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Calcium in PDB 5f2l: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate

Enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate

All present enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate:
4.1.2.40;

Protein crystallography data

The structure of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate, PDB code: 5f2l was solved by C.Lowkam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.19 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.966, 108.029, 237.423, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.9

Other elements in 5f2l:

The structure of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate (pdb code 5f2l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate, PDB code: 5f2l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5f2l

Go back to Calcium Binding Sites List in 5f2l
Calcium binding site 1 out of 7 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3002

b:29.9
occ:1.00
 OE2 B:GLU84 2.2 31.1 1.0
OE2 B:GLU83 2.3 35.9 1.0
O A:GLU238 2.3 23.2 1.0
O A:HOH3169 2.3 35.2 1.0
O A:THR241 2.4 19.2 1.0
OE2 A:GLU238 2.5 27.4 1.0
CD B:GLU83 3.3 38.6 1.0
HA A:ASP242 3.3 29.0 0.6
HG3 A:GLU238 3.3 29.1 1.0
HA A:ASP242 3.4 30.4 0.4
C A:GLU238 3.4 21.7 1.0
CD B:GLU84 3.5 30.2 1.0
C A:THR241 3.5 23.0 1.0
HG3 B:GLU83 3.5 44.0 1.0
CD A:GLU238 3.5 25.7 1.0
O A:HOH3197 3.7 43.7 1.0
HG2 B:GLU83 3.7 44.0 1.0
H A:THR241 3.8 25.6 0.6
CG B:GLU83 3.8 36.7 1.0
H A:THR241 3.9 25.6 0.4
HA A:ALA239 3.9 28.9 1.0
CG A:GLU238 3.9 24.2 1.0
HZ2 A:LYS325 4.0 70.2 1.0
HG3 B:GLU84 4.1 30.2 1.0
HA A:GLU238 4.1 24.4 1.0
CA A:ASP242 4.1 24.1 0.6
CA A:ASP242 4.2 25.3 0.4
N A:ASP242 4.2 23.9 0.6
N A:ASP242 4.2 23.9 0.4
CA A:GLU238 4.3 20.3 1.0
CG B:GLU84 4.3 25.2 1.0
OE1 B:GLU84 4.3 33.2 1.0
O B:HOH671 4.3 39.5 1.0
OE1 B:GLU83 4.4 42.0 1.0
HB3 A:ASP242 4.4 40.8 0.4
N A:ALA239 4.4 22.3 1.0
HB2 A:ASP242 4.4 35.0 0.6
O A:HOH3367 4.4 32.6 1.0
O B:HOH734 4.4 40.4 1.0
N A:THR241 4.5 21.4 1.0
CA A:ALA239 4.5 24.1 1.0
HG23 A:THR241 4.5 29.0 1.0
HG2 B:GLU84 4.6 30.2 1.0
OD1 A:ASP242 4.6 28.3 0.6
CA A:THR241 4.6 23.4 1.0
OE1 A:GLU238 4.6 25.7 1.0
HG2 A:GLU238 4.7 29.1 1.0
CB A:GLU238 4.7 19.7 1.0
CB A:ASP242 4.8 29.1 0.6
CB A:ASP242 4.8 34.0 0.4
C A:ALA239 4.9 23.3 1.0
NZ A:LYS325 4.9 58.5 1.0
HG22 A:THR241 4.9 29.0 1.0
HE1 A:TYR245 4.9 27.3 1.0
H A:SER240 5.0 26.6 0.6

Calcium binding site 2 out of 7 in 5f2l

Go back to Calcium Binding Sites List in 5f2l
Calcium binding site 2 out of 7 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:39.1
occ:1.00
 O B:HOH662 2.4 35.7 1.0
O B:HOH889 2.4 39.3 1.0
O A:HOH3460 2.5 34.5 1.0
O A:HOH3343 2.5 33.2 1.0
O A:HOH3357 2.5 37.2 1.0
O A:HOH3240 2.5 37.4 1.0
O A:HOH3316 2.7 24.9 1.0
HB2 A:GLU197 3.7 32.5 1.0
O A:HOH3407 4.0 48.1 1.0
H A:GLU197 4.0 26.3 1.0
O A:HOH3102 4.2 41.0 1.0
O A:HOH3252 4.3 32.5 1.0
O A:HOH3103 4.4 66.4 1.0
HD1 B:PHE63 4.5 36.1 1.0
O A:HOH3452 4.5 36.3 1.0
O A:HOH3524 4.6 25.2 1.0
O A:HOH3450 4.6 49.6 1.0
CB A:GLU197 4.6 27.1 1.0
N A:GLU197 4.6 21.9 1.0
O B:PRO62 4.6 25.9 1.0
HA B:PHE63 4.6 28.4 1.0
O A:SER195 4.7 21.7 1.0
OE1 A:GLU197 4.8 56.1 1.0
HA A:LYS196 4.8 23.9 1.0
O A:HOH3484 4.8 32.8 1.0
O B:HOH898 4.8 34.2 1.0
HA A:GLU197 4.9 27.7 1.0
HB3 A:GLU197 5.0 32.5 1.0

Calcium binding site 3 out of 7 in 5f2l

Go back to Calcium Binding Sites List in 5f2l
Calcium binding site 3 out of 7 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:38.4
occ:1.00
 OD2 C:ASP259 2.4 52.3 1.0
OD1 C:ASP259 2.5 50.8 1.0
O C:HOH560 2.5 35.5 1.0
CG C:ASP259 2.8 49.5 1.0
O C:HOH709 3.0 47.0 1.0
HD2 C:LYS255 4.3 66.0 1.0
CB C:ASP259 4.3 45.3 1.0
HB3 C:LYS255 4.3 60.5 1.0
O C:LYS255 4.4 48.3 1.0
O C:HOH605 4.4 46.3 1.0
O C:HOH642 4.5 45.2 1.0
HB2 C:ASP259 4.6 54.4 1.0
O C:HOH712 4.7 53.4 1.0
HB3 C:ASP259 4.7 54.4 1.0
HA C:ASP259 4.8 55.3 1.0
O C:HOH612 4.8 54.6 1.0

Calcium binding site 4 out of 7 in 5f2l

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Calcium binding site 4 out of 7 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:86.7
occ:1.00
 O C:HOH761 2.4 49.5 1.0
O C:HOH737 3.0 50.8 1.0
O C:HOH748 4.6 36.3 1.0
O C:HOH540 4.6 35.7 1.0

Calcium binding site 5 out of 7 in 5f2l

Go back to Calcium Binding Sites List in 5f2l
Calcium binding site 5 out of 7 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:0.6
occ:1.00
 O C:HOH523 2.6 61.2 1.0
O C:GLU84 2.7 63.7 1.0
O C:HOH564 2.7 48.8 1.0
O C:HOH532 3.1 40.2 1.0
HA C:GLU84 3.5 77.2 1.0
C C:GLU84 3.6 57.4 1.0
HB3 C:GLU84 3.7 95.2 1.0
HA C:LYS14 3.9 46.2 1.0
CA C:GLU84 4.0 64.4 1.0
O C:HOH705 4.1 64.2 1.0
CB C:GLU84 4.3 79.3 1.0
O C:LYS14 4.4 36.6 1.0
HG2 C:GLU84 4.6 0.3 1.0
HG22 C:VAL17 4.6 58.5 1.0
O C:SER16 4.7 40.2 1.0
O C:GLU13 4.8 40.6 1.0
CA C:LYS14 4.8 38.5 1.0
N C:ALA85 4.8 47.1 1.0
HA C:ALA85 4.8 48.6 1.0
CG C:GLU84 4.9 96.9 1.0
HG3 C:GLU84 4.9 0.3 1.0
C C:LYS14 4.9 35.1 1.0
O C:HOH538 5.0 48.5 1.0

Calcium binding site 6 out of 7 in 5f2l

Go back to Calcium Binding Sites List in 5f2l
Calcium binding site 6 out of 7 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:30.2
occ:1.00
 O B:GLU238 2.3 26.2 1.0
O B:HOH577 2.3 33.7 1.0
O B:THR241 2.4 21.7 1.0
OE2 B:GLU238 2.5 32.6 1.0
HA B:ASP242 3.3 28.9 0.7
HG3 B:GLU238 3.4 30.6 1.0
HA B:ASP242 3.4 29.3 0.3
C B:GLU238 3.5 25.0 1.0
C B:THR241 3.5 23.9 1.0
CD B:GLU238 3.6 29.2 1.0
HA B:ALA239 3.7 31.1 1.0
H B:THR241 3.7 27.1 0.6
O B:HOH589 3.8 34.9 1.0
HZ2 B:LYS325 4.0 62.5 1.0
CG B:GLU238 4.0 25.5 1.0
CA B:ASP242 4.2 24.0 0.7
HA B:GLU238 4.2 26.4 1.0
CA B:ASP242 4.2 24.4 0.3
N B:ASP242 4.3 23.9 0.7
N B:ASP242 4.3 23.6 0.3
O B:HOH619 4.3 41.3 1.0
N B:ALA239 4.4 25.0 1.0
CA B:ALA239 4.4 26.0 1.0
CA B:GLU238 4.4 22.0 1.0
HB3 B:ASP242 4.4 33.4 0.3
N B:THR241 4.4 22.6 1.0
HB2 B:ASP242 4.5 34.7 0.7
HG23 B:THR241 4.5 27.6 1.0
CA B:THR241 4.6 23.3 1.0
OD1 B:ASP242 4.6 35.2 0.7
OE1 B:GLU238 4.7 28.8 1.0
HG2 B:GLU238 4.7 30.6 1.0
NZ B:LYS325 4.8 52.1 1.0
C B:ALA239 4.8 24.7 1.0
CB B:GLU238 4.8 22.4 1.0
CB B:ASP242 4.8 27.8 0.3
CB B:ASP242 4.8 28.9 0.7
HZ3 B:LYS325 4.8 62.5 1.0
HG22 B:THR241 4.9 27.6 1.0
H B:SER240 4.9 28.3 0.6
HB2 B:ASP242 5.0 33.4 0.3
H B:SER240 5.0 28.3 0.4

Calcium binding site 7 out of 7 in 5f2l

Go back to Calcium Binding Sites List in 5f2l
Calcium binding site 7 out of 7 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Talitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:41.2
occ:1.00
 O B:HOH765 2.5 37.7 1.0
O B:HOH866 2.5 35.7 1.0
O B:HOH720 2.5 38.1 1.0
O B:HOH639 2.6 30.2 1.0
O B:HOH724 2.7 25.2 1.0
HB2 B:GLU197 3.7 26.7 1.0
H B:GLU197 4.0 22.5 1.0
O B:HOH815 4.2 51.0 1.0
O B:HOH644 4.4 32.0 1.0
O B:HOH504 4.4 35.5 1.0
O B:HOH506 4.4 84.4 1.0
O B:HOH929 4.4 28.7 1.0
O B:HOH833 4.6 36.6 1.0
N B:GLU197 4.6 18.8 1.0
O B:HOH836 4.6 56.0 1.0
CB B:GLU197 4.6 22.3 1.0
O B:SER195 4.6 20.4 1.0
HA B:LYS196 4.8 19.9 1.0
OE1 B:GLU197 4.8 41.2 1.0
O B:HOH882 4.9 35.1 1.0
HA B:GLU197 4.9 24.0 1.0
HB3 B:GLU197 5.0 26.7 1.0

Reference:

C.Lowkam, B.Liotard, J.Sygusch. Non-Stereospecific Substrate Cleavage By Tagatose-Bisphosphate Class I Aldolase To Be Published.
Page generated: Sun Jul 14 19:02:46 2024

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