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Calcium in PDB 5f4w: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp

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

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

Protein crystallography data

The structure of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp, PDB code: 5f4w was solved by C.Lowkam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.955, 107.373, 237.730, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.6

Other elements in 5f4w:

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

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp (pdb code 5f4w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp, PDB code: 5f4w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5f4w

Go back to Calcium Binding Sites List in 5f4w
Calcium binding site 1 out of 4 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp


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

b:22.2
occ:0.50
 O C:HOH905 2.3 43.7 1.0
O C:HOH839 2.5 72.4 1.0
O A:HOH3423 3.0 52.1 1.0
O C:HOH931 3.0 45.4 1.0
O A:HOH3115 3.8 41.7 1.0
O C:HOH719 3.8 37.4 1.0
O A:HOH3485 3.9 66.9 1.0
OE2 A:GLU140 3.9 37.5 1.0
O C:HOH887 4.3 77.0 1.0
O B:HOH792 4.3 38.8 1.0
O B:HOH733 4.3 49.4 1.0
HH12 B:ARG115 4.4 39.3 1.0
NH1 B:ARG115 4.4 32.7 1.0
O A:HOH3259 4.5 60.9 1.0
O B:HOH540 4.5 38.8 1.0
HH11 B:ARG115 4.6 39.3 1.0
CD A:GLU140 4.6 36.3 1.0
CZ B:ARG115 4.6 30.6 1.0
O C:HOH750 4.8 47.1 1.0
HH22 B:ARG115 4.8 37.8 1.0
NH2 B:ARG115 4.8 31.5 1.0
O B:HOH717 4.9 35.6 1.0
O C:ASP316 4.9 35.1 1.0
OE1 A:GLU140 4.9 37.9 1.0

Calcium binding site 2 out of 4 in 5f4w

Go back to Calcium Binding Sites List in 5f4w
Calcium binding site 2 out of 4 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp


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

b:30.0
occ:1.00
 OE2 C:GLU84 2.2 41.0 1.0
O A:GLU238 2.2 32.4 1.0
O C:HOH777 2.3 48.3 1.0
O A:THR241 2.4 27.3 1.0
OE2 A:GLU238 2.4 39.1 1.0
OE1 C:GLU83 2.5 52.5 1.0
HG3 A:GLU238 3.3 40.5 1.0
C A:GLU238 3.4 30.6 1.0
CD C:GLU84 3.4 38.5 1.0
CD A:GLU238 3.5 37.1 1.0
CD C:GLU83 3.5 52.1 1.0
HA A:ASP242 3.6 38.5 1.0
O A:HOH3117 3.6 37.2 1.0
C A:THR241 3.6 27.5 1.0
H A:THR241 3.7 31.1 0.6
HG3 C:GLU83 3.7 52.8 1.0
HA A:ALA239 3.7 33.7 1.0
H A:THR241 3.8 31.1 0.4
CG A:GLU238 3.9 33.8 1.0
HG2 C:GLU83 3.9 52.8 1.0
CG C:GLU83 4.0 44.0 1.0
HA A:GLU238 4.1 35.9 1.0
HG3 C:GLU84 4.2 43.2 1.0
OE1 C:GLU84 4.2 42.3 1.0
HG23 A:THR241 4.3 29.6 1.0
N A:ALA239 4.3 27.0 1.0
CA A:GLU238 4.3 29.9 1.0
N A:ASP242 4.4 30.5 1.0
CA A:ASP242 4.4 32.1 1.0
CA A:ALA239 4.4 28.1 1.0
CG C:GLU84 4.4 36.0 1.0
O A:HOH3403 4.4 69.2 1.0
N A:THR241 4.4 25.9 1.0
OE1 A:GLU238 4.6 35.8 1.0
O A:HOH3401 4.6 42.6 1.0
CA A:THR241 4.6 27.3 1.0
HD3 A:LYS325 4.6 70.5 1.0
OE2 C:GLU83 4.6 52.4 1.0
HG22 A:THR241 4.7 29.6 1.0
HG2 A:GLU238 4.7 40.5 1.0
HG2 C:GLU84 4.7 43.2 1.0
HE1 A:TYR245 4.7 27.7 1.0
HZ1 A:LYS325 4.7 57.3 1.0
CB A:GLU238 4.7 30.8 1.0
C A:ALA239 4.8 28.5 1.0
CG2 A:THR241 4.9 24.6 1.0
H A:SER240 4.9 30.6 0.6
H A:SER240 4.9 30.4 0.4

Calcium binding site 3 out of 4 in 5f4w

Go back to Calcium Binding Sites List in 5f4w
Calcium binding site 3 out of 4 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp


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

b:21.8
occ:0.50
 O C:HOH814 2.6 62.5 1.0
O C:ALA37 2.6 56.8 1.0
O C:GLN40 2.6 60.8 1.0
O C:HOH512 3.2 41.4 1.0
HA C:THR41 3.3 79.6 1.0
C C:ALA37 3.7 55.2 1.0
C C:GLN40 3.7 61.7 1.0
HB1 C:ALA37 3.7 62.4 1.0
O C:THR41 3.8 62.2 1.0
H C:GLN40 3.9 72.6 1.0
CA C:THR41 4.1 66.3 1.0
HA C:GLN38 4.3 73.2 1.0
C C:THR41 4.3 63.1 1.0
HA C:ALA37 4.3 62.9 1.0
N C:THR41 4.4 64.8 1.0
CA C:ALA37 4.5 52.4 1.0
CB C:ALA37 4.5 52.0 1.0
N C:GLN40 4.6 60.5 1.0
O C:HOH846 4.6 59.4 1.0
N C:GLN38 4.7 59.6 1.0
CA C:GLN38 4.8 61.0 1.0
CA C:GLN40 4.8 62.1 1.0
C C:GLN38 4.9 61.8 1.0
HB3 C:ALA37 5.0 62.4 1.0
HB3 C:GLN40 5.0 75.1 1.0

Calcium binding site 4 out of 4 in 5f4w

Go back to Calcium Binding Sites List in 5f4w
Calcium binding site 4 out of 4 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Tbp


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

b:36.1
occ:1.00
 O D:HOH679 2.4 59.5 1.0
O D:GLU84 2.4 51.9 1.0
O D:HOH734 2.4 68.3 1.0
O D:HOH532 2.6 35.2 1.0
O D:HOH528 3.0 41.8 1.0
C D:GLU84 3.5 51.4 1.0
HA D:GLU84 3.6 66.6 1.0
HB3 D:GLU84 3.8 74.3 1.0
HG22 D:VAL17 4.0 51.3 1.0
CA D:GLU84 4.0 55.5 1.0
O D:SER16 4.2 37.3 1.0
HG3 D:GLU84 4.3 81.2 1.0
CB D:GLU84 4.4 61.9 1.0
HA D:ALA85 4.4 38.7 1.0
O D:LYS14 4.4 31.9 1.0
HA D:LYS14 4.6 39.4 1.0
N D:ALA85 4.6 33.7 1.0
HA D:SER65 4.7 36.2 1.0
HG23 D:VAL17 4.7 51.3 1.0
O D:SER65 4.7 29.6 1.0
CG2 D:VAL17 4.7 42.8 1.0
O D:HOH756 4.8 52.9 1.0
CG D:GLU84 4.9 67.7 1.0
CA D:ALA85 5.0 32.3 1.0

Reference:

C.Lowkam, B.Liotard, J.Sygusch. Non-Stereospecific Substrate Cleavage By Tagatose-Bisphosphate Class I Aldolase To Be Published.
Page generated: Sat Dec 12 05:24:43 2020

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