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Sodium in PDB 4a22: Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate

Enzymatic activity of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate:
4.1.2.13;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, PDB code: 4a22 was solved by M.Coincon, M.De La Paz Santangelo, P.M.Gest, M.E.Guerin, H.Pham, G.Ryan, S.E.Puckett, J.S.Spencer, M.Gonzalez-Juarrero, R.Daher, A.J.Lenaerts, D.Schnappinger, M.Therisod, S.Ehrt, M.Jackson, J.Sygusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.42 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 335.386, 42.977, 102.601, 90.00, 99.39, 90.00
R / Rfree (%) 17.9 / 22.1

Other elements in 4a22:

The structure of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate (pdb code 4a22). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate, PDB code: 4a22:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4a22

Go back to Sodium Binding Sites List in 4a22
Sodium binding site 1 out of 6 in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1345

b:33.6
occ:1.00
 O17 A:TD41344 2.5 21.3 0.6
O A:GLY213 2.6 39.5 1.0
O A:SER255 2.7 26.2 1.0
O A:VAL211 2.8 36.4 1.0
O3 A:SO41349 3.0 28.2 0.4
O A:GLY253 3.1 31.8 1.0
O A:HOH2193 3.2 48.9 1.0
HB2 A:SER255 3.3 26.4 1.0
HA2 A:GLY253 3.4 31.4 1.0
C A:GLY253 3.4 37.5 1.0
H A:GLY213 3.5 38.5 1.0
HA3 A:GLY253 3.5 31.4 1.0
CA A:GLY253 3.6 26.3 1.0
C A:SER255 3.7 33.0 1.0
C A:GLY213 3.7 42.5 1.0
H A:SER255 3.7 38.9 1.0
N A:GLY213 3.8 32.2 1.0
N A:SER255 3.8 32.5 1.0
O A:HOH2178 3.8 28.3 1.0
HA A:HIS212 3.9 45.1 1.0
C A:VAL211 4.0 37.5 1.0
O4 A:SO41349 4.1 22.6 0.4
P16 A:TD41344 4.1 22.5 0.6
CA A:SER255 4.1 29.3 1.0
S A:SO41349 4.1 23.8 0.4
CB A:SER255 4.1 22.1 1.0
N A:GLY254 4.2 31.6 1.0
HA A:VAL214 4.3 52.2 1.0
C A:GLY254 4.3 34.6 1.0
CA A:GLY213 4.3 37.4 1.0
C A:HIS212 4.3 45.6 1.0
HG A:SER257 4.4 44.9 1.0
HG23 A:VAL214 4.4 50.3 1.0
H A:VAL211 4.5 42.5 1.0
HG21 A:VAL214 4.5 50.3 1.0
CA A:HIS212 4.5 37.7 1.0
O19 A:TD41344 4.6 21.3 0.6
H A:GLY254 4.6 37.8 1.0
O A:HOH2195 4.7 45.5 1.0
HB3 A:SER255 4.7 26.4 1.0
O15 A:TD41344 4.7 27.8 0.6
N A:VAL214 4.7 33.5 1.0
N A:HIS212 4.7 32.9 1.0
O1 A:SO41349 4.8 28.5 0.4
CA A:GLY254 4.8 27.6 1.0
HA3 A:GLY256 4.8 27.8 1.0
HG22 A:VAL220 4.8 54.9 1.0
HE2 A:TYR215 4.8 60.4 1.0
N A:GLY256 4.8 26.3 1.0
HA2 A:GLY213 4.9 44.8 1.0
HB A:VAL211 4.9 39.7 1.0
O A:GLY254 4.9 29.3 1.0
CG2 A:VAL214 4.9 42.0 1.0
CA A:VAL214 5.0 43.6 1.0

Sodium binding site 2 out of 6 in 4a22

Go back to Sodium Binding Sites List in 4a22
Sodium binding site 2 out of 6 in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1346

b:31.8
occ:1.00
 HE2 A:HIS93 2.4 27.7 1.0
HD22 A:ASN274 2.5 29.3 1.0
HZ3 A:LYS272 2.9 24.2 1.0
OD1 A:ASP95 2.9 33.7 1.0
HZ2 A:LYS272 2.9 24.2 1.0
OE2 A:GLU159 2.9 38.0 1.0
HA A:ASP95 3.1 25.9 1.0
HE1 A:HIS252 3.2 47.6 1.0
NE2 A:HIS93 3.2 23.2 1.0
OE1 A:GLU159 3.2 27.4 1.0
ND2 A:ASN274 3.3 24.5 1.0
NZ A:LYS272 3.3 20.3 1.0
CD A:GLU159 3.4 36.1 1.0
HE2 A:HIS252 3.4 30.0 1.0
HD2 A:HIS93 3.4 24.0 1.0
HB2 A:MET129 3.4 18.5 1.0
SD A:MET129 3.5 29.6 1.0
OE1 A:GLN51 3.5 24.2 1.0
CE1 A:HIS252 3.6 39.8 1.0
HZ1 A:LYS272 3.6 24.2 1.0
HD21 A:ASN274 3.6 29.3 1.0
NE2 A:HIS252 3.7 25.1 1.0
CD2 A:HIS93 3.7 20.1 1.0
CG A:ASP95 3.8 38.8 1.0
HE22 A:GLN51 3.9 31.5 1.0
HO01 A:TD41344 3.9 26.9 0.6
CA A:ASP95 4.0 21.7 1.0
CB A:MET129 4.1 15.5 1.0
CG A:ASN274 4.2 28.5 1.0
HG12 A:VAL250 4.2 23.9 1.0
HB3 A:MET129 4.2 18.5 1.0
CD A:GLN51 4.3 27.0 1.0
OD1 A:ASN274 4.3 29.3 1.0
CB A:ASP95 4.4 23.1 1.0
CG A:MET129 4.4 19.1 1.0
CE1 A:HIS93 4.4 18.9 1.0
NE2 A:GLN51 4.4 26.4 1.0
H A:HIS96 4.5 31.3 1.0
HB2 A:ASP95 4.5 27.7 1.0
OD2 A:ASP95 4.6 35.4 1.0
HE1 A:MET129 4.6 27.2 1.0
HG3 A:MET129 4.6 22.8 1.0
O A:THR94 4.6 17.8 1.0
ND1 A:HIS252 4.6 35.7 1.0
CE A:LYS272 4.6 19.7 1.0
HE3 A:LYS272 4.6 23.6 1.0
CE A:MET129 4.6 22.8 1.0
O01 A:TD41344 4.7 22.4 0.6
HE2 A:MET129 4.7 27.2 1.0
HE1 A:HIS93 4.7 22.6 1.0
N A:HIS96 4.7 26.2 1.0
C A:ASP95 4.7 25.6 1.0
CG A:GLU159 4.8 21.8 1.0
CD2 A:HIS252 4.8 25.0 1.0
HB3 A:GLU159 4.9 18.7 1.0
HG2 A:GLU159 5.0 26.0 1.0
CG A:HIS93 5.0 17.9 1.0

Sodium binding site 3 out of 6 in 4a22

Go back to Sodium Binding Sites List in 4a22
Sodium binding site 3 out of 6 in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1347

b:25.2
occ:1.00
 HB2 A:CYS97 2.7 23.0 1.0
HG1 A:THR94 2.7 21.4 1.0
H A:MET129 2.7 12.9 1.0
OG1 A:THR94 2.7 17.9 1.0
O A:ASP95 2.7 37.2 1.0
O A:MET129 2.9 20.2 1.0
HG23 A:VAL106 3.0 23.2 1.0
HB A:THR94 3.0 20.6 1.0
HG21 A:VAL106 3.2 23.2 1.0
HG22 A:VAL106 3.3 23.2 1.0
CG2 A:VAL106 3.3 19.5 1.0
HB3 A:CYS97 3.3 23.0 1.0
CB A:THR94 3.4 17.3 1.0
N A:MET129 3.4 10.9 1.0
HB3 A:MET129 3.4 18.5 1.0
CB A:CYS97 3.4 19.3 1.0
O A:THR94 3.4 17.8 1.0
HE2 A:TYR105 3.5 22.0 1.0
C A:THR94 3.5 19.5 1.0
HD2 A:TYR105 3.6 23.1 1.0
C A:ASP95 3.7 25.6 1.0
C A:MET129 3.8 18.2 1.0
N A:ASP95 3.9 15.3 1.0
HB3 A:HIS128 3.9 10.6 1.0
H A:CYS97 3.9 29.8 1.0
CA A:MET129 3.9 10.2 1.0
CE2 A:TYR105 4.0 18.4 1.0
N A:CYS97 4.0 24.9 1.0
CD2 A:TYR105 4.0 19.4 1.0
CA A:THR94 4.1 17.7 1.0
HA A:HIS128 4.1 12.4 1.0
CB A:MET129 4.1 15.5 1.0
H A:ASP95 4.2 18.2 1.0
HD1 A:HIS128 4.2 19.9 1.0
CA A:CYS97 4.3 18.7 1.0
C A:HIS96 4.3 22.2 1.0
CA A:ASP95 4.4 21.7 1.0
C A:HIS128 4.4 15.7 1.0
CA A:HIS128 4.6 10.5 1.0
CB A:HIS128 4.6 8.9 1.0
HA A:ASP95 4.6 25.9 1.0
HG22 A:THR94 4.7 16.6 1.0
CG2 A:THR94 4.7 13.9 1.0
HB2 A:MET129 4.7 18.5 1.0
SG A:CYS97 4.7 28.8 1.0
N A:HIS96 4.7 26.2 1.0
HA A:HIS96 4.8 28.6 1.0
HA A:THR94 4.8 21.1 1.0
HA A:CYS97 4.8 22.4 1.0
H A:THR94 4.8 17.7 1.0
CB A:VAL106 4.8 21.2 1.0
O A:HIS96 4.8 24.9 1.0
CA A:HIS96 4.8 23.9 1.0
HA A:MET129 4.9 12.1 1.0
ND1 A:HIS128 4.9 16.7 1.0
HG2 A:MET129 5.0 22.8 1.0
N A:THR94 5.0 14.8 1.0

Sodium binding site 4 out of 6 in 4a22

Go back to Sodium Binding Sites List in 4a22
Sodium binding site 4 out of 6 in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1348

b:46.3
occ:1.00
 O17 B:TD41344 2.4 34.4 0.3
O B:GLY213 2.6 46.9 1.0
O B:VAL211 2.7 36.0 1.0
O2 B:SO41346 2.8 38.5 0.7
O B:SER255 2.9 44.8 1.0
HA2 B:GLY253 3.1 67.9 1.0
H B:GLY213 3.3 64.8 1.0
O B:HOH2192 3.4 50.0 1.0
HA3 B:GLY253 3.4 67.9 1.0
O B:GLY253 3.4 55.9 1.0
C B:GLY253 3.4 54.5 1.0
CA B:GLY253 3.5 56.7 1.0
HA B:HIS212 3.5 53.8 1.0
N B:GLY213 3.5 54.1 1.0
C B:GLY213 3.6 59.9 1.0
HB2 B:SER255 3.6 53.8 1.0
O B:HOH2174 3.8 28.8 1.0
C B:VAL211 3.9 49.1 1.0
S B:SO41346 3.9 34.9 0.7
H B:SER255 3.9 54.7 1.0
C B:HIS212 3.9 46.8 1.0
C B:SER255 4.0 46.6 1.0
P16 B:TD41344 4.0 35.3 0.3
N B:SER255 4.0 45.7 1.0
O3 B:SO41346 4.1 32.4 0.7
CA B:HIS212 4.1 45.0 1.0
CA B:GLY213 4.1 56.7 1.0
N B:GLY254 4.2 43.9 1.0
O1 B:SO41346 4.3 39.6 0.7
HA B:VAL214 4.3 64.3 1.0
HG21 B:VAL214 4.3 70.7 1.0
CA B:SER255 4.4 45.0 1.0
CB B:SER255 4.4 44.9 1.0
C B:GLY254 4.5 41.6 1.0
N B:HIS212 4.5 47.9 1.0
HE1 B:TYR215 4.5 83.5 1.0
H B:VAL211 4.6 58.4 1.0
H B:GLY254 4.6 52.6 1.0
O19 B:TD41344 4.6 26.8 0.3
HA2 B:GLY213 4.7 67.9 1.0
N B:VAL214 4.7 50.0 1.0
O15 B:TD41344 4.7 28.5 0.3
O B:HIS212 4.7 45.0 1.0
HD1 B:TYR215 4.9 91.2 1.0
HA3 B:GLY213 4.9 67.9 1.0
CA B:GLY254 4.9 42.4 1.0
N B:GLY253 4.9 51.7 1.0
O B:GLY254 4.9 40.0 1.0
O18 B:TD41344 5.0 29.4 0.3
HB B:VAL211 5.0 63.4 1.0
O B:HOH2176 5.0 45.9 1.0
CA B:VAL214 5.0 53.7 1.0

Sodium binding site 5 out of 6 in 4a22

Go back to Sodium Binding Sites List in 4a22
Sodium binding site 5 out of 6 in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1346

b:71.6
occ:1.00
 O C:GLY213 2.1 89.8 1.0
O1 C:SO41344 2.4 55.9 1.0
O C:SER255 2.5 42.7 1.0
H C:GLY213 2.7 0.9 1.0
HB2 C:SER255 3.1 61.6 1.0
HA2 C:GLY253 3.2 90.3 1.0
C C:GLY213 3.2 95.0 1.0
O C:VAL211 3.3 81.0 1.0
N C:GLY213 3.3 90.8 1.0
O C:HOH2148 3.4 41.5 1.0
C C:SER255 3.5 59.0 1.0
H C:SER255 3.5 72.0 1.0
C C:GLY253 3.6 75.2 1.0
N C:SER255 3.6 60.1 1.0
HG21 C:VAL214 3.6 0.8 1.0
O C:GLY253 3.6 78.1 1.0
CA C:GLY253 3.7 75.3 1.0
S C:SO41344 3.8 51.7 1.0
CA C:SER255 3.8 62.6 1.0
CA C:GLY213 3.9 94.5 1.0
CB C:SER255 3.9 51.5 1.0
HA C:HIS212 3.9 94.7 1.0
HA3 C:GLY253 3.9 90.3 1.0
HA C:VAL214 4.0 0.7 1.0
N C:GLY254 4.1 62.4 1.0
C C:GLY254 4.2 63.7 1.0
C C:HIS212 4.2 81.3 1.0
HB3 C:SER255 4.3 61.6 1.0
O4 C:SO41344 4.3 38.2 1.0
N C:VAL214 4.3 93.6 1.0
O3 C:SO41344 4.4 43.3 1.0
C C:VAL211 4.4 88.6 1.0
H C:GLY254 4.4 74.8 1.0
HA3 C:GLY213 4.5 0.3 1.0
CA C:HIS212 4.5 79.0 1.0
HA2 C:GLY213 4.5 0.3 1.0
CG2 C:VAL214 4.6 90.0 1.0
CA C:VAL214 4.7 90.7 1.0
N C:GLY256 4.7 69.0 1.0
HE2 C:TYR215 4.7 0.7 1.0
CA C:GLY254 4.7 59.7 1.0
O2 C:SO41344 4.7 44.2 1.0
HG13 C:VAL211 4.7 97.5 1.0
HA3 C:GLY256 4.8 96.9 1.0
O C:GLY254 4.8 61.5 1.0
HA C:SER255 4.8 75.0 1.0
HB C:THR277 4.8 38.8 1.0
HG23 C:VAL214 4.8 0.8 1.0
HG C:SER257 4.9 96.2 1.0
OG C:SER255 4.9 34.5 1.0
N C:HIS212 4.9 88.3 1.0

Sodium binding site 6 out of 6 in 4a22

Go back to Sodium Binding Sites List in 4a22
Sodium binding site 6 out of 6 in the Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Mycobacterium Tuberculosis Fructose 1,6-Bisphosphate Aldolase Bound to N-(4-Hydroxybutyl)- Glycolohydroxamic Acid Bis- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1346

b:73.1
occ:1.00
 O D:GLY213 2.2 0.6 1.0
O1 D:SO41344 2.6 55.4 1.0
HA2 D:GLY253 2.8 57.0 1.0
O D:SER255 3.0 55.9 1.0
H D:GLY213 3.0 0.7 1.0
O D:VAL211 3.2 96.1 1.0
N D:GLY213 3.2 0.2 1.0
C D:GLY213 3.2 98.8 1.0
CA D:GLY253 3.5 47.6 1.0
HB2 D:SER255 3.5 56.0 1.0
C D:GLY253 3.5 52.2 1.0
HA D:HIS212 3.5 0.6 1.0
H D:SER255 3.6 74.3 1.0
HA3 D:GLY253 3.6 57.0 1.0
C D:HIS212 3.7 0.2 1.0
O D:GLY253 3.7 49.9 1.0
CA D:GLY213 3.8 95.6 1.0
N D:SER255 4.0 62.0 1.0
C D:SER255 4.0 60.5 1.0
HG21 D:VAL214 4.0 0.8 1.0
S D:SO41344 4.1 49.0 1.0
CA D:HIS212 4.1 0.6 1.0
N D:GLY254 4.2 79.4 1.0
HA D:VAL214 4.2 0.3 1.0
C D:VAL211 4.2 97.4 1.0
CA D:SER255 4.3 57.0 1.0
CB D:SER255 4.3 46.8 1.0
O D:HIS212 4.3 0.2 1.0
HA2 D:GLY213 4.4 0.6 1.0
N D:VAL214 4.4 0.0 1.0
H D:GLY254 4.4 95.2 1.0
HA3 D:GLY213 4.4 0.6 1.0
O3 D:SO41344 4.6 40.0 1.0
N D:HIS212 4.6 0.1 1.0
C D:GLY254 4.7 83.2 1.0
HE1 D:TYR215 4.7 0.4 1.0
O4 D:SO41344 4.7 52.4 1.0
HB3 D:SER255 4.8 56.0 1.0
CA D:VAL214 4.8 0.0 1.0
N D:GLY253 4.8 41.3 1.0
HG D:SER257 4.8 45.8 1.0
O2 D:SO41344 4.9 34.4 1.0
H D:GLY253 4.9 49.5 1.0
CA D:GLY254 5.0 84.1 1.0
HD1 D:TYR215 5.0 0.4 1.0
CG2 D:VAL214 5.0 88.3 1.0

Reference:

M.De La Paz Santangelo, P.M.Gest, M.E.Guerin, M.Coincon, H.Pham, G.Ryan, S.E.Puckett, J.S.Spencer, M.Gonzalez-Juarrero, R.Daher, A.J.Lenaerts, D.Schnappinger, M.Therisod, S.Ehrt, J.Sygusch, M.Jackson. Glycolytic and Non-Glycolytic Functions of Mycobacterium Tuberculosis Fructose-1,6-Bisphosphate Aldolase, An Essential Enzyme Produced By Replicating and Non-Replicating Bacilli. J. Biol. Chem. V. 286 40219 2011.
ISSN: ESSN 1083-351X
PubMed: 21949126
DOI: 10.1074/JBC.M111.259440
Page generated: Mon Oct 7 14:17:16 2024

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