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Calcium in PDB 3mhg: Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes

Enzymatic activity of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes

All present enzymatic activity of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes:
4.1.2.40;

Protein crystallography data

The structure of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes, PDB code: 3mhg was solved by C.Lowkam, B.Liotard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.52 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.092, 108.182, 238.708, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.6

Calcium Binding Sites:

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

Calcium binding site 1 out of 7 in 3mhg

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Calcium binding site 1 out of 7 in the Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca327

b:15.3
occ:1.00
 O A:PRO62 4.5 8.5 1.0

Calcium binding site 2 out of 7 in 3mhg

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Calcium binding site 2 out of 7 in the Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca328

b:19.8
occ:1.00
 O A:HOH1835 2.5 12.9 1.0
O C:HOH379 2.6 16.5 1.0
O A:HOH554 2.6 12.4 1.0
O A:HOH557 2.7 10.1 1.0
O A:HOH558 2.7 21.2 1.0
O A:HOH560 2.7 28.1 1.0
O A:HOH561 2.7 21.5 1.0
O A:HOH559 4.4 15.3 1.0
O C:HOH376 4.4 9.4 1.0
O A:HOH562 4.5 14.9 1.0
O A:HOH1489 4.5 35.3 1.0
O C:PRO62 4.5 10.1 1.0
CB A:GLU197 4.5 9.9 1.0
O A:HOH555 4.6 31.5 1.0
N A:GLU197 4.6 5.1 1.0
O C:HOH377 4.6 18.3 1.0
O A:HOH552 4.6 14.6 1.0
O A:HOH556 4.6 21.9 1.0
O A:SER195 4.6 6.2 1.0
OE1 A:GLU197 4.7 44.4 1.0
O C:HOH1810 4.9 22.2 1.0
O A:HOH336 4.9 45.1 1.0
CA A:GLU197 5.0 9.7 1.0

Calcium binding site 3 out of 7 in 3mhg

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Calcium binding site 3 out of 7 in the Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca329

b:14.4
occ:1.00
 O A:GLU238 2.3 10.2 1.0
OE2 C:GLU84 2.4 19.4 1.0
O A:THR241 2.4 5.8 1.0
OE1 C:GLU83 2.5 20.4 1.0
O A:HOH1268 2.6 21.7 1.0
OE2 A:GLU238 2.7 25.1 1.0
CD C:GLU83 3.4 36.9 1.0
C A:GLU238 3.5 11.8 1.0
C A:THR241 3.6 11.2 1.0
CD A:GLU238 3.6 22.0 1.0
CD C:GLU84 3.6 14.4 1.0
O A:HOH2326 3.7 27.4 1.0
CG C:GLU83 3.7 24.1 1.0
CG A:GLU238 3.9 15.2 1.0
CA A:ASP242 4.2 10.7 1.0
O C:HOH538 4.3 33.5 1.0
N A:ASP242 4.3 9.3 1.0
O C:HOH1300 4.4 31.6 1.0
CA A:GLU238 4.4 10.8 1.0
N A:ALA239 4.4 9.9 1.0
CA A:ALA239 4.4 12.4 1.0
CG C:GLU84 4.4 13.7 1.0
N A:THR241 4.4 8.8 1.0
OE1 C:GLU84 4.4 19.7 1.0
OE2 C:GLU83 4.4 38.9 1.0
O A:HOH754 4.5 28.4 1.0
O A:HOH579 4.5 22.1 1.0
CA A:THR241 4.6 6.6 1.0
OE1 A:GLU238 4.7 14.6 1.0
OD1 A:ASP242 4.7 22.6 1.0
CB A:GLU238 4.8 9.2 1.0
C A:ALA239 4.8 14.7 1.0
CB A:ASP242 4.9 15.8 1.0

Calcium binding site 4 out of 7 in 3mhg

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Calcium binding site 4 out of 7 in the Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca327

b:21.9
occ:1.00
 OD1 B:ASP259 2.6 17.5 1.0
O B:HOH893 2.6 15.8 1.0
O B:HOH1580 2.7 30.8 1.0
O B:HOH2129 2.7 18.9 1.0
OD2 B:ASP259 2.7 22.3 1.0
CG B:ASP259 3.0 21.3 1.0
O B:HOH1293 4.2 26.7 1.0
O B:HOH897 4.3 24.9 1.0
O B:HOH2419 4.3 28.8 1.0
O B:HOH895 4.4 29.0 1.0
CB B:ASP259 4.5 14.3 1.0
O B:HOH892 4.6 46.8 1.0
O B:LYS255 4.7 15.4 1.0
O B:HOH920 4.9 37.0 1.0

Calcium binding site 5 out of 7 in 3mhg

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Calcium binding site 5 out of 7 in the Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca327

b:17.1
occ:1.00
 O C:GLU238 2.4 13.6 1.0
O C:THR241 2.4 8.0 1.0
O C:HOH1277 2.6 25.0 1.0
OE2 C:GLU238 2.7 22.5 1.0
C C:GLU238 3.5 14.1 1.0
C C:THR241 3.6 11.6 1.0
CD C:GLU238 3.6 25.4 1.0
O C:HOH1319 3.9 22.8 1.0
CG C:GLU238 4.0 16.7 1.0
O C:HOH442 4.1 28.1 1.0
CA C:ASP242 4.2 8.9 1.0
N C:ASP242 4.3 5.8 1.0
CA C:GLU238 4.4 11.3 1.0
N C:THR241 4.4 10.2 1.0
N C:ALA239 4.4 9.5 1.0
O C:HOH366 4.5 32.6 1.0
CA C:ALA239 4.5 10.8 1.0
O C:HOH1520 4.6 33.0 1.0
O C:HOH440 4.6 36.3 1.0
CA C:THR241 4.6 7.7 1.0
OD1 C:ASP242 4.7 21.3 1.0
OE1 C:GLU238 4.7 18.0 1.0
CB C:GLU238 4.8 11.4 1.0
C C:ALA239 4.8 14.1 1.0
CB C:ASP242 4.9 14.3 1.0

Calcium binding site 6 out of 7 in 3mhg

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Calcium binding site 6 out of 7 in the Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca328

b:52.5
occ:1.00
 O C:GLN40 2.6 33.6 1.0
O C:ALA37 2.7 25.6 1.0
O C:HOH495 2.8 37.7 1.0
O C:HOH779 2.8 26.9 1.0
O C:HOH1812 2.8 40.9 1.0
C C:GLN40 3.7 37.2 1.0
C C:ALA37 3.9 29.3 1.0
CA C:THR41 3.9 41.4 1.0
O C:THR41 3.9 36.6 1.0
C C:THR41 4.2 38.3 1.0
O C:HOH1889 4.2 43.1 1.0
N C:THR41 4.2 41.3 1.0
O C:HOH1778 4.3 53.7 1.0
CA C:ALA37 4.5 27.5 1.0
CB C:ALA37 4.7 23.8 1.0
O C:HOH682 4.7 36.7 1.0
N C:GLN40 4.7 27.4 1.0
CA C:GLN40 4.9 24.8 1.0
O C:HOH782 4.9 31.8 1.0
N C:GLN38 4.9 25.1 1.0

Calcium binding site 7 out of 7 in 3mhg

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Calcium binding site 7 out of 7 in the Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Dihydroxyacetone Phosphate Carbanion Intermediate in Tagatose-1,6- Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca327

b:62.3
occ:1.00
 O D:GLU84 2.7 29.5 1.0
O D:HOH1282 2.8 24.0 1.0
O D:HOH1820 2.8 35.7 1.0
O D:HOH2164 2.9 66.1 1.0
O D:HOH2165 3.0 54.0 1.0
O D:HOH959 3.1 23.4 1.0
O D:HOH803 3.6 52.0 1.0
O D:HOH2241 3.7 36.6 1.0
C D:GLU84 3.7 26.4 1.0
OE2 D:GLU84 3.9 86.7 1.0
O D:SER16 4.2 15.8 1.0
CA D:GLU84 4.2 30.3 1.0
CB D:GLU84 4.2 40.5 1.0
CG2 D:VAL17 4.5 23.8 1.0
O D:LYS14 4.6 17.8 1.0
CD D:GLU84 4.8 78.1 1.0
O D:SER65 4.8 14.9 1.0
N D:ALA85 4.9 18.7 1.0

Reference:

C.Lowkam, B.Liotard, J.Sygusch. Structure of A Class I Tagatose-1,6-Bisphosphate Aldolase: Investigation Into An Apparent Loss of Stereospecificity. J.Biol.Chem. V. 285 21143 2010.
ISSN: ISSN 0021-9258
PubMed: 20427286
DOI: 10.1074/JBC.M109.080358
Page generated: Tue Jul 8 14:35:21 2025

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