Atomistry » Calcium » PDB 5eyh-5fjs » 5f4s
Atomistry »
  Calcium »
    PDB 5eyh-5fjs »
      5f4s »

Calcium in PDB 5f4s: Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp

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

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

Protein crystallography data

The structure of Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp, PDB code: 5f4s was solved by C.Lowkam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.10 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.011, 109.141, 238.335, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.9

Other elements in 5f4s:

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

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp (pdb code 5f4s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp, PDB code: 5f4s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 1 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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

b:33.0
occ:1.00
 O B:HOH646 2.3 34.6 1.0
O A:HOH3454 2.5 30.7 1.0
O A:HOH3298 2.5 26.6 1.0
O A:HOH3277 2.5 19.3 1.0
O A:HOH3341 2.6 20.2 1.0
O B:HOH834 2.6 38.2 1.0
O B:HOH853 2.7 50.1 1.0
HB2 A:GLU197 3.7 28.8 1.0
H A:GLU197 4.0 18.4 1.0
O A:HOH3395 4.2 49.2 1.0
HD1 B:PHE63 4.3 25.5 1.0
O A:HOH3513 4.3 23.6 1.0
O A:HOH3211 4.4 28.8 1.0
HA B:PHE63 4.4 26.6 1.0
O A:HOH3496 4.4 30.8 1.0
O A:HOH3507 4.4 22.3 1.0
N A:GLU197 4.6 15.3 1.0
CB A:GLU197 4.6 24.0 1.0
O B:PRO62 4.6 17.3 1.0
O A:SER195 4.6 15.2 1.0
HA A:LYS196 4.6 19.2 1.0
O B:HOH867 4.6 26.8 1.0
O A:HOH3493 4.7 18.2 1.0
HG21 A:ILE2 4.7 46.5 0.6
OE1 A:GLU197 4.8 70.3 1.0
HG22 A:ILE2 4.8 46.5 0.6
HB3 A:GLU197 4.9 28.8 1.0
O B:HOH625 4.9 36.2 1.0
HA A:GLU197 5.0 22.0 1.0

Calcium binding site 2 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 2 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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

b:22.3
occ:1.00
 O A:HOH3263 2.3 30.2 1.0
O A:GLU238 2.3 19.6 1.0
OE2 B:GLU84 2.3 29.5 1.0
O A:THR241 2.4 16.1 1.0
OE1 B:GLU83 2.5 33.4 1.0
OE2 A:GLU238 2.6 29.7 1.0
HG3 A:GLU238 3.3 24.6 1.0
HA A:ASP242 3.4 26.4 1.0
C A:GLU238 3.5 15.5 1.0
CD B:GLU84 3.5 25.1 1.0
C A:THR241 3.5 20.3 1.0
CD A:GLU238 3.6 23.5 1.0
CD B:GLU83 3.6 44.9 1.0
HA A:ALA239 3.7 24.3 1.0
H A:THR241 3.7 17.1 0.5
O A:HOH3294 3.8 35.7 1.0
H A:THR241 3.8 17.1 0.5
CG A:GLU238 3.9 20.5 1.0
HG2 B:GLU83 3.9 46.6 1.0
HG3 B:GLU84 4.1 24.9 1.0
O B:HOH602 4.1 41.3 1.0
HB3 B:GLU83 4.1 24.6 1.0
HA A:GLU238 4.2 23.4 1.0
CA A:ASP242 4.2 22.0 1.0
N A:ASP242 4.3 17.7 1.0
CG B:GLU83 4.3 38.8 1.0
OE1 B:GLU84 4.3 24.4 1.0
N A:ALA239 4.4 17.4 1.0
CA A:GLU238 4.4 19.5 1.0
CG B:GLU84 4.4 20.7 1.0
O B:HOH766 4.4 38.7 1.0
CA A:ALA239 4.4 20.2 1.0
N A:THR241 4.5 14.2 1.0
OD1 A:ASP242 4.5 26.2 1.0
HG23 A:THR241 4.6 26.6 1.0
HB2 A:ASP242 4.6 32.9 1.0
OE2 B:GLU83 4.6 52.6 1.0
O A:HOH3420 4.6 42.1 1.0
OE1 A:GLU238 4.6 22.7 1.0
CA A:THR241 4.6 14.6 1.0
HG2 B:GLU84 4.7 24.9 1.0
HG2 A:GLU238 4.7 24.6 1.0
O A:HOH3235 4.7 34.5 1.0
CB B:GLU83 4.7 20.5 1.0
CB A:GLU238 4.7 23.7 1.0
C A:ALA239 4.8 22.0 1.0
CB A:ASP242 4.9 27.4 1.0
HG22 A:THR241 5.0 26.6 1.0
HE1 A:TYR245 5.0 20.3 1.0

Calcium binding site 3 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 3 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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

b:33.0
occ:1.00
 O B:HOH833 2.5 29.6 1.0
O B:HOH686 2.5 22.3 1.0
O B:HOH668 2.5 22.9 1.0
O B:HOH635 2.6 32.8 1.0
HB2 B:GLU197 3.6 22.9 1.0
H B:GLU197 4.0 16.8 1.0
O B:HOH547 4.3 26.4 1.0
O B:HOH890 4.4 23.3 1.0
CB B:GLU197 4.5 19.1 1.0
N B:GLU197 4.5 14.0 1.0
O B:HOH669 4.5 49.2 1.0
HA B:LYS196 4.6 15.3 1.0
O B:HOH864 4.6 25.4 1.0
O B:SER195 4.6 16.8 1.0
O B:HOH861 4.7 24.2 1.0
O B:HOH805 4.8 49.3 1.0
OE1 B:GLU197 4.8 61.6 1.0
HB3 B:GLU197 4.8 22.9 1.0
O B:HOH850 4.9 28.0 1.0
HA B:GLU197 4.9 25.4 1.0
CA B:GLU197 5.0 21.2 1.0

Calcium binding site 4 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 4 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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

b:24.5
occ:1.00
 O B:HOH651 2.2 29.7 1.0
O B:GLU238 2.2 25.5 1.0
O B:THR241 2.3 16.3 1.0
OE2 B:GLU238 2.5 40.6 1.0
HA B:ASP242 3.3 28.1 1.0
HE3 B:MET326 3.4 45.3 0.8
HG3 B:GLU238 3.4 32.7 1.0
C B:GLU238 3.4 13.4 1.0
C B:THR241 3.5 17.1 1.0
CD B:GLU238 3.5 27.9 1.0
H B:THR241 3.7 21.6 1.0
HA B:ALA239 3.7 21.9 1.0
CG B:GLU238 4.0 27.3 1.0
CA B:ASP242 4.1 23.4 1.0
N B:ASP242 4.2 20.5 1.0
CE B:MET326 4.2 47.7 0.8
HA B:GLU238 4.2 20.4 1.0
HE2 B:MET326 4.2 45.3 0.8
N B:ALA239 4.3 15.2 1.0
CA B:ALA239 4.4 18.3 1.0
N B:THR241 4.4 18.0 1.0
CA B:GLU238 4.4 17.0 1.0
HE1 B:MET326 4.5 45.3 0.8
HG23 B:THR241 4.5 24.4 1.0
O B:HOH773 4.5 42.4 1.0
CA B:THR241 4.6 15.0 1.0
OD1 B:ASP242 4.6 45.7 1.0
OE1 B:GLU238 4.6 25.9 1.0
HB2 B:ASP242 4.6 41.7 1.0
O B:HOH573 4.6 42.1 1.0
HG2 B:GLU238 4.7 32.7 1.0
C B:ALA239 4.8 20.6 1.0
CB B:GLU238 4.8 23.7 1.0
CB B:ASP242 4.9 34.7 1.0
H B:SER240 4.9 24.1 1.0
H B:ASP242 4.9 24.6 1.0
HE1 B:TYR245 5.0 20.8 1.0
HG22 B:THR241 5.0 24.4 1.0

Calcium binding site 5 out of 5 in 5f4s

Go back to Calcium Binding Sites List in 5f4s
Calcium binding site 5 out of 5 in the Tagatose-1,6-Bisphosphate Aldolase From Streptococcus Pyogenes in Complex with Fbp


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

b:42.5
occ:1.00
 OD1 C:ASP259 2.3 41.4 1.0
OD2 C:ASP259 2.6 47.5 1.0
CG C:ASP259 2.8 48.0 1.0
HG3 C:LYS255 3.7 54.5 1.0
CB C:ASP259 4.3 42.6 1.0
O C:HOH664 4.3 35.9 1.0
O C:HOH588 4.4 41.8 1.0
HE3 C:LYS255 4.4 69.1 1.0
HG2 C:LYS255 4.5 54.5 1.0
CG C:LYS255 4.5 45.4 1.0
O C:LYS255 4.5 39.6 1.0
O C:HOH517 4.7 45.6 1.0
HB3 C:ASP259 4.7 51.1 1.0
HB2 C:ASP259 4.7 51.1 1.0
HA C:ASP259 4.8 49.4 1.0
H C:ASP259 4.9 47.5 1.0

Reference:

C.Lowkam, B.Liotard, J.Sygusch. Non-Stereospecific Substrate Cleavage By Tagatose-Bisphosphate Class I Aldolase To Be Published.
Page generated: Sun Jul 14 19:04:47 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy