Calcium in PDB 5ff7: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P

Enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P

All present enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P:
4.1.2.40;

Protein crystallography data

The structure of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P, PDB code: 5ff7 was solved by C.Low-Kam, B.Liotard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.85 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.081, 108.190, 238.040, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P (pdb code 5ff7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P, PDB code: 5ff7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5ff7

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Calcium binding site 1 out of 6 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P


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 Dhap and G3P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:55.5
occ:0.55
 OE2 C:GLU84 2.4 51.6 1.0
O A:GLU238 2.4 29.3 1.0
O A:HOH3244 2.5 97.5 1.0
O A:THR241 2.5 21.4 1.0
OE2 A:GLU238 2.6 41.9 1.0
OE1 C:GLU83 3.0 57.8 1.0
HG3 A:GLU238 3.2 43.1 1.0
HA A:ASP242 3.4 34.1 1.0
CD A:GLU238 3.5 39.6 1.0
C A:GLU238 3.6 23.9 1.0
CD C:GLU84 3.6 46.6 1.0
C A:THR241 3.7 25.6 1.0
CG A:GLU238 3.9 35.9 1.0
CD C:GLU83 3.9 64.0 1.0
H A:THR241 3.9 29.2 1.0
HA A:ALA239 4.0 26.8 1.0
HB3 C:GLU83 4.1 53.4 1.0
HA A:GLU238 4.2 29.1 1.0
O C:HOH657 4.2 49.5 1.0
HG3 C:GLU84 4.3 51.4 1.0
CA A:ASP242 4.3 28.4 1.0
O A:HOH3352 4.4 37.7 1.0
CA A:GLU238 4.4 24.2 1.0
N A:ASP242 4.4 28.3 1.0
O C:HOH638 4.5 38.5 1.0
OE1 C:GLU84 4.5 54.8 1.0
HE2 A:LYS325 4.5 64.8 0.9
CG C:GLU84 4.5 42.8 1.0
N A:ALA239 4.6 24.3 1.0
HG2 A:GLU238 4.6 43.1 1.0
HG23 A:THR241 4.6 34.7 1.0
OE2 C:GLU83 4.6 79.1 1.0
OE1 A:GLU238 4.6 35.0 1.0
N A:THR241 4.6 24.3 1.0
CA A:ALA239 4.6 22.4 1.0
HG2 C:GLU83 4.7 63.4 1.0
HG2 C:GLU84 4.7 51.4 1.0
CB A:GLU238 4.7 29.4 1.0
CG C:GLU83 4.8 52.8 1.0
OD1 A:ASP242 4.8 91.2 1.0
CA A:THR241 4.8 26.5 1.0
HB2 A:ASP242 4.8 51.6 1.0
CB C:GLU83 4.9 44.5 1.0

Calcium binding site 2 out of 6 in 5ff7

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Calcium binding site 2 out of 6 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P


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 Dhap and G3P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3004

b:63.1
occ:1.00
 OE2 A:GLU83 2.3 47.5 1.0
OE2 A:GLU84 2.4 45.1 1.0
CD A:GLU83 3.4 63.5 1.0
CD A:GLU84 3.6 40.3 1.0
HG3 A:GLU83 3.7 71.2 1.0
HG2 A:GLU83 3.9 71.2 1.0
CG A:GLU83 3.9 59.3 1.0
HG3 A:GLU84 4.1 52.2 1.0
O A:HOH3176 4.3 44.5 1.0
CG A:GLU84 4.4 43.5 1.0
OE1 A:GLU83 4.4 60.0 1.0
OE1 A:GLU84 4.5 41.3 1.0
HG2 A:GLU84 4.6 52.2 1.0

Calcium binding site 3 out of 6 in 5ff7

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Calcium binding site 3 out of 6 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P


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 Dhap and G3P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3005

b:45.8
occ:0.78
 O A:HOH3436 2.5 46.0 1.0
O A:HOH3217 2.7 66.1 1.0
O A:HOH3383 3.1 47.8 1.0
O A:HOH3400 3.3 51.9 1.0
HA A:LYS317 4.3 29.6 1.0
O A:LYS317 4.4 28.6 1.0
O A:ALA319 4.4 26.5 1.0
O A:HOH3366 4.5 51.1 1.0
C A:LYS317 4.7 23.1 1.0
O A:ASP316 4.9 39.0 1.0

Calcium binding site 4 out of 6 in 5ff7

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Calcium binding site 4 out of 6 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P


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 Dhap and G3P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:47.8
occ:0.46
 O B:HOH666 2.5 49.1 1.0
O B:HOH560 2.5 85.4 1.0
HB3 B:ASN312 3.0 53.4 1.0
O B:HOH581 3.4 45.0 1.0
O B:HOH626 3.8 58.2 1.0
CB B:ASN312 3.9 44.5 1.0
OD1 B:ASP316 3.9 92.7 1.0
CG B:ASN312 4.0 45.7 1.0
HG B:SER22 4.1 61.9 1.0
OD2 B:ASP316 4.2 86.8 1.0
OD1 B:ASN312 4.4 42.0 1.0
O B:HOH540 4.4 46.7 1.0
ND2 B:ASN312 4.4 45.3 1.0
HB2 B:ASN312 4.5 53.4 1.0
HD22 B:ASN312 4.5 54.3 1.0
CG B:ASP316 4.5 76.2 1.0
HA B:ASN312 4.6 54.0 1.0
O B:ASN312 4.8 41.9 1.0
HG11 B:VAL17 4.8 60.2 1.0
CA B:ASN312 4.8 45.0 1.0
HD21 B:ASN312 4.8 54.3 1.0
OG B:SER22 4.9 51.6 1.0
HB B:VAL17 5.0 57.5 1.0

Calcium binding site 5 out of 6 in 5ff7

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Calcium binding site 5 out of 6 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P


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 Dhap and G3P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:47.6
occ:0.68
 O C:HOH808 2.6 57.5 1.0
O C:HOH721 2.7 54.0 1.0
O A:HOH3439 2.7 70.4 1.0
O A:HOH3289 2.7 52.5 1.0
O C:HOH788 3.2 40.6 1.0
O C:HOH622 3.4 46.7 1.0
O C:HOH772 3.7 62.1 1.0
O B:HOH673 3.8 35.5 1.0
O C:HOH756 3.8 66.1 1.0
O A:HOH3273 4.2 58.5 1.0
HA C:LYS317 4.3 31.4 1.0
O C:LYS317 4.5 30.5 1.0
O B:HOH523 4.7 39.4 1.0
C C:LYS317 4.9 22.5 1.0
O A:HOH3355 4.9 72.0 1.0

Calcium binding site 6 out of 6 in 5ff7

Go back to Calcium Binding Sites List in 5ff7
Calcium binding site 6 out of 6 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Dhap and G3P


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 Dhap and G3P within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:57.3
occ:1.00
 OD1 D:ASP259 2.5 79.5 1.0
OD2 D:ASP259 2.5 72.8 1.0
O D:HOH670 2.6 45.4 1.0
O D:HOH613 2.8 88.7 1.0
CG D:ASP259 2.8 72.3 1.0
O D:HOH641 4.0 72.9 1.0
CB D:ASP259 4.3 57.8 1.0
O D:HOH519 4.4 45.9 1.0
HB3 D:LYS255 4.5 64.5 1.0
HD2 D:LYS255 4.5 84.0 1.0
O D:LYS255 4.7 47.7 1.0
HB2 D:ASP259 4.7 69.4 1.0
HA D:ASP259 4.8 63.8 1.0
HB3 D:ASP259 4.8 69.4 1.0
H D:ASP259 5.0 62.1 1.0

Reference:

C.Low-Kam, B.Liotard, J.Sygusch. Non-Stereospecific Substrate Cleavage By Tagatose-Bisphosphate Class I Aldolase To Be Published.
Page generated: Sat Dec 12 05:25:00 2020

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