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Calcium in PDB 5f2m: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate

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

All present enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate, PDB code: 5f2m was solved by C.Lowkam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.20 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.985, 107.837, 237.810, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate (pdb code 5f2m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate, PDB code: 5f2m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5f2m

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Calcium binding site 1 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3002

b:27.7
occ:1.00
 O A:HOH3279 2.4 21.4 1.0
O B:HOH929 2.4 33.1 1.0
O A:HOH3418 2.4 24.5 1.0
O A:HOH3324 2.4 26.6 1.0
O B:HOH921 2.5 28.4 1.0
O B:HOH735 2.5 28.0 1.0
O A:HOH3323 2.7 21.1 1.0
HB2 A:GLU197 3.6 29.7 1.0
O B:HOH969 3.7 66.3 1.0
H A:GLU197 3.9 20.9 1.0
O A:HOH3172 4.4 27.2 1.0
HD1 B:PHE63 4.4 31.9 1.0
O A:HOH3475 4.4 21.4 1.0
O A:HOH3408 4.5 45.4 1.0
O A:HOH3455 4.5 25.5 1.0
HA B:PHE63 4.5 25.6 1.0
N A:GLU197 4.5 17.4 1.0
O A:HOH3401 4.5 47.8 1.0
CB A:GLU197 4.5 24.8 1.0
O B:HOH954 4.6 20.6 1.0
O A:HOH3463 4.6 23.5 1.0
O B:PRO62 4.6 23.9 1.0
O A:SER195 4.6 17.7 1.0
O A:HOH3447 4.7 28.5 1.0
HA A:LYS196 4.7 19.5 1.0
OE1 A:GLU197 4.8 52.4 1.0
HA A:GLU197 4.9 24.4 1.0
O A:HOH3372 4.9 54.5 1.0
CA A:GLU197 5.0 20.4 1.0
HB3 A:GLU197 5.0 29.7 1.0

Calcium binding site 2 out of 10 in 5f2m

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Calcium binding site 2 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:25.3
occ:1.00
 OE2 B:GLU84 2.2 31.4 1.0
O A:HOH3272 2.3 27.0 1.0
O A:GLU238 2.3 25.0 1.0
O A:THR241 2.4 18.2 1.0
OE2 A:GLU238 2.4 31.0 1.0
OE1 B:GLU83 2.5 35.9 1.0
O A:HOH3123 2.9 86.7 1.0
HG3 A:GLU238 3.3 34.0 1.0
HA A:ASP242 3.4 27.2 1.0
CD A:GLU238 3.5 29.4 1.0
C A:GLU238 3.5 24.7 1.0
CD B:GLU84 3.5 29.5 1.0
C A:THR241 3.5 19.1 1.0
CD B:GLU83 3.7 41.2 1.0
H A:THR241 3.7 25.3 0.6
H A:THR241 3.8 25.3 0.4
HA A:ALA239 3.8 29.7 1.0
CG A:GLU238 3.9 28.3 1.0
O B:HOH645 4.1 46.1 1.0
HG2 B:GLU83 4.1 45.7 1.0
HA A:GLU238 4.1 29.9 1.0
HG3 B:GLU84 4.2 30.4 1.0
HB3 B:GLU83 4.2 38.1 1.0
CA A:ASP242 4.2 22.6 1.0
N A:ASP242 4.2 20.9 1.0
OE1 B:GLU84 4.3 31.9 1.0
CA A:GLU238 4.3 24.9 1.0
CG B:GLU84 4.4 25.4 1.0
CG B:GLU83 4.4 38.1 1.0
N A:ALA239 4.4 23.3 1.0
N A:THR241 4.4 21.1 1.0
CA A:ALA239 4.5 24.8 1.0
HG23 A:THR241 4.5 25.8 1.0
OE1 A:GLU238 4.5 29.3 1.0
HB2 A:ASP242 4.5 35.3 1.0
O B:HOH830 4.6 43.3 1.0
OD1 A:ASP242 4.6 35.8 1.0
O A:HOH3412 4.6 40.3 1.0
CA A:THR241 4.6 20.0 1.0
HG2 A:GLU238 4.6 34.0 1.0
OE2 B:GLU83 4.7 46.8 1.0
HG2 B:GLU84 4.7 30.4 1.0
CB A:GLU238 4.7 25.9 1.0
O A:HOH3108 4.7 51.0 1.0
HE3 A:LYS325 4.8 60.6 1.0
CB B:GLU83 4.8 31.8 1.0
CB A:ASP242 4.9 29.4 1.0
HG22 A:THR241 4.9 25.8 1.0
C A:ALA239 4.9 23.8 1.0
HE1 A:TYR245 4.9 26.2 1.0
HE2 A:LYS325 5.0 60.6 1.0
H A:SER240 5.0 28.1 0.4

Calcium binding site 3 out of 10 in 5f2m

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Calcium binding site 3 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3004

b:62.3
occ:1.00
 O A:HOH3350 2.3 85.2 1.0
O A:HOH3468 3.3 65.8 1.0
O A:HOH3396 3.6 61.5 1.0
O A:HOH3129 3.6 58.6 1.0
HA A:LYS317 4.5 30.1 1.0
O A:ALA319 4.6 23.6 1.0
O A:HOH3143 4.8 63.2 1.0
O A:LYS317 4.9 27.4 1.0
O A:ASP316 4.9 30.7 1.0
O A:HOH3196 4.9 40.0 1.0
C A:LYS317 5.0 23.9 1.0

Calcium binding site 4 out of 10 in 5f2m

Go back to Calcium Binding Sites List in 5f2m
Calcium binding site 4 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:26.5
occ:1.00
 O B:HOH670 2.2 32.8 1.0
O B:GLU238 2.3 22.4 1.0
O B:THR241 2.3 17.3 1.0
OE2 B:GLU238 2.6 39.0 1.0
HG3 B:GLU238 3.4 34.2 1.0
HA B:ASP242 3.4 27.2 1.0
C B:GLU238 3.4 21.8 1.0
C B:THR241 3.5 20.1 1.0
CD B:GLU238 3.6 33.5 1.0
HA B:ALA239 3.7 28.9 1.0
H B:THR241 3.7 23.9 0.6
O B:HOH510 3.7 48.8 1.0
H B:THR241 3.8 23.9 0.4
CG B:GLU238 4.0 28.5 1.0
HA B:GLU238 4.2 25.0 1.0
CA B:ASP242 4.2 22.7 1.0
N B:ASP242 4.3 21.6 1.0
N B:ALA239 4.3 22.1 1.0
CA B:ALA239 4.3 24.1 1.0
CA B:GLU238 4.4 20.8 1.0
HG23 B:THR241 4.4 23.5 1.0
N B:THR241 4.4 20.0 1.0
O B:HOH843 4.4 53.2 1.0
CA B:THR241 4.6 19.0 1.0
OD1 B:ASP242 4.6 35.0 1.0
OE1 B:GLU238 4.7 31.6 1.0
HG2 B:GLU238 4.7 34.2 1.0
C B:ALA239 4.7 23.6 1.0
HB2 B:ASP242 4.8 34.5 1.0
HG22 B:THR241 4.8 23.5 1.0
CB B:GLU238 4.8 22.8 1.0
O B:HOH507 4.8 45.6 1.0
HZ3 B:LYS325 4.9 72.6 1.0
H B:SER240 4.9 26.5 0.6
H B:SER240 5.0 26.5 0.4
CB B:ASP242 5.0 28.7 1.0

Calcium binding site 5 out of 10 in 5f2m

Go back to Calcium Binding Sites List in 5f2m
Calcium binding site 5 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:28.5
occ:1.00
 O B:HOH741 2.3 22.5 1.0
O B:HOH893 2.4 25.5 1.0
O B:HOH803 2.6 19.1 1.0
O B:HOH736 2.6 28.1 1.0
HB2 B:GLU197 3.7 28.0 1.0
H B:GLU197 4.0 20.7 1.0
O B:HOH647 4.2 24.0 1.0
O B:HOH958 4.3 29.0 1.0
O B:HOH963 4.4 19.6 1.0
O B:HOH887 4.5 40.7 1.0
O B:HOH950 4.5 26.6 1.0
N B:GLU197 4.5 17.2 1.0
O B:HOH882 4.6 58.9 1.0
O B:SER195 4.6 18.0 1.0
CB B:GLU197 4.6 23.3 1.0
HA B:LYS196 4.7 19.1 1.0
O B:HOH916 4.7 27.4 1.0
HA B:GLU197 4.8 24.8 1.0
O B:HOH838 4.9 60.7 1.0
CA B:GLU197 5.0 20.7 1.0
OE1 B:GLU197 5.0 40.3 1.0

Calcium binding site 6 out of 10 in 5f2m

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Calcium binding site 6 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:86.8
occ:1.00
 O B:HOH875 2.5 85.1 1.0
O B:HOH992 2.7 64.4 1.0
O C:HOH729 2.7 55.2 1.0
O B:HOH742 2.7 60.2 1.0
O B:HOH877 2.8 50.8 1.0
O B:HOH915 3.2 71.0 1.0
O A:HOH3488 3.3 63.3 1.0
O B:HOH817 4.3 53.2 1.0
HA B:LYS317 4.6 27.5 1.0
O A:HOH3236 4.7 49.3 1.0
O C:HOH540 4.7 31.9 1.0
O B:HOH543 4.8 51.6 1.0
O C:HOH739 4.8 39.4 1.0
O B:ALA319 4.8 22.2 1.0
O B:ASP316 5.0 31.6 1.0

Calcium binding site 7 out of 10 in 5f2m

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Calcium binding site 7 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-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 Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:60.1
occ:1.00
 O B:ALA37 2.5 42.1 1.0
O B:GLN40 2.6 43.4 1.0
O B:HOH780 2.6 66.4 1.0
O B:HOH589 3.0 42.7 1.0
O B:HOH881 3.1 69.6 1.0
HA B:THR41 3.3 65.3 1.0
C B:GLN40 3.7 45.7 1.0
C B:ALA37 3.7 40.5 1.0
O B:THR41 3.9 51.9 1.0
H B:GLN40 3.9 50.0 1.0
HB1 B:ALA37 4.0 45.0 1.0
CA B:THR41 4.0 54.4 1.0
C B:THR41 4.3 52.2 1.0
HA B:ALA37 4.3 44.5 1.0
N B:THR41 4.3 51.0 1.0
HA B:GLN38 4.4 56.5 1.0
CA B:ALA37 4.5 37.0 1.0
N B:GLN40 4.6 41.7 1.0
O B:HOH922 4.6 42.3 1.0
N B:GLN38 4.7 44.0 1.0
CB B:ALA37 4.7 37.5 1.0
C B:GLN38 4.7 45.6 1.0
CA B:GLN40 4.8 44.0 1.0
CA B:GLN38 4.8 47.1 1.0
O B:GLN38 4.8 48.1 1.0

Calcium binding site 8 out of 10 in 5f2m

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Calcium binding site 8 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:63.0
occ:1.00
 O C:HOH546 2.4 38.8 1.0
O C:GLU84 2.4 58.4 1.0
O C:HOH502 2.5 73.0 1.0
O C:HOH584 2.7 63.9 1.0
O C:HOH591 3.0 47.5 1.0
HB3 C:GLU84 3.4 92.5 1.0
C C:GLU84 3.5 58.3 1.0
HA C:GLU84 3.8 82.0 1.0
CA C:GLU84 4.1 68.3 1.0
HG22 C:VAL17 4.1 55.1 1.0
O C:SER16 4.1 41.8 1.0
CB C:GLU84 4.1 77.1 1.0
HA C:LYS14 4.3 48.2 1.0
HA C:ALA85 4.3 52.6 1.0
O C:LYS14 4.3 36.6 1.0
N C:ALA85 4.6 50.0 1.0
HG3 C:GLU84 4.7 0.1 1.0
O C:SER65 4.8 38.1 1.0
HA C:SER65 4.8 42.8 1.0
HB2 C:GLU84 4.8 92.5 1.0
O C:GLU13 4.9 37.2 1.0
CA C:ALA85 4.9 43.8 1.0
C C:LYS14 5.0 36.0 1.0
CG2 C:VAL17 5.0 45.9 1.0
CG C:GLU84 5.0 88.4 1.0
H C:GLY86 5.0 44.9 1.0

Calcium binding site 9 out of 10 in 5f2m

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Calcium binding site 9 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:32.8
occ:1.00
 O D:HOH695 2.4 42.9 1.0
OD2 D:ASP259 2.4 42.7 1.0
OD1 D:ASP259 2.5 42.0 1.0
O D:HOH597 2.6 29.8 1.0
CG D:ASP259 2.8 42.0 1.0
HD2 D:LYS255 4.2 59.2 1.0
O D:HOH643 4.3 39.2 1.0
HB3 D:LYS255 4.3 52.6 1.0
CB D:ASP259 4.3 41.3 1.0
O D:HOH594 4.6 43.6 1.0
O D:HOH673 4.6 37.7 1.0
O D:LYS255 4.6 42.5 1.0
O D:HOH540 4.6 37.1 1.0
HB2 D:ASP259 4.7 49.5 1.0
HB3 D:ASP259 4.7 49.5 1.0
HA D:ASP259 4.9 48.4 1.0

Calcium binding site 10 out of 10 in 5f2m

Go back to Calcium Binding Sites List in 5f2m
Calcium binding site 10 out of 10 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Competitive Inhibitor Hexitol-1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:83.0
occ:1.00
 O D:HOH715 2.5 55.6 1.0
O D:HOH785 2.6 62.6 1.0
O D:HOH683 2.8 70.2 1.0
O D:HOH735 2.9 61.5 1.0
O D:HOH634 3.4 66.0 1.0
OD1 D:ASP316 4.1 61.0 1.0
HG11 D:VAL17 4.2 54.9 1.0
OD2 D:ASP316 4.3 65.4 1.0
O D:HOH669 4.5 50.5 1.0
CG D:ASP316 4.6 61.5 1.0
HB3 D:ASN312 4.9 45.8 1.0
HG12 D:VAL17 4.9 54.9 1.0
O D:HOH736 4.9 54.3 1.0
CG1 D:VAL17 5.0 45.8 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 19:02:50 2024

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