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Sodium in PDB 7l00: Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor

Enzymatic activity of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor:
1.13.12.16; 1.3.1.9;

Protein crystallography data

The structure of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor, PDB code: 7l00 was solved by A.Akhtar, B.D.Santarsiero, K.E.Hevener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.69 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.9, 66.15, 101.78, 90, 90.09, 90
R / Rfree (%) 14.4 / 18.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor (pdb code 7l00). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor, PDB code: 7l00:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7l00

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Sodium binding site 1 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:40.4
occ:1.00
O A:VAL283 2.7 28.0 1.0
O A:LEU210 2.8 29.8 1.0
O A:ALA280 2.8 20.1 1.0
O A:ALA212 3.0 22.6 1.0
O A:VAL209 3.1 23.2 1.0
O A:ALA281 3.2 23.3 1.0
C A:LEU210 3.4 27.4 1.0
C A:ALA281 3.4 21.4 1.0
CA A:ALA281 3.7 19.1 1.0
N A:ALA212 3.7 22.3 1.0
C A:VAL283 3.8 25.7 1.0
C A:ALA280 3.8 18.4 1.0
O A:HOH591 4.0 44.7 1.0
C A:ALA212 4.0 21.9 1.0
N A:VAL283 4.0 20.6 1.0
CA A:LEU210 4.1 26.2 1.0
N A:LYS211 4.2 26.4 1.0
CA A:ALA212 4.2 20.8 1.0
C A:LYS211 4.2 24.1 1.0
C A:VAL209 4.2 23.5 1.0
N A:MET282 4.2 20.3 1.0
N A:ALA281 4.2 19.1 1.0
CB A:ALA212 4.3 19.5 1.0
CA A:VAL283 4.4 22.0 1.0
CA A:LYS211 4.4 27.2 1.0
N A:LEU210 4.7 23.4 1.0
C A:MET282 4.7 21.8 1.0
CG A:LYS284 4.7 36.2 1.0
CB A:VAL283 4.8 21.7 1.0
N A:LYS284 4.9 27.3 1.0
CA A:MET282 4.9 21.4 1.0
O A:LYS211 5.0 24.0 1.0
CB A:ALA281 5.0 18.9 1.0
NZ A:LYS284 5.0 44.0 1.0

Sodium binding site 2 out of 8 in 7l00

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Sodium binding site 2 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:37.8
occ:1.00
OE2 A:GLU136 2.6 33.6 1.0
O A:GLY141 2.7 21.8 1.0
N12 A:XCJ402 2.7 22.8 1.0
O A:HIS143 3.1 35.3 1.0
CD A:GLU136 3.4 30.4 1.0
C1' A:FMN401 3.4 21.8 1.0
OE1 A:GLU136 3.4 31.1 1.0
N A:HIS143 3.5 24.6 1.0
C14 A:XCJ402 3.5 22.3 1.0
C A:HIS143 3.6 29.9 1.0
C13 A:XCJ402 3.6 23.8 1.0
C10 A:XCJ402 3.7 24.2 1.0
N09 A:XCJ402 3.7 24.8 1.0
C A:GLY142 3.8 22.4 1.0
C A:GLY141 3.8 21.5 1.0
N10 A:FMN401 3.9 22.4 1.0
C16 A:XCJ402 4.0 27.2 1.0
CA A:GLY142 4.0 21.9 1.0
C15 A:XCJ402 4.1 24.5 1.0
CA A:HIS143 4.1 27.2 1.0
N A:ILE144 4.3 26.8 1.0
N A:GLY142 4.4 22.5 1.0
CG2 A:ILE144 4.4 28.2 1.0
CA A:ILE144 4.4 25.2 1.0
C9A A:FMN401 4.4 21.5 1.0
C10 A:FMN401 4.5 23.8 1.0
O A:GLY142 4.5 23.1 1.0
N1 A:FMN401 4.6 24.1 1.0
C9 A:FMN401 4.6 21.4 1.0
O25 A:XCJ402 4.8 26.9 1.0
CB A:HIS143 4.8 32.1 1.0
C2' A:FMN401 4.8 23.1 1.0
CG A:GLU136 4.8 26.6 1.0
O A:HOH556 4.8 26.6 1.0
C4' A:FMN401 5.0 21.3 1.0

Sodium binding site 3 out of 8 in 7l00

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Sodium binding site 3 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:31.4
occ:1.00
O B:GLY141 2.6 19.9 1.0
O B:HIS143 2.7 33.1 1.0
N12 B:XCJ402 2.7 20.1 1.0
OE1 B:GLU136 2.8 31.7 1.0
C1' B:FMN401 3.3 16.8 1.0
OE2 B:GLU136 3.3 28.1 1.0
CD B:GLU136 3.4 27.7 1.0
N B:HIS143 3.5 21.0 1.0
C B:HIS143 3.5 26.4 1.0
C14 B:XCJ402 3.5 21.7 1.0
C13 B:XCJ402 3.6 21.9 1.0
N09 B:XCJ402 3.6 21.2 1.0
C10 B:XCJ402 3.7 21.1 1.0
C B:GLY141 3.8 18.1 1.0
N10 B:FMN401 3.8 18.0 1.0
C B:GLY142 3.8 19.7 1.0
CA B:GLY142 4.0 19.2 1.0
C16 B:XCJ402 4.0 24.6 1.0
CA B:HIS143 4.1 24.6 1.0
C15 B:XCJ402 4.2 22.8 1.0
N B:GLY142 4.3 18.6 1.0
C9A B:FMN401 4.3 17.9 1.0
C10 B:FMN401 4.4 17.7 1.0
C9 B:FMN401 4.4 17.0 1.0
N B:ILE144 4.5 21.8 1.0
O B:GLY142 4.5 19.9 1.0
N1 B:FMN401 4.5 18.5 1.0
CG2 B:ILE144 4.5 21.7 1.0
CA B:ILE144 4.6 20.8 1.0
C2' B:FMN401 4.7 16.5 1.0
CB B:HIS143 4.8 29.8 1.0
O25 B:XCJ402 4.8 22.9 1.0
CG B:GLU136 4.9 23.7 1.0
C4' B:FMN401 4.9 16.9 1.0
O B:HOH589 5.0 23.5 1.0
CA B:GLY141 5.0 17.2 1.0

Sodium binding site 4 out of 8 in 7l00

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Sodium binding site 4 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:32.0
occ:1.00
O B:VAL283 2.8 24.3 1.0
O B:ALA280 2.8 17.0 1.0
O B:LEU210 2.8 21.8 1.0
O B:ALA212 3.0 21.7 1.0
O B:VAL209 3.1 19.3 1.0
O B:ALA281 3.2 19.6 1.0
O B:HOH608 3.2 34.5 1.0
C B:LEU210 3.5 21.7 1.0
C B:ALA281 3.5 19.1 1.0
CA B:ALA281 3.7 17.9 1.0
N B:ALA212 3.7 19.8 1.0
C B:ALA280 3.8 16.8 1.0
C B:VAL283 3.9 22.7 1.0
O B:HOH556 3.9 31.7 1.0
C B:ALA212 3.9 20.9 1.0
CA B:LEU210 4.0 20.7 1.0
N B:VAL283 4.0 19.2 1.0
O B:HOH536 4.0 42.0 1.0
CA B:ALA212 4.2 20.0 1.0
C B:VAL209 4.2 18.8 1.0
CB B:ALA212 4.2 20.9 1.0
N B:ALA281 4.2 17.5 1.0
C B:LYS211 4.3 22.1 1.0
N B:LYS211 4.3 21.1 1.0
N B:MET282 4.4 19.7 1.0
CA B:VAL283 4.4 20.2 1.0
N B:LEU210 4.6 19.0 1.0
CA B:LYS211 4.7 23.8 1.0
C B:MET282 4.7 20.1 1.0
CB B:VAL283 4.8 19.7 1.0
CA B:MET282 5.0 20.0 1.0
CD B:LYS284 5.0 34.7 1.0
N B:LYS284 5.0 23.8 1.0

Sodium binding site 5 out of 8 in 7l00

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Sodium binding site 5 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:33.7
occ:1.00
O C:HIS143 2.5 35.7 1.0
N12 C:XCJ402 2.7 24.9 1.0
O C:GLY141 2.7 22.3 1.0
OE1 C:GLU136 2.8 38.3 1.0
C1' C:FMN401 3.3 21.1 1.0
OE2 C:GLU136 3.3 33.8 1.0
C14 C:XCJ402 3.4 27.7 1.0
CD C:GLU136 3.4 33.7 1.0
C C:HIS143 3.5 31.5 1.0
N C:HIS143 3.5 25.6 1.0
C13 C:XCJ402 3.6 28.1 1.0
C10 C:XCJ402 3.7 25.5 1.0
N09 C:XCJ402 3.7 26.2 1.0
N10 C:FMN401 3.7 22.5 1.0
C C:GLY142 3.8 23.8 1.0
C C:GLY141 3.8 22.4 1.0
C16 C:XCJ402 4.0 31.5 1.0
CA C:GLY142 4.0 22.9 1.0
CA C:HIS143 4.0 30.1 1.0
C15 C:XCJ402 4.1 29.3 1.0
C9A C:FMN401 4.3 22.5 1.0
C10 C:FMN401 4.3 23.4 1.0
N C:GLY142 4.4 23.9 1.0
O C:GLY142 4.4 24.5 1.0
N1 C:FMN401 4.5 24.3 1.0
C9 C:FMN401 4.5 22.5 1.0
N C:ILE144 4.5 27.3 1.0
CB C:HIS143 4.6 34.9 1.0
CG2 C:ILE144 4.7 27.7 1.0
CA C:ILE144 4.7 26.6 1.0
C2' C:FMN401 4.7 21.3 1.0
O25 C:XCJ402 4.8 30.1 1.0
C4' C:FMN401 4.9 20.6 1.0
CG C:GLU136 4.9 27.8 1.0

Sodium binding site 6 out of 8 in 7l00

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Sodium binding site 6 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:34.8
occ:1.00
O C:LEU210 2.8 25.4 1.0
O C:VAL283 2.9 25.8 1.0
O C:ALA280 2.9 19.6 1.0
O C:VAL209 3.0 23.6 1.0
O C:ALA212 3.0 23.4 1.0
O C:ALA281 3.2 21.0 1.0
C C:LEU210 3.4 25.4 1.0
C C:ALA281 3.5 20.6 1.0
CA C:ALA281 3.7 19.3 1.0
N C:ALA212 3.8 24.9 1.0
C C:ALA280 3.9 19.3 1.0
CA C:LEU210 3.9 24.4 1.0
O C:HOH578 3.9 32.5 1.0
C C:VAL283 3.9 23.9 1.0
C C:ALA212 4.0 23.2 1.0
N C:VAL283 4.1 19.1 1.0
C C:VAL209 4.1 23.4 1.0
CA C:ALA212 4.2 23.3 1.0
N C:ALA281 4.3 19.1 1.0
CB C:ALA212 4.3 22.5 1.0
N C:LYS211 4.3 26.4 1.0
C C:LYS211 4.3 28.1 1.0
N C:MET282 4.4 19.3 1.0
N C:LEU210 4.5 22.5 1.0
CA C:VAL283 4.5 20.8 1.0
CA C:LYS211 4.7 29.0 1.0
C C:MET282 4.8 19.4 1.0
CB C:VAL283 4.9 22.0 1.0
CB C:ALA281 5.0 18.9 1.0
O C:LYS211 5.0 28.9 1.0

Sodium binding site 7 out of 8 in 7l00

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Sodium binding site 7 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:41.6
occ:1.00
O D:LEU210 2.7 34.3 1.0
O D:ALA212 2.8 29.6 1.0
O D:ALA280 2.9 24.8 1.0
O D:VAL283 2.9 30.4 1.0
O D:VAL209 3.1 28.8 1.0
O D:HOH591 3.2 47.1 1.0
O D:ALA281 3.2 27.2 1.0
C D:LEU210 3.4 32.2 1.0
C D:ALA281 3.5 25.5 1.0
O D:HOH509 3.6 53.5 1.0
N D:ALA212 3.6 31.6 1.0
CA D:ALA281 3.7 23.4 1.0
C D:ALA212 3.8 30.5 1.0
C D:ALA280 3.9 23.1 1.0
C D:VAL283 4.0 29.5 1.0
O D:HOH564 4.1 45.9 1.0
CA D:ALA212 4.1 30.2 1.0
CA D:LEU210 4.1 30.7 1.0
C D:LYS211 4.1 33.2 1.0
N D:VAL283 4.2 26.0 1.0
N D:LYS211 4.2 32.6 1.0
CB D:ALA212 4.2 29.9 1.0
C D:VAL209 4.3 28.6 1.0
N D:ALA281 4.3 22.6 1.0
N D:MET282 4.4 24.6 1.0
CA D:LYS211 4.4 35.8 1.0
CA D:VAL283 4.6 27.0 1.0
N D:LEU210 4.7 29.3 1.0
C D:MET282 4.9 26.1 1.0
O D:LYS211 4.9 33.8 1.0
CB D:VAL283 5.0 27.1 1.0
CD D:LYS284 5.0 42.1 1.0

Sodium binding site 8 out of 8 in 7l00

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Sodium binding site 8 out of 8 in the Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:34.2
occ:1.00
O D:HIS143 2.3 26.8 0.3
N12 D:XCJ402 2.7 23.8 1.0
O D:GLY141 2.7 22.7 1.0
OE2 D:GLU136 2.8 30.8 1.0
C D:HIS143 3.3 25.1 0.3
N D:HIS143 3.4 23.0 0.7
O D:HIS143 3.4 23.9 0.7
C1' D:FMN401 3.4 21.6 1.0
OE1 D:GLU136 3.4 27.0 1.0
CD D:GLU136 3.5 26.1 1.0
N D:HIS143 3.5 23.5 0.3
C14 D:XCJ402 3.6 22.5 1.0
C D:HIS143 3.6 24.0 0.7
C10 D:XCJ402 3.6 24.9 1.0
C13 D:XCJ402 3.6 23.7 1.0
N09 D:XCJ402 3.6 24.6 1.0
C D:GLY142 3.7 22.8 1.0
C D:GLY141 3.8 21.6 1.0
N10 D:FMN401 3.9 23.3 1.0
CA D:GLY142 3.9 22.7 1.0
CA D:HIS143 4.0 24.9 0.3
C16 D:XCJ402 4.0 25.1 1.0
CA D:HIS143 4.0 24.5 0.7
C15 D:XCJ402 4.1 23.6 1.0
N D:ILE144 4.2 23.4 1.0
N D:GLY142 4.3 22.1 1.0
O D:GLY142 4.4 22.4 1.0
CA D:ILE144 4.4 23.5 1.0
C9A D:FMN401 4.4 24.1 1.0
C10 D:FMN401 4.4 23.6 1.0
CG2 D:ILE144 4.5 25.0 1.0
N1 D:FMN401 4.5 22.7 1.0
C9 D:FMN401 4.6 23.4 1.0
CB D:HIS143 4.6 26.4 0.3
O D:HOH510 4.7 25.2 1.0
CB D:HIS143 4.8 26.8 0.7
O25 D:XCJ402 4.8 23.5 1.0
C2' D:FMN401 4.9 21.6 1.0
CG D:GLU136 4.9 20.8 1.0

Reference:

J.A.Jones, K.E.Hevener, L.Alghanim, A.Akhtar, B.D.Santarsiero. Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor To Be Published.
Page generated: Fri Dec 24 09:55:57 2021

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