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Calcium in PDB 3mhf: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes

Enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes

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

Protein crystallography data

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

Resolution Low / High (Å) 43.55 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.863, 105.590, 238.160, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes (pdb code 3mhf). 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, PDB code: 3mhf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3mhf

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Calcium binding site 1 out of 7 in the 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 Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca327

b:22.4
occ:1.00
 OE2 A:GLU84 2.4 32.1 1.0
OE1 A:GLU83 2.5 31.7 1.0
CD A:GLU83 3.5 43.9 1.0
CD A:GLU84 3.6 29.3 1.0
CG A:GLU83 3.9 32.3 1.0
O A:HOH413 4.3 32.7 1.0
O A:HOH1284 4.3 36.2 1.0
O A:HOH892 4.4 35.0 1.0
OE1 A:GLU84 4.4 26.1 1.0
CG A:GLU84 4.5 22.2 1.0
OE2 A:GLU83 4.5 41.8 1.0

Calcium binding site 2 out of 7 in 3mhf

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Calcium binding site 2 out of 7 in the 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 Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca328

b:22.1
occ:1.00
 O A:GLU238 2.3 18.1 1.0
OE2 C:GLU84 2.4 28.5 1.0
OE1 C:GLU83 2.4 30.8 1.0
O A:THR241 2.5 15.1 1.0
O A:HOH392 2.5 29.2 1.0
OE2 A:GLU238 2.6 27.1 1.0
CD C:GLU83 3.5 34.3 1.0
C A:GLU238 3.5 16.4 1.0
CD C:GLU84 3.6 25.0 1.0
CD A:GLU238 3.6 21.1 1.0
C A:THR241 3.6 12.8 1.0
O A:HOH576 3.7 25.2 1.0
CG C:GLU83 3.8 25.9 1.0
CG A:GLU238 4.0 21.6 1.0
O C:HOH619 4.2 40.6 1.0
CA A:ASP242 4.2 17.0 1.0
N A:ASP242 4.3 12.8 1.0
CA A:GLU238 4.3 17.0 1.0
O A:HOH702 4.4 39.2 1.0
O C:HOH1010 4.4 37.6 1.0
N A:ALA239 4.4 13.8 1.0
OE1 C:GLU84 4.4 27.8 1.0
CG C:GLU84 4.4 15.6 1.0
O A:HOH1787 4.4 26.2 1.0
CA A:ALA239 4.5 17.8 1.0
N A:THR241 4.5 16.1 1.0
OE2 C:GLU83 4.6 31.8 1.0
OE1 A:GLU238 4.7 22.7 1.0
OD1 A:ASP242 4.7 41.9 1.0
CA A:THR241 4.7 13.3 1.0
CB A:GLU238 4.8 21.3 1.0
C A:ALA239 4.9 20.7 1.0
CB A:ASP242 4.9 22.4 1.0

Calcium binding site 3 out of 7 in 3mhf

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Calcium binding site 3 out of 7 in the 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 Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca329

b:45.7
occ:1.00
 O C:HOH722 2.6 31.0 1.0
O A:HOH559 2.7 33.1 1.0
O A:HOH1672 2.8 18.8 1.0
O C:HOH595 2.8 41.8 1.0
O A:HOH375 2.9 32.6 1.0
O C:HOH1953 2.9 53.9 1.0
O C:HOH763 3.1 47.4 1.0
O A:HOH362 4.4 34.1 1.0
O C:HOH373 4.4 22.4 1.0
O A:HOH390 4.5 23.9 1.0
O C:PRO62 4.6 17.9 1.0
CB A:GLU197 4.6 15.0 1.0
N A:GLU197 4.7 10.8 1.0
O A:SER195 4.7 14.4 1.0
O A:HOH674 4.7 27.3 1.0
O C:HOH554 4.7 24.4 1.0
O A:HOH680 4.8 31.2 1.0
OE1 A:GLU197 4.8 55.6 1.0

Calcium binding site 4 out of 7 in 3mhf

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Calcium binding site 4 out of 7 in the 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 Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca330

b:43.5
occ:1.00
 O A:HOH355 2.6 28.3 1.0
O A:HOH855 2.7 27.4 1.0
O A:HOH403 2.9 33.5 1.0
O A:HOH998 3.1 46.8 1.0
O A:HOH885 4.5 29.4 1.0
O A:HOH374 4.7 23.1 1.0
O A:PRO62 4.7 20.1 1.0
O A:HOH409 4.9 34.7 1.0

Calcium binding site 5 out of 7 in 3mhf

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Calcium binding site 5 out of 7 in the 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 Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca327

b:71.3
occ:1.00
 O B:HOH699 3.1 56.8 1.0
O B:HOH2138 3.1 64.7 1.0
O B:HOH398 3.1 33.5 1.0
O B:HOH1740 3.1 62.7 1.0
O B:HOH2137 4.0 53.0 1.0
CG B:ASN312 4.0 37.4 1.0
CB B:ASN312 4.1 27.9 1.0
O B:HOH418 4.1 39.7 1.0
OD1 B:ASP316 4.3 61.7 1.0
OD1 B:ASN312 4.3 31.9 1.0
ND2 B:ASN312 4.4 32.1 1.0
OG B:SER22 4.6 32.2 1.0
OD2 B:ASP316 4.7 62.5 1.0
O B:HOH1158 4.7 46.9 1.0
CG B:ASP316 4.9 52.8 1.0
CA B:ASN312 4.9 30.8 1.0
O B:ASN312 4.9 27.7 1.0
O B:HOH2139 5.0 52.9 1.0

Calcium binding site 6 out of 7 in 3mhf

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Calcium binding site 6 out of 7 in the 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 Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca327

b:80.5
occ:1.00
 O C:HOH356 3.0 70.8 1.0
O C:HOH2050 3.1 41.5 1.0
O A:HOH2130 3.1 51.1 1.0
O C:HOH392 3.1 26.8 1.0
O C:HOH810 3.2 46.0 1.0
O C:HOH757 3.3 49.4 1.0
O A:HOH700 3.8 41.9 1.0
O C:LYS317 4.4 18.0 1.0
O B:HOH557 4.6 26.8 1.0
O C:HOH1368 4.7 43.5 1.0
O C:ALA319 4.7 17.5 1.0
C C:LYS317 4.8 17.5 1.0
O C:HOH450 5.0 45.6 1.0

Calcium binding site 7 out of 7 in 3mhf

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Calcium binding site 7 out of 7 in the 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 Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca327

b:28.1
occ:1.00
 OD1 D:ASP259 2.5 26.4 1.0
O D:HOH364 2.6 28.7 1.0
OD2 D:ASP259 2.7 26.5 1.0
CG D:ASP259 2.9 31.9 1.0
O D:HOH1141 4.3 40.5 1.0
O D:HOH647 4.3 38.1 1.0
CB D:ASP259 4.4 23.7 1.0
O D:LYS255 4.6 21.5 1.0
O D:HOH1218 4.6 35.9 1.0
O D:HOH412 4.9 34.3 1.0
O D:HOH1140 5.0 33.9 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: Sat Jul 13 13:36:06 2024

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