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Calcium in PDB 5f2i: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant

Enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant

All present enzymatic activity of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant:
4.1.2.40;

Protein crystallography data

The structure of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant, PDB code: 5f2i was solved by C.Lowkam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.37 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.079, 98.542, 237.969, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.2

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant (pdb code 5f2i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant, PDB code: 5f2i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 5f2i

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Calcium binding site 1 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:53.4
occ:1.00
 O A:HOH788 2.5 60.4 1.0
O A:HOH825 2.6 55.6 1.0
O A:HOH695 2.6 43.1 1.0
O A:HOH677 2.6 26.0 1.0
O A:HOH572 2.7 30.0 1.0
O A:HOH808 3.5 0.6 1.0
O A:ALA319 4.5 24.5 1.0
HA A:LYS317 4.5 27.5 1.0
O A:HOH769 4.6 60.4 1.0
O A:HOH569 4.7 43.6 1.0
O A:HOH723 4.7 42.8 1.0
O A:LYS317 4.9 22.8 1.0
O A:ASP316 4.9 28.1 1.0

Calcium binding site 2 out of 11 in 5f2i

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Calcium binding site 2 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.2
occ:1.00
 OE2 B:GLU84 2.2 32.4 1.0
O A:GLU238 2.3 21.7 1.0
OE1 B:GLU83 2.3 35.6 1.0
O A:THR241 2.4 18.6 1.0
OE2 A:GLU238 2.4 26.7 1.0
O A:HOH644 2.4 27.4 1.0
HG3 A:GLU238 3.1 29.4 1.0
HA A:ASP242 3.3 30.7 0.5
CD B:GLU83 3.4 35.1 1.0
CD A:GLU238 3.4 25.8 1.0
HA A:ASP242 3.4 29.4 0.5
HG3 B:GLU83 3.4 38.6 1.0
C A:GLU238 3.4 20.8 1.0
CD B:GLU84 3.4 30.2 1.0
C A:THR241 3.5 22.6 1.0
HG2 B:GLU83 3.7 38.6 1.0
CG B:GLU83 3.7 32.1 1.0
CG A:GLU238 3.7 24.5 1.0
H A:THR241 3.8 26.9 1.0
HA A:ALA239 3.9 27.9 1.0
HG3 B:GLU84 3.9 34.3 1.0
HA A:GLU238 4.1 24.3 1.0
CA A:ASP242 4.1 25.6 0.5
CG B:GLU84 4.2 28.6 1.0
CA A:ASP242 4.2 24.5 0.5
N A:ASP242 4.2 25.8 0.5
N A:ASP242 4.2 25.8 0.5
O A:HOH520 4.3 27.7 1.0
CA A:GLU238 4.3 20.3 1.0
O A:HOH756 4.3 30.3 1.0
OE1 B:GLU84 4.4 29.6 1.0
HG2 B:GLU84 4.4 34.3 1.0
HB2 A:ASP242 4.4 37.5 0.5
HB3 A:ASP242 4.4 37.5 0.5
N A:ALA239 4.4 20.8 1.0
O B:HOH678 4.4 42.2 1.0
N A:THR241 4.5 22.4 1.0
HG2 A:GLU238 4.5 29.4 1.0
O B:HOH515 4.5 43.7 1.0
OE2 B:GLU83 4.5 36.5 1.0
HG23 A:THR241 4.5 25.4 1.0
OE1 A:GLU238 4.5 25.0 1.0
CA A:ALA239 4.5 23.3 1.0
CA A:THR241 4.6 22.1 1.0
CB A:GLU238 4.6 22.3 1.0
OD1 A:ASP242 4.7 30.9 0.5
HE2 A:LYS325 4.7 47.4 1.0
CB A:ASP242 4.8 31.3 0.5
HE1 A:TYR245 4.8 24.7 1.0
CB A:ASP242 4.8 31.2 0.5
HG22 A:THR241 4.9 25.4 1.0
C A:ALA239 4.9 23.1 1.0
H A:SER240 5.0 25.9 1.0

Calcium binding site 3 out of 11 in 5f2i

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Calcium binding site 3 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:83.4
occ:1.00
 O A:GLN40 2.4 60.6 1.0
O A:HOH571 2.6 43.7 1.0
O A:ALA37 2.6 78.0 1.0
HA A:THR41 3.1 89.9 1.0
C A:GLN40 3.5 65.2 1.0
C A:ALA37 3.9 71.5 1.0
H A:GLN40 3.9 78.8 1.0
CA A:THR41 3.9 74.9 1.0
O A:THR41 4.1 74.0 1.0
N A:THR41 4.1 70.6 1.0
HA A:GLN38 4.2 87.6 1.0
HB1 A:ALA37 4.2 80.5 1.0
C A:THR41 4.3 73.6 1.0
N A:GLN40 4.5 65.7 1.0
HA A:ALA37 4.6 79.5 1.0
CA A:GLN40 4.6 65.1 1.0
HG22 A:THR41 4.7 0.2 1.0
CA A:ALA37 4.7 66.3 1.0
N A:GLN38 4.8 69.3 1.0
CA A:GLN38 4.8 73.0 1.0
C A:GLN38 4.8 75.0 1.0
HG3 A:GLN40 4.9 69.1 1.0
CB A:ALA37 5.0 67.1 1.0
H A:THR41 5.0 84.8 1.0

Calcium binding site 4 out of 11 in 5f2i

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Calcium binding site 4 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:70.9
occ:1.00
 O B:HOH797 2.5 47.7 1.0
O B:HOH827 2.5 34.5 1.0
O A:HOH586 2.6 34.9 1.0
O A:HOH768 2.6 36.7 1.0
O A:HOH537 2.7 37.8 1.0
O B:PRO62 2.8 26.3 1.0
O B:HOH806 2.9 32.9 1.0
O A:HOH832 3.7 38.0 1.0
HA B:PHE63 3.7 29.6 1.0
O A:HOH611 4.0 46.9 1.0
C B:PRO62 4.0 25.4 1.0
OD2 A:ASP242 4.1 36.7 0.5
O A:HOH640 4.5 30.1 1.0
O B:HOH753 4.5 36.8 1.0
HD1 B:PHE63 4.5 35.2 1.0
CA B:PHE63 4.6 24.6 1.0
O A:HOH731 4.7 38.3 1.0
OD1 A:ASP242 4.7 33.6 0.5
O B:HOH628 4.7 27.6 1.0
N B:PHE63 4.7 24.1 1.0
CG A:ASP242 4.8 32.6 0.5
HA B:PRO62 4.9 30.3 1.0
O A:HOH619 4.9 18.9 1.0

Calcium binding site 5 out of 11 in 5f2i

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Calcium binding site 5 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:61.0
occ:1.00
 O B:HOH730 2.4 45.7 1.0
O B:HOH535 2.4 45.4 1.0
O B:ALA37 2.4 39.2 1.0
O B:GLN40 2.5 49.1 1.0
O B:HOH689 2.5 33.9 1.0
HA B:THR41 3.5 62.5 1.0
O B:HOH763 3.5 60.4 1.0
C B:ALA37 3.6 38.8 1.0
HB1 B:ALA37 3.7 44.9 1.0
C B:GLN40 3.7 49.1 1.0
H B:GLN40 3.9 55.4 1.0
HA B:ALA37 4.0 43.8 1.0
O B:THR41 4.1 52.8 1.0
CA B:THR41 4.2 52.1 1.0
CA B:ALA37 4.2 36.5 1.0
N B:THR41 4.4 50.3 1.0
CB B:ALA37 4.4 37.4 1.0
HA B:GLN38 4.4 53.9 1.0
C B:THR41 4.4 52.3 1.0
N B:GLN40 4.6 46.1 1.0
N B:GLN38 4.6 40.3 1.0
O B:HOH810 4.7 53.1 1.0
HG3 B:GLN40 4.8 55.0 1.0
CA B:GLN40 4.8 48.2 1.0
CA B:GLN38 4.9 44.9 1.0
HB3 B:ALA37 4.9 44.9 1.0
C B:GLN38 4.9 45.7 1.0

Calcium binding site 6 out of 11 in 5f2i

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Calcium binding site 6 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:25.1
occ:1.00
 O B:GLU238 2.2 26.5 1.0
O B:THR241 2.4 23.5 1.0
OE2 B:GLU238 2.4 33.4 1.0
O B:HOH510 3.0 64.2 1.0
HG3 B:GLU238 3.2 36.2 1.0
CD B:GLU238 3.4 31.1 1.0
C B:GLU238 3.4 26.4 1.0
HA B:ASP242 3.5 39.1 1.0
C B:THR241 3.6 26.9 1.0
HA B:ALA239 3.8 34.8 1.0
CG B:GLU238 3.8 30.1 1.0
H B:THR241 3.8 31.2 1.0
HA B:GLU238 4.1 31.0 1.0
HZ1 B:LYS325 4.3 57.9 1.0
CA B:GLU238 4.3 25.8 1.0
CA B:ASP242 4.3 32.6 1.0
N B:ASP242 4.3 29.3 1.0
N B:ALA239 4.3 27.3 1.0
O B:HOH683 4.4 51.2 1.0
OE1 B:GLU238 4.4 29.8 1.0
CA B:ALA239 4.4 29.0 1.0
HE3 B:LYS325 4.5 57.8 1.0
HZ2 B:LYS325 4.5 57.9 1.0
HG2 B:GLU238 4.5 36.2 1.0
N B:THR241 4.5 26.0 1.0
HG23 B:THR241 4.5 25.3 1.0
CB B:GLU238 4.6 27.4 1.0
O B:HOH668 4.7 39.6 1.0
CA B:THR241 4.7 25.7 1.0
HE1 B:TYR245 4.8 24.9 1.0
NZ B:LYS325 4.8 48.2 1.0
HB3 B:ASP242 4.8 48.0 1.0
C B:ALA239 4.9 29.1 1.0
H B:SER240 5.0 32.9 1.0
HG22 B:THR241 5.0 25.3 1.0

Calcium binding site 7 out of 11 in 5f2i

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Calcium binding site 7 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:67.6
occ:1.00
 O B:HOH793 2.5 40.3 1.0
O B:HOH677 2.5 37.1 1.0
O B:HOH643 2.6 40.1 1.0
O B:HOH695 2.7 27.9 1.0
O B:HOH598 2.8 48.3 1.0
HB2 B:GLU197 3.7 31.9 1.0
O B:HOH596 3.8 46.9 1.0
H B:GLU197 4.1 22.4 1.0
O B:HOH693 4.3 33.1 1.0
O B:HOH825 4.4 31.2 1.0
CB B:GLU197 4.5 26.6 1.0
O B:SER195 4.6 21.3 1.0
N B:GLU197 4.6 18.6 1.0
HA B:LYS196 4.6 22.9 1.0
HB3 B:GLU197 4.7 31.9 1.0
OD2 B:ASP242 4.7 50.2 1.0
O B:HOH817 4.8 31.9 1.0
O B:HOH551 4.8 48.3 1.0
HA B:GLU197 4.9 24.6 1.0
OE1 B:GLU197 4.9 39.9 1.0
O B:HOH619 5.0 30.0 1.0
CA B:GLU197 5.0 20.5 1.0

Calcium binding site 8 out of 11 in 5f2i

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Calcium binding site 8 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:27.1
occ:1.00
 O C:HOH624 2.2 30.5 1.0
O C:HOH578 2.3 24.0 1.0
OD1 C:ASP259 2.5 35.5 1.0
OD2 C:ASP259 2.6 34.6 1.0
CG C:ASP259 2.8 34.1 1.0
HD2 C:LYS255 4.1 47.9 1.0
HB3 C:LYS255 4.1 43.1 1.0
CB C:ASP259 4.3 32.2 1.0
O C:LYS255 4.4 30.5 1.0
O C:HOH518 4.5 33.0 1.0
O C:HOH675 4.5 41.9 1.0
O C:HOH552 4.6 37.2 1.0
O C:HOH622 4.6 35.9 1.0
O C:HOH524 4.7 37.0 1.0
HB2 C:ASP259 4.7 38.6 1.0
HA C:ASP259 4.8 37.2 1.0
HB3 C:ASP259 4.8 38.6 1.0
H C:ASP259 4.9 36.5 1.0
CD C:LYS255 4.9 39.9 1.0

Calcium binding site 9 out of 11 in 5f2i

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Calcium binding site 9 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:50.7
occ:1.00
 O C:HOH527 2.4 43.2 1.0
O C:HOH656 2.5 36.7 1.0
O C:HOH677 2.5 41.3 1.0
O C:GLU13 2.6 34.0 1.0
O C:SER16 2.8 36.3 1.0
O C:HOH636 2.9 51.0 1.0
HA C:VAL17 3.3 45.4 1.0
HB3 C:GLU13 3.5 44.8 1.0
C C:GLU13 3.6 34.9 1.0
C C:SER16 3.6 35.2 1.0
HA C:GLU13 3.6 41.4 1.0
H C:ASP18 3.7 51.4 1.0
HB2 C:SER16 4.0 43.7 1.0
O C:HOH731 4.0 64.3 1.0
CA C:GLU13 4.0 34.5 1.0
CA C:VAL17 4.1 37.8 1.0
H C:SER16 4.2 39.5 1.0
CB C:GLU13 4.2 37.3 1.0
N C:VAL17 4.2 35.2 1.0
O C:HOH665 4.3 69.6 1.0
N C:ASP18 4.3 42.9 1.0
HG2 C:GLU13 4.5 46.2 1.0
CA C:SER16 4.6 34.5 1.0
HA C:LYS14 4.6 46.7 1.0
H C:GLY19 4.6 48.2 1.0
HG22 C:VAL17 4.6 47.4 1.0
N C:LYS14 4.7 36.0 1.0
CB C:SER16 4.7 36.4 1.0
C C:VAL17 4.7 39.5 1.0
N C:SER16 4.7 32.9 1.0
O C:HOH501 4.9 59.3 1.0
HB2 C:GLU13 4.9 44.8 1.0
CG C:GLU13 5.0 38.5 1.0

Calcium binding site 10 out of 11 in 5f2i

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Calcium binding site 10 out of 11 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes GLU163GLN Mutant


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 GLU163GLN Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:35.8
occ:1.00
 O D:HOH550 2.3 32.8 1.0
O D:GLU13 2.4 33.0 1.0
O D:SER16 2.4 32.0 1.0
O D:HOH728 2.6 34.2 1.0
O D:HOH697 2.7 37.5 1.0
O D:HOH743 2.8 36.6 1.0
O D:HOH649 2.9 35.3 1.0
HA D:VAL17 3.4 41.6 1.0
C D:SER16 3.4 31.7 1.0
C D:GLU13 3.4 32.9 1.0
H D:SER16 3.7 37.1 1.0
HB2 D:SER16 3.8 38.1 1.0
HA D:GLU13 3.9 39.4 1.0
HB3 D:GLU13 3.9 43.3 1.0
H D:ASP18 3.9 44.6 1.0
CA D:GLU13 4.1 32.9 1.0
HA D:LYS14 4.1 42.9 1.0
CA D:VAL17 4.2 34.6 1.0
N D:VAL17 4.2 32.1 1.0
CA D:SER16 4.3 30.8 1.0
N D:SER16 4.4 30.9 1.0
N D:LYS14 4.4 32.8 1.0
CB D:SER16 4.5 31.7 1.0
CB D:GLU13 4.5 36.1 1.0
N D:ASP18 4.5 37.2 1.0
H D:GLY19 4.6 42.3 1.0
O D:HOH583 4.6 29.4 1.0
HG22 D:VAL17 4.7 42.9 1.0
CA D:LYS14 4.7 35.8 1.0
C D:VAL17 4.9 35.5 1.0
C D:LYS14 4.9 32.5 1.0
HG2 D:GLU13 5.0 46.3 1.0
H D:VAL17 5.0 38.6 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 05:48:40 2025

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