4.6 36.9 1.0
O B:GLU147 4.9 34.4 1.0
CB B:GLU147 5.0 30.6 1.0

Cobalt binding site 6 out of 8 in 5fat

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Cobalt binding site 6 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co304

b:60.9
occ:1.00
 ND1 B:HIS90 2.8 38.5 1.0
ND1 A:HIS178 3.1 30.2 1.0
CE1 B:HIS90 3.2 39.6 1.0
CE1 A:HIS178 3.9 29.8 1.0
CG B:HIS90 3.9 33.9 1.0
CG A:HIS178 4.1 29.5 1.0
CA A:HIS178 4.2 27.5 1.0
CB A:HIS178 4.3 27.2 1.0
NE2 B:HIS90 4.4 42.9 1.0
CB B:HIS90 4.6 33.2 1.0
O A:HIS178 4.6 26.2 1.0
CD2 B:HIS90 4.8 41.6 1.0
C A:HIS178 4.8 28.0 1.0
CE2 A:TYR177 4.9 22.5 1.0
O A:TYR177 5.0 26.4 1.0

Cobalt binding site 7 out of 8 in 5fat

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Cobalt binding site 7 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co306

b:29.9
occ:1.00
 CO B:CO307 1.4 30.3 1.0
OE1 B:GLU147 2.3 35.5 1.0
OE2 B:GLU147 2.7 25.3 1.0
ND1 B:HIS140 2.8 35.5 1.0
CD B:GLU147 2.8 29.6 1.0
CE1 B:HIS140 3.6 38.1 1.0
CG B:HIS140 3.8 36.9 1.0
CB B:HIS140 4.0 30.8 1.0
CA B:HIS140 4.1 29.8 1.0
O B:HIS140 4.1 31.5 1.0
CG B:GLU147 4.3 30.0 1.0
OD1 B:ASP143 4.4 31.6 1.0
C B:HIS140 4.5 28.6 1.0
NE2 B:HIS140 4.8 34.8 1.0
CD2 B:HIS140 4.9 32.4 1.0
CB B:GLU147 4.9 30.6 1.0

Cobalt binding site 8 out of 8 in 5fat

Go back to Cobalt Binding Sites List in 5fat
Cobalt binding site 8 out of 8 in the Oxa-48 in Complex with Fpi-1602


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Oxa-48 in Complex with Fpi-1602 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co307

b:30.3
occ:1.00
 CO B:CO306 1.4 29.9 1.0
OE1 B:GLU147 2.3 35.5 1.0
OE2 B:GLU147 2.6 25.3 1.0
CD B:GLU147 2.7 29.6 1.0
ND1 B:HIS140 3.9 35.5 1.0
OD1 B:ASP143 4.2 31.6 1.0
CG B:GLU147 4.2 30.0 1.0
CE1 B:HIS140 4.5 38.1 1.0
O B:HIS140 4.9 31.5 1.0
CG B:HIS140 5.0 36.9 1.0

Reference:

A.M.King, D.T.King, S.French, E.Brouillette, A.Asli, J.A.Alexander, M.Vuckovic, S.N.Maiti, T.R.Parr, E.D.Brown, F.Malouin, N.C.Strynadka, G.D.Wright. Structural and Kinetic Characterization of Diazabicyclooctanes As Dual Inhibitors of Both Serine-Beta-Lactamases and Penicillin-Binding Proteins. Acs Chem.Biol. V. 11 864 2016.
ISSN: ESSN 1554-8937
PubMed: 26731698
DOI: 10.1021/ACSCHEMBIO.5B00944
Page generated: Tue Jul 30 17:53:00 2024

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