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Calcium in PDB 5f4s: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp

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

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

Protein crystallography data

The structure of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp, PDB code: 5f4s was solved by C.Lowkam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.10 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.011, 109.141, 238.335, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.9

Other elements in 5f4s:

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

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp (pdb code 5f4s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp, PDB code: 5f4s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 1 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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 Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3004

b:33.0
occ:1.00
 O B:HOH646 2.3 34.6 1.0
O A:HOH3454 2.5 30.7 1.0
O A:HOH3298 2.5 26.6 1.0
O A:HOH3277 2.5 19.3 1.0
O A:HOH3341 2.6 20.2 1.0
O B:HOH834 2.6 38.2 1.0
O B:HOH853 2.7 50.1 1.0
HB2 A:GLU197 3.7 28.8 1.0
H A:GLU197 4.0 18.4 1.0
O A:HOH3395 4.2 49.2 1.0
HD1 B:PHE63 4.3 25.5 1.0
O A:HOH3513 4.3 23.6 1.0
O A:HOH3211 4.4 28.8 1.0
HA B:PHE63 4.4 26.6 1.0
O A:HOH3496 4.4 30.8 1.0
O A:HOH3507 4.4 22.3 1.0
N A:GLU197 4.6 15.3 1.0
CB A:GLU197 4.6 24.0 1.0
O B:PRO62 4.6 17.3 1.0
O A:SER195 4.6 15.2 1.0
HA A:LYS196 4.6 19.2 1.0
O B:HOH867 4.6 26.8 1.0
O A:HOH3493 4.7 18.2 1.0
HG21 A:ILE2 4.7 46.5 0.6
OE1 A:GLU197 4.8 70.3 1.0
HG22 A:ILE2 4.8 46.5 0.6
HB3 A:GLU197 4.9 28.8 1.0
O B:HOH625 4.9 36.2 1.0
HA A:GLU197 5.0 22.0 1.0

Calcium binding site 2 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 2 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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 Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3005

b:22.3
occ:1.00
 O A:HOH3263 2.3 30.2 1.0
O A:GLU238 2.3 19.6 1.0
OE2 B:GLU84 2.3 29.5 1.0
O A:THR241 2.4 16.1 1.0
OE1 B:GLU83 2.5 33.4 1.0
OE2 A:GLU238 2.6 29.7 1.0
HG3 A:GLU238 3.3 24.6 1.0
HA A:ASP242 3.4 26.4 1.0
C A:GLU238 3.5 15.5 1.0
CD B:GLU84 3.5 25.1 1.0
C A:THR241 3.5 20.3 1.0
CD A:GLU238 3.6 23.5 1.0
CD B:GLU83 3.6 44.9 1.0
HA A:ALA239 3.7 24.3 1.0
H A:THR241 3.7 17.1 0.5
O A:HOH3294 3.8 35.7 1.0
H A:THR241 3.8 17.1 0.5
CG A:GLU238 3.9 20.5 1.0
HG2 B:GLU83 3.9 46.6 1.0
HG3 B:GLU84 4.1 24.9 1.0
O B:HOH602 4.1 41.3 1.0
HB3 B:GLU83 4.1 24.6 1.0
HA A:GLU238 4.2 23.4 1.0
CA A:ASP242 4.2 22.0 1.0
N A:ASP242 4.3 17.7 1.0
CG B:GLU83 4.3 38.8 1.0
OE1 B:GLU84 4.3 24.4 1.0
N A:ALA239 4.4 17.4 1.0
CA A:GLU238 4.4 19.5 1.0
CG B:GLU84 4.4 20.7 1.0
O B:HOH766 4.4 38.7 1.0
CA A:ALA239 4.4 20.2 1.0
N A:THR241 4.5 14.2 1.0
OD1 A:ASP242 4.5 26.2 1.0
HG23 A:THR241 4.6 26.6 1.0
HB2 A:ASP242 4.6 32.9 1.0
OE2 B:GLU83 4.6 52.6 1.0
O A:HOH3420 4.6 42.1 1.0
OE1 A:GLU238 4.6 22.7 1.0
CA A:THR241 4.6 14.6 1.0
HG2 B:GLU84 4.7 24.9 1.0
HG2 A:GLU238 4.7 24.6 1.0
O A:HOH3235 4.7 34.5 1.0
CB B:GLU83 4.7 20.5 1.0
CB A:GLU238 4.7 23.7 1.0
C A:ALA239 4.8 22.0 1.0
CB A:ASP242 4.9 27.4 1.0
HG22 A:THR241 5.0 26.6 1.0
HE1 A:TYR245 5.0 20.3 1.0

Calcium binding site 3 out of 5 in 5f4s

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Calcium binding site 3 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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 Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:33.0
occ:1.00
 O B:HOH833 2.5 29.6 1.0
O B:HOH686 2.5 22.3 1.0
O B:HOH668 2.5 22.9 1.0
O B:HOH635 2.6 32.8 1.0
HB2 B:GLU197 3.6 22.9 1.0
H B:GLU197 4.0 16.8 1.0
O B:HOH547 4.3 26.4 1.0
O B:HOH890 4.4 23.3 1.0
CB B:GLU197 4.5 19.1 1.0
N B:GLU197 4.5 14.0 1.0
O B:HOH669 4.5 49.2 1.0
HA B:LYS196 4.6 15.3 1.0
O B:HOH864 4.6 25.4 1.0
O B:SER195 4.6 16.8 1.0
O B:HOH861 4.7 24.2 1.0
O B:HOH805 4.8 49.3 1.0
OE1 B:GLU197 4.8 61.6 1.0
HB3 B:GLU197 4.8 22.9 1.0
O B:HOH850 4.9 28.0 1.0
HA B:GLU197 4.9 25.4 1.0
CA B:GLU197 5.0 21.2 1.0

Calcium binding site 4 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 4 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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 Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:24.5
occ:1.00
 O B:HOH651 2.2 29.7 1.0
O B:GLU238 2.2 25.5 1.0
O B:THR241 2.3 16.3 1.0
OE2 B:GLU238 2.5 40.6 1.0
HA B:ASP242 3.3 28.1 1.0
HE3 B:MET326 3.4 45.3 0.8
HG3 B:GLU238 3.4 32.7 1.0
C B:GLU238 3.4 13.4 1.0
C B:THR241 3.5 17.1 1.0
CD B:GLU238 3.5 27.9 1.0
H B:THR241 3.7 21.6 1.0
HA B:ALA239 3.7 21.9 1.0
CG B:GLU238 4.0 27.3 1.0
CA B:ASP242 4.1 23.4 1.0
N B:ASP242 4.2 20.5 1.0
CE B:MET326 4.2 47.7 0.8
HA B:GLU238 4.2 20.4 1.0
HE2 B:MET326 4.2 45.3 0.8
N B:ALA239 4.3 15.2 1.0
CA B:ALA239 4.4 18.3 1.0
N B:THR241 4.4 18.0 1.0
CA B:GLU238 4.4 17.0 1.0
HE1 B:MET326 4.5 45.3 0.8
HG23 B:THR241 4.5 24.4 1.0
O B:HOH773 4.5 42.4 1.0
CA B:THR241 4.6 15.0 1.0
OD1 B:ASP242 4.6 45.7 1.0
OE1 B:GLU238 4.6 25.9 1.0
HB2 B:ASP242 4.6 41.7 1.0
O B:HOH573 4.6 42.1 1.0
HG2 B:GLU238 4.7 32.7 1.0
C B:ALA239 4.8 20.6 1.0
CB B:GLU238 4.8 23.7 1.0
CB B:ASP242 4.9 34.7 1.0
H B:SER240 4.9 24.1 1.0
H B:ASP242 4.9 24.6 1.0
HE1 B:TYR245 5.0 20.8 1.0
HG22 B:THR241 5.0 24.4 1.0

Calcium binding site 5 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 5 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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 Fbp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:42.5
occ:1.00
 OD1 C:ASP259 2.3 41.4 1.0
OD2 C:ASP259 2.6 47.5 1.0
CG C:ASP259 2.8 48.0 1.0
HG3 C:LYS255 3.7 54.5 1.0
CB C:ASP259 4.3 42.6 1.0
O C:HOH664 4.3 35.9 1.0
O C:HOH588 4.4 41.8 1.0
HE3 C:LYS255 4.4 69.1 1.0
HG2 C:LYS255 4.5 54.5 1.0
CG C:LYS255 4.5 45.4 1.0
O C:LYS255 4.5 39.6 1.0
O C:HOH517 4.7 45.6 1.0
HB3 C:ASP259 4.7 51.1 1.0
HB2 C:ASP259 4.7 51.1 1.0
HA C:ASP259 4.8 49.4 1.0
H C:ASP259 4.9 47.5 1.0

Reference:

C.Lowkam, B.Liotard, J.Sygusch. Non-Stereospecific Substrate Cleavage By Tagatose-Bisphosphate Class I Aldolase To Be Published.
Page generated: Wed Jul 9 05:51:16 2025

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