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Sodium in PDB 5vbx: Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli

Enzymatic activity of Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli

All present enzymatic activity of Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli:
2.7.8.7;

Protein crystallography data

The structure of Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli, PDB code: 5vbx was solved by A.M.Marcella, A.W.Barb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.60 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.376, 69.522, 59.894, 90.00, 109.55, 90.00
R / Rfree (%) 19.2 / 24.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli (pdb code 5vbx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli, PDB code: 5vbx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 5vbx

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Sodium binding site 1 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:34.8
occ:1.00
 OE1 A:GLU12 2.8 36.1 1.0
OH A:TYR117 2.9 22.9 1.0
N C:HIS116 2.9 19.2 1.0
CB C:GLU114 3.2 23.8 1.0
CD2 C:HIS116 3.3 32.0 1.0
N C:ARG115 3.3 22.1 1.0
CE2 A:TYR117 3.4 24.0 1.0
CD A:GLU12 3.4 34.6 1.0
CB C:HIS116 3.5 19.4 1.0
CZ A:TYR117 3.6 24.5 1.0
CB A:GLU12 3.7 19.7 1.0
CG A:GLU12 3.7 23.6 1.0
CG C:HIS116 3.7 31.7 1.0
CA C:HIS116 3.7 20.9 1.0
C C:ARG115 3.8 28.7 1.0
CA C:ARG115 3.8 26.1 1.0
C C:GLU114 3.9 25.1 1.0
CB C:ARG115 3.9 29.0 1.0
CA C:GLU114 4.1 23.8 1.0
CG C:GLU114 4.1 34.5 1.0
OE2 C:GLU114 4.2 48.2 1.0
N C:TYR117 4.3 18.4 1.0
OE2 A:GLU12 4.3 44.9 1.0
C C:HIS116 4.5 20.5 1.0
NE2 C:HIS116 4.5 35.2 1.0
CD C:GLU114 4.5 40.2 1.0
CD2 A:TYR117 4.6 23.3 1.0
O C:GLU114 4.6 25.4 1.0
CD2 C:TYR117 4.9 17.6 1.0
CA A:GLU12 4.9 19.2 1.0
CE1 A:TYR117 4.9 24.4 1.0
CG C:ARG115 4.9 37.4 1.0
ND1 C:HIS116 5.0 33.4 1.0
O C:ARG115 5.0 25.9 1.0

Sodium binding site 2 out of 9 in 5vbx

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Sodium binding site 2 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:44.0
occ:1.00
 O A:GLY24 2.4 40.6 1.0
OG A:SER23 2.8 48.0 1.0
N A:LEU27 3.1 31.3 1.0
C A:GLY24 3.2 40.8 1.0
C A:SER23 3.3 45.3 1.0
O A:SER23 3.4 48.8 1.0
N A:ARG26 3.4 35.9 1.0
N A:GLY24 3.5 43.3 1.0
O A:VAL19 3.6 34.5 1.0
CB A:LEU27 3.7 31.6 1.0
CB A:ARG26 3.8 32.5 1.0
CB A:SER23 3.8 44.4 1.0
CA A:ILE20 3.8 38.4 1.0
CA A:ARG26 3.9 33.2 1.0
CA A:GLY24 3.9 41.1 1.0
CG1 A:VAL19 3.9 32.8 1.0
C A:ARG26 3.9 32.9 1.0
CA A:LEU27 4.0 35.1 1.0
CA A:SER23 4.0 47.3 1.0
C A:ASP25 4.0 34.4 1.0
N A:ASP25 4.1 40.0 1.0
C A:VAL19 4.1 35.6 1.0
N A:ILE20 4.2 33.5 1.0
N A:SER23 4.4 46.8 1.0
CG1 A:ILE20 4.4 33.9 1.0
CA A:ASP25 4.4 39.7 1.0
O A:ILE20 4.5 43.3 1.0
O A:HOH346 4.6 45.2 1.0
C A:ILE20 4.6 43.3 1.0
CB A:ILE20 4.7 34.7 1.0
O A:ASP25 4.8 37.2 1.0
N A:ALA28 4.9 28.8 1.0

Sodium binding site 3 out of 9 in 5vbx

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Sodium binding site 3 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:32.0
occ:1.00
 N A:HIS116 2.8 20.1 1.0
OH B:TYR117 2.8 20.8 1.0
OE1 B:GLU12 2.9 26.2 1.0
N A:ARG115 3.2 23.6 1.0
CD2 A:HIS116 3.3 35.2 1.0
CB A:HIS116 3.4 25.2 1.0
CB A:GLU114 3.5 18.5 1.0
CE1 B:TYR117 3.5 21.7 1.0
CD B:GLU12 3.6 31.6 1.0
CG A:HIS116 3.6 29.7 1.0
CA A:HIS116 3.6 23.5 1.0
CZ B:TYR117 3.6 20.5 1.0
C A:ARG115 3.7 24.6 1.0
CA A:ARG115 3.7 27.8 1.0
CB A:ARG115 3.9 33.2 1.0
C A:GLU114 3.9 25.4 1.0
CB B:GLU12 4.0 19.7 1.0
CG A:ARG115 4.0 43.4 1.0
CG B:GLU12 4.0 28.3 1.0
N A:TYR117 4.3 18.6 1.0
CA A:GLU114 4.3 21.3 1.0
OE1 A:GLU114 4.3 37.4 1.0
C A:HIS116 4.4 19.3 1.0
OE2 B:GLU12 4.4 36.7 1.0
NE2 A:HIS116 4.4 38.3 1.0
CG A:GLU114 4.5 27.5 1.0
NE A:ARG115 4.5 58.4 1.0
O A:GLU114 4.7 25.4 1.0
CD A:GLU114 4.7 33.8 1.0
ND1 A:HIS116 4.8 37.5 1.0
CD1 A:TYR117 4.8 23.9 1.0
CD1 B:TYR117 4.8 20.3 1.0
O A:ARG115 4.8 21.6 1.0
CD A:ARG115 4.9 51.4 1.0
CE2 B:TYR117 4.9 18.6 1.0
O B:HOH311 5.0 35.1 1.0

Sodium binding site 4 out of 9 in 5vbx

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Sodium binding site 4 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:35.9
occ:1.00
 OH C:TYR117 2.6 22.7 1.0
N B:HIS116 3.0 21.0 1.0
OE2 C:GLU12 3.0 39.3 1.0
ND1 B:HIS116 3.0 39.6 1.0
N B:ARG115 3.4 23.0 1.0
CB B:HIS116 3.4 29.9 1.0
CE1 C:TYR117 3.4 18.8 1.0
CB B:GLU114 3.4 27.4 1.0
CZ C:TYR117 3.5 21.7 1.0
CD C:GLU12 3.6 35.6 1.0
CG B:HIS116 3.6 36.2 1.0
CA B:HIS116 3.7 25.5 1.0
CB C:GLU12 3.8 24.2 1.0
CB B:ARG115 3.8 29.6 1.0
CG C:GLU12 3.9 30.6 1.0
CA B:ARG115 3.9 24.1 1.0
C B:ARG115 3.9 23.2 1.0
C B:GLU114 4.1 27.4 1.0
OE2 B:GLU114 4.1 34.5 1.0
CE1 B:HIS116 4.2 43.2 1.0
CG B:GLU114 4.3 24.9 1.0
N B:TYR117 4.3 21.8 1.0
CA B:GLU114 4.4 26.5 1.0
OE1 C:GLU12 4.4 37.2 1.0
C B:HIS116 4.5 18.7 1.0
CD B:GLU114 4.5 30.7 1.0
CG B:ARG115 4.5 35.0 1.0
O C:HOH310 4.7 44.9 1.0
CD1 C:TYR117 4.7 17.9 1.0
CD2 B:TYR117 4.7 19.8 1.0
CE2 C:TYR117 4.8 20.2 1.0
CD2 B:HIS116 4.9 37.2 1.0
NE B:ARG115 4.9 39.8 1.0
O B:GLU114 4.9 24.3 1.0

Sodium binding site 5 out of 9 in 5vbx

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Sodium binding site 5 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na205

b:35.1
occ:1.00
 N C:LEU89 3.0 23.1 1.0
O C:MET107 3.2 36.8 1.0
CA C:ARG88 3.4 25.7 1.0
NE C:ARG88 3.7 47.9 1.0
C C:ARG88 3.7 22.7 1.0
CB C:ARG88 3.7 26.9 1.0
CB C:MET107 3.7 23.6 1.0
CD C:ARG88 3.8 37.4 1.0
CA C:LEU89 4.0 21.8 1.0
O C:LEU89 4.0 25.4 1.0
C C:MET107 4.1 30.3 1.0
CB C:LEU89 4.1 22.1 1.0
O C:HOH320 4.2 40.8 1.0
CE C:MET107 4.3 32.8 1.0
CG2 C:VAL109 4.3 17.6 1.0
CG C:LEU89 4.4 23.7 1.0
CG C:ARG88 4.4 29.8 1.0
CA C:MET107 4.4 22.7 1.0
O C:PRO87 4.5 23.8 1.0
C C:LEU89 4.5 24.3 1.0
N C:ARG88 4.7 25.1 1.0
CG C:MET107 4.8 27.6 1.0
CZ C:ARG88 4.9 59.7 1.0
N C:MET107 4.9 23.1 1.0
O C:ARG88 4.9 23.5 1.0
SD C:MET107 5.0 33.4 1.0

Sodium binding site 6 out of 9 in 5vbx

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Sodium binding site 6 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na206

b:39.3
occ:1.00
 O C:GLY24 2.5 36.7 1.0
OG C:SER23 2.8 33.6 1.0
N C:LEU27 2.9 22.7 1.0
CB C:LEU27 3.4 21.2 1.0
N C:ARG26 3.4 24.9 1.0
C C:GLY24 3.4 33.3 1.0
C C:SER23 3.5 31.4 1.0
O C:SER23 3.5 32.3 1.0
O C:VAL19 3.6 32.0 1.0
O C:HOH317 3.7 39.4 1.0
CA C:LEU27 3.7 21.7 1.0
N C:GLY24 3.8 31.7 1.0
C C:ARG26 3.8 23.4 1.0
CB C:ARG26 3.8 25.6 1.0
CG1 C:VAL19 3.9 27.9 1.0
CB C:SER23 3.9 34.8 1.0
CA C:ARG26 3.9 24.5 1.0
CA C:ILE20 3.9 34.2 1.0
C C:ASP25 4.1 30.2 1.0
C C:VAL19 4.1 27.0 1.0
O C:HOH316 4.1 40.4 1.0
CA C:SER23 4.1 30.0 1.0
CA C:GLY24 4.2 30.8 1.0
N C:ILE20 4.2 25.7 1.0
N C:ASP25 4.3 33.7 1.0
N C:SER23 4.5 31.3 1.0
CA C:ASP25 4.5 33.7 1.0
CG1 C:ILE20 4.5 31.6 1.0
O C:ILE20 4.7 33.9 1.0
C C:ILE20 4.7 37.1 1.0
CB C:ILE20 4.8 34.5 1.0
CG C:LEU27 4.8 26.1 1.0
N C:ALA28 4.8 23.8 1.0
O C:ASP25 4.8 27.8 1.0
C C:LEU27 4.9 22.5 1.0
CB C:VAL19 5.0 26.7 1.0

Sodium binding site 7 out of 9 in 5vbx

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Sodium binding site 7 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na207

b:37.6
occ:1.00
 N C:ASN81 3.0 21.7 1.0
O C:HOH307 3.1 26.9 1.0
NA C:NA209 3.6 45.8 1.0
CB C:ASN81 3.7 26.0 1.0
CA C:ASN81 3.8 23.5 1.0
O C:ASN81 3.8 26.6 1.0
ND2 C:ASN81 3.9 30.6 1.0
CA C:PHE80 3.9 21.5 1.0
C C:PHE80 3.9 24.8 1.0
CB C:PHE80 4.0 22.6 1.0
CG C:ASN81 4.1 28.5 1.0
C C:ASN81 4.3 27.3 1.0
O C:HOH347 4.6 32.8 1.0
O C:HOH340 4.7 26.4 1.0

Sodium binding site 8 out of 9 in 5vbx

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Sodium binding site 8 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


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 Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na208

b:36.3
occ:1.00
 O C:HOH314 2.7 46.0 1.0
N C:ALA14 2.8 27.5 1.0
O C:HIS116 2.9 24.9 1.0
O C:HOH328 2.9 35.9 1.0
CB C:ALA14 3.2 27.3 1.0
CA C:HIS116 3.5 20.9 1.0
N C:ILE13 3.5 23.8 1.0
CG C:GLU12 3.5 30.6 1.0
CB C:HIS116 3.5 19.4 1.0
C C:HIS116 3.6 20.5 1.0
CA C:ALA14 3.6 25.1 1.0
ND1 C:HIS116 3.7 33.4 1.0
C C:ILE13 3.8 27.3 1.0
CA C:ILE13 3.9 22.0 1.0
CB C:ILE13 4.0 23.8 1.0
C C:GLU12 4.1 23.6 1.0
CG C:HIS116 4.1 31.7 1.0
OE1 C:GLU12 4.2 37.2 1.0
CD C:GLU12 4.4 35.6 1.0
CA C:GLU12 4.4 23.0 1.0
CB C:GLU12 4.6 24.2 1.0
O C:ARG115 4.8 25.9 1.0
C C:ALA14 4.8 24.4 1.0
O C:GLU12 4.8 19.5 1.0
N C:HIS116 4.8 19.2 1.0
CG2 C:ILE13 4.8 23.5 1.0
N C:ARG15 4.9 20.4 1.0
N C:TYR117 4.9 18.4 1.0
CE1 C:HIS116 4.9 36.6 1.0
NH1 C:ARG115 5.0 44.0 1.0
O C:ILE13 5.0 32.7 1.0

Sodium binding site 9 out of 9 in 5vbx

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Sodium binding site 9 out of 9 in the Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Holo-[Acyl-Carrier-Protein] Synthase (Acps) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na209

b:45.8
occ:1.00
 NH2 C:ARG53 3.4 42.0 1.0
O C:HOH359 3.4 53.7 1.0
NA C:NA207 3.6 37.6 1.0
NH1 C:ARG53 3.9 31.8 1.0
CZ C:ARG53 4.1 33.1 1.0
O C:HOH347 4.2 32.8 1.0
O C:HOH340 4.3 26.4 1.0
CE1 C:PHE49 4.4 21.9 1.0
ND2 C:ASN81 4.6 30.6 1.0
CD1 C:ILE39 4.8 33.2 1.0

Reference:

A.M.Marcella, S.J.Culbertson, M.A.Shogren-Knaak, A.W.Barb. Structure, High Affinity, and Negative Cooperativity of the Escherichia Coli Holo-(Acyl Carrier Protein):Holo-(Acyl Carrier Protein) Synthase Complex. J. Mol. Biol. V. 429 3763 2017.
ISSN: ESSN 1089-8638
PubMed: 29054754
DOI: 10.1016/J.JMB.2017.10.015
Page generated: Tue Oct 8 00:48:02 2024

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