Calcium in PDB 7c8h: Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate

Enzymatic activity of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate

All present enzymatic activity of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate:
4.1.2.22;

Protein crystallography data

The structure of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate, PDB code: 7c8h was solved by K.Nakata, T.Kashiwagi, E.Nango, H.Miyano, T.Mizukoshi, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.80 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 144.62, 185.8, 162.89, 90, 99.61, 90
R / Rfree (%) 16.1 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate (pdb code 7c8h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate, PDB code: 7c8h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7c8h

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Calcium binding site 1 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:60.6
occ:1.00
O2B A:TPP900 2.1 47.0 1.0
O1A A:TPP900 2.2 47.5 1.0
OD1 A:ASP182 2.2 36.2 1.0
OD1 A:ASN215 2.3 40.5 1.0
O A:TYR217 2.3 45.0 1.0
O A:HOH1028 2.3 34.3 1.0
PB A:TPP900 3.0 40.4 1.0
CG A:ASN215 3.1 37.4 1.0
PA A:TPP900 3.2 44.9 1.0
ND2 A:ASN215 3.3 35.8 1.0
O3A A:TPP900 3.3 46.6 1.0
CG A:ASP182 3.4 37.9 1.0
O1B A:TPP900 3.4 48.6 1.0
C A:TYR217 3.6 40.8 1.0
OD2 A:ASP182 4.0 40.6 1.0
N A:ASP182 4.0 38.6 1.0
O A:HIS213 4.0 34.7 1.0
O7 A:TPP900 4.1 43.9 1.0
NZ A:LYS300 4.2 40.7 1.0
N A:GLY183 4.3 38.5 1.0
N A:TYR217 4.3 42.5 1.0
O2A A:TPP900 4.3 37.7 1.0
O3B A:TPP900 4.3 42.7 1.0
N A:LYS218 4.4 37.9 1.0
CD A:LYS300 4.4 41.1 1.0
CB A:ASN215 4.5 39.0 1.0
CB A:ASP182 4.5 39.5 1.0
CA A:LYS218 4.5 38.9 1.0
CA A:TYR217 4.6 41.0 1.0
N A:ASN215 4.6 32.5 1.0
CA A:ASP182 4.6 39.1 1.0
CG2 A:THR223 4.7 35.3 1.0
CE A:LYS300 4.7 42.4 1.0
C A:ASN215 4.8 37.9 1.0
CA A:ASN215 4.8 35.4 1.0
N A:GLY216 4.9 37.8 1.0
C A:ASP182 4.9 37.5 1.0
C A:GLY181 4.9 38.2 1.0
CA A:GLY181 4.9 42.3 1.0

Calcium binding site 2 out of 8 in 7c8h

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Calcium binding site 2 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:55.7
occ:1.00
O1A B:TPP903 2.1 43.6 1.0
OD1 B:ASP182 2.2 31.4 1.0
OD1 B:ASN215 2.2 31.4 1.0
O1B B:TPP903 2.2 39.3 1.0
O B:TYR217 2.3 37.7 1.0
O B:HOH1010 2.5 35.4 1.0
PB B:TPP903 3.1 46.5 1.0
CG B:ASN215 3.1 38.3 1.0
PA B:TPP903 3.3 44.9 1.0
CG B:ASP182 3.3 32.8 1.0
O3A B:TPP903 3.4 45.3 1.0
ND2 B:ASN215 3.5 36.9 1.0
C B:TYR217 3.5 33.3 1.0
O2B B:TPP903 3.5 43.3 1.0
OD2 B:ASP182 3.9 35.5 1.0
N B:ASP182 4.0 36.5 1.0
O B:HIS213 4.1 41.6 1.0
N B:TYR217 4.1 39.4 1.0
O7 B:TPP903 4.1 41.2 1.0
N B:GLY183 4.2 37.0 1.0
NZ B:LYS300 4.2 40.0 1.0
N B:LYS218 4.4 36.9 1.0
O2A B:TPP903 4.4 37.5 1.0
O3B B:TPP903 4.4 52.6 1.0
CA B:TYR217 4.4 35.2 1.0
CB B:ASN215 4.5 40.0 1.0
CB B:ASP182 4.5 34.3 1.0
CG2 B:THR223 4.5 39.2 1.0
N B:ASN215 4.5 35.0 1.0
CA B:LYS218 4.6 36.7 1.0
CA B:ASP182 4.6 36.0 1.0
CD B:LYS300 4.7 36.5 1.0
N B:GLY216 4.7 41.9 1.0
CA B:ASN215 4.8 37.5 1.0
C B:ASN215 4.8 39.0 1.0
C B:ASP182 4.8 35.5 1.0
CE B:LYS300 4.8 38.7 1.0
C B:GLY181 4.9 36.8 1.0

Calcium binding site 3 out of 8 in 7c8h

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Calcium binding site 3 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca901

b:70.1
occ:1.00
OD1 C:ASP182 2.1 73.6 1.0
O C:TYR217 2.2 47.2 1.0
O3B C:TPP900 2.3 57.3 1.0
O2A C:TPP900 2.3 66.3 1.0
O C:HOH1058 2.3 42.1 1.0
OD1 C:ASN215 2.4 58.7 1.0
CG C:ASN215 3.0 57.9 1.0
ND2 C:ASN215 3.2 50.1 1.0
CG C:ASP182 3.3 60.4 1.0
PB C:TPP900 3.4 63.3 1.0
C C:TYR217 3.4 52.1 1.0
PA C:TPP900 3.5 60.3 1.0
O3A C:TPP900 3.7 63.7 1.0
O2B C:TPP900 3.9 53.2 1.0
OD2 C:ASP182 3.9 53.0 1.0
N C:TYR217 4.0 53.6 1.0
N C:ASP182 4.0 47.7 1.0
O C:HIS213 4.0 45.2 1.0
N C:GLY183 4.3 54.3 1.0
CG2 C:THR223 4.3 57.1 1.0
CB C:ASN215 4.3 59.6 1.0
N C:LYS218 4.3 54.1 1.0
O7 C:TPP900 4.3 60.3 1.0
CA C:TYR217 4.4 53.9 1.0
N C:ASN215 4.4 59.4 1.0
NZ C:LYS300 4.4 47.6 1.0
CB C:ASP182 4.4 56.9 1.0
N C:GLY216 4.5 45.9 1.0
CA C:LYS218 4.5 60.2 1.0
C C:ASN215 4.6 52.2 1.0
O1A C:TPP900 4.6 65.5 1.0
CA C:ASP182 4.6 54.4 1.0
CA C:ASN215 4.6 56.7 1.0
CE C:LYS300 4.7 46.7 1.0
O1B C:TPP900 4.7 90.6 1.0
CD C:LYS300 4.8 51.9 1.0
C C:ASP182 4.9 52.2 1.0

Calcium binding site 4 out of 8 in 7c8h

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Calcium binding site 4 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca904

b:71.6
occ:1.00
OD1 D:ASP182 1.9 61.5 1.0
O2A D:TPP903 2.1 64.1 1.0
O1B D:TPP903 2.2 58.9 1.0
O D:HOH1049 2.2 39.3 1.0
O D:TYR217 2.4 42.6 1.0
OD1 D:ASN215 2.5 48.5 1.0
CG D:ASP182 3.0 52.2 1.0
CG D:ASN215 3.1 45.8 1.0
ND2 D:ASN215 3.2 44.6 1.0
PA D:TPP903 3.2 54.1 1.0
PB D:TPP903 3.3 55.1 1.0
O3A D:TPP903 3.5 60.5 1.0
C D:TYR217 3.6 50.7 1.0
OD2 D:ASP182 3.6 49.5 1.0
N D:ASP182 3.7 53.5 1.0
O2B D:TPP903 3.8 50.9 1.0
N D:GLY183 3.9 47.9 1.0
O D:HIS213 4.0 44.9 1.0
N D:TYR217 4.1 48.5 1.0
O1A D:TPP903 4.1 56.9 1.0
CB D:ASP182 4.2 57.3 1.0
O7 D:TPP903 4.3 60.0 1.0
CG2 D:THR223 4.3 52.4 1.0
CA D:ASP182 4.3 56.5 1.0
N D:ASN215 4.3 54.6 1.0
CB D:ASN215 4.4 49.1 1.0
CA D:TYR217 4.5 50.5 1.0
N D:LYS218 4.5 54.4 1.0
C D:GLY181 4.5 49.3 1.0
O3B D:TPP903 4.6 83.1 1.0
C D:ASP182 4.6 49.5 1.0
N D:GLY216 4.6 43.5 1.0
CA D:GLY181 4.7 53.2 1.0
CA D:ASN215 4.7 53.1 1.0
CA D:LYS218 4.7 56.0 1.0
NZ D:LYS300 4.7 53.8 1.0
C D:ASN215 4.7 48.2 1.0
CE D:LYS300 4.8 52.5 1.0
CA D:GLY183 4.9 50.1 1.0

Calcium binding site 5 out of 8 in 7c8h

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Calcium binding site 5 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca903

b:62.8
occ:1.00
OD1 E:ASN215 2.1 44.7 1.0
O2A E:TPP902 2.1 49.3 1.0
OD1 E:ASP182 2.2 45.2 1.0
O2B E:TPP902 2.2 40.5 1.0
O E:TYR217 2.2 41.7 1.0
O E:HOH1017 2.4 40.0 1.0
CG E:ASN215 2.9 40.2 1.0
ND2 E:ASN215 3.2 39.0 1.0
PB E:TPP902 3.2 43.3 1.0
CG E:ASP182 3.3 44.4 1.0
PA E:TPP902 3.3 45.6 1.0
C E:TYR217 3.4 38.5 1.0
O3A E:TPP902 3.5 46.0 1.0
O1B E:TPP902 3.7 45.9 1.0
OD2 E:ASP182 3.8 41.6 1.0
N E:ASP182 3.9 47.8 1.0
N E:TYR217 4.0 39.9 1.0
O E:HIS213 4.0 36.0 1.0
N E:GLY183 4.1 42.4 1.0
NZ E:LYS300 4.2 47.4 1.0
O7 E:TPP902 4.3 45.9 1.0
N E:LYS218 4.3 40.3 1.0
CA E:TYR217 4.3 37.8 1.0
CB E:ASN215 4.3 41.4 1.0
O1A E:TPP902 4.3 46.5 1.0
N E:ASN215 4.3 41.5 1.0
CG2 E:THR223 4.4 50.7 1.0
CB E:ASP182 4.5 46.8 1.0
O3B E:TPP902 4.5 50.4 1.0
N E:GLY216 4.5 39.9 1.0
CA E:ASP182 4.6 44.1 1.0
CA E:LYS218 4.6 39.8 1.0
CD E:LYS300 4.6 45.4 1.0
CA E:ASN215 4.7 42.3 1.0
CE E:LYS300 4.7 43.4 1.0
C E:ASN215 4.7 38.9 1.0
C E:ASP182 4.8 42.5 1.0
C E:GLY181 4.9 49.7 1.0
CA E:GLY181 5.0 50.0 1.0
CA E:GLY183 5.0 42.7 1.0

Calcium binding site 6 out of 8 in 7c8h

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Calcium binding site 6 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca901

b:79.6
occ:1.00
O3B F:TPP900 2.0 54.1 1.0
OD1 F:ASP182 2.1 45.4 1.0
O1A F:TPP900 2.1 48.5 1.0
O F:TYR217 2.2 51.8 1.0
OD1 F:ASN215 2.3 51.5 1.0
O F:HOH1031 2.5 43.9 1.0
PA F:TPP900 3.2 52.3 1.0
PB F:TPP900 3.2 58.6 1.0
CG F:ASN215 3.2 49.9 1.0
CG F:ASP182 3.2 47.7 1.0
O3A F:TPP900 3.4 60.8 1.0
C F:TYR217 3.5 52.2 1.0
ND2 F:ASN215 3.5 48.5 1.0
O2B F:TPP900 3.8 63.4 1.0
OD2 F:ASP182 3.9 45.6 1.0
NZ F:LYS300 3.9 57.0 1.0
N F:ASP182 4.0 40.8 1.0
O7 F:TPP900 4.0 58.7 1.0
N F:GLY183 4.1 54.8 1.0
O F:HIS213 4.2 45.9 1.0
CG2 F:THR223 4.2 45.8 1.0
N F:TYR217 4.3 45.6 1.0
N F:LYS218 4.3 56.0 1.0
O2A F:TPP900 4.4 54.8 1.0
CB F:ASP182 4.4 47.7 1.0
CA F:LYS218 4.4 59.9 1.0
O1B F:TPP900 4.4 69.2 1.0
CA F:TYR217 4.5 46.6 1.0
CA F:ASP182 4.5 45.6 1.0
CB F:ASN215 4.6 51.2 1.0
N F:ASN215 4.6 46.1 1.0
CD F:LYS300 4.7 56.7 1.0
C F:ASP182 4.7 49.0 1.0
C F:GLY181 4.8 41.2 1.0
CE F:LYS300 4.8 54.8 1.0
N F:GLY216 4.8 49.5 1.0
CA F:GLY181 4.8 41.2 1.0
CA F:ASN215 4.9 50.9 1.0
CA F:GLY183 5.0 52.1 1.0
C F:ASN215 5.0 49.2 1.0

Calcium binding site 7 out of 8 in 7c8h

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Calcium binding site 7 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca902

b:70.2
occ:1.00
O2A G:TPP901 2.1 39.8 1.0
OD1 G:ASP182 2.4 42.7 1.0
OD1 G:ASN215 2.4 46.9 1.0
O2B G:TPP901 2.4 44.5 1.0
O G:TYR217 2.5 41.2 1.0
CG G:ASN215 3.1 45.9 1.0
PB G:TPP901 3.2 39.3 1.0
O1B G:TPP901 3.2 38.1 1.0
PA G:TPP901 3.3 41.0 1.0
ND2 G:ASN215 3.3 50.9 1.0
CG G:ASP182 3.4 42.4 1.0
O3A G:TPP901 3.4 41.1 1.0
O G:HIS213 3.7 38.3 1.0
C G:TYR217 3.7 38.0 1.0
N G:ASP182 3.8 40.1 1.0
OD2 G:ASP182 4.0 39.5 1.0
N G:GLY183 4.2 43.1 1.0
O1A G:TPP901 4.2 39.2 1.0
O7 G:TPP901 4.3 42.6 1.0
CB G:ASP182 4.3 43.7 1.0
N G:TYR217 4.4 39.8 1.0
N G:ASN215 4.4 41.2 1.0
NZ G:LYS300 4.4 45.3 1.0
CB G:ASN215 4.5 43.8 1.0
CA G:ASP182 4.5 40.4 1.0
N G:LYS218 4.6 37.8 1.0
O3B G:TPP901 4.6 42.8 1.0
CA G:GLY181 4.7 39.7 1.0
CA G:TYR217 4.7 37.2 1.0
CG2 G:THR223 4.7 37.0 1.0
C G:GLY181 4.7 40.8 1.0
C G:ASP182 4.8 44.6 1.0
N G:GLY216 4.8 42.2 1.0
CA G:LYS218 4.8 38.0 1.0
CA G:ASN215 4.8 45.2 1.0
CD G:LYS300 4.9 35.8 1.0
C G:HIS213 4.9 37.5 1.0
CE G:LYS300 4.9 38.0 1.0
C G:ASN215 5.0 44.4 1.0

Calcium binding site 8 out of 8 in 7c8h

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Calcium binding site 8 out of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca903

b:69.9
occ:1.00
O1A H:TPP902 2.0 49.0 1.0
O1B H:TPP902 2.1 47.3 1.0
OD1 H:ASN215 2.2 48.6 1.0
O H:TYR217 2.2 40.4 1.0
OD1 H:ASP182 2.3 41.9 1.0
O H:HOH1019 2.4 44.9 1.0
PB H:TPP902 3.0 48.0 1.0
PA H:TPP902 3.0 43.0 1.0
CG H:ASN215 3.1 46.2 1.0
O3A H:TPP902 3.1 47.3 1.0
ND2 H:ASN215 3.3 45.5 1.0
CG H:ASP182 3.4 40.4 1.0
C H:TYR217 3.5 39.6 1.0
O2B H:TPP902 3.5 47.0 1.0
N H:ASP182 3.9 34.9 1.0
O7 H:TPP902 4.0 47.4 1.0
OD2 H:ASP182 4.1 36.9 1.0
N H:GLY183 4.1 43.5 1.0
O2A H:TPP902 4.2 48.0 1.0
NZ H:LYS300 4.2 47.0 1.0
O H:HIS213 4.2 40.8 1.0
N H:TYR217 4.2 37.0 1.0
N H:LYS218 4.3 43.7 1.0
O3B H:TPP902 4.4 47.6 1.0
CG2 H:THR223 4.4 43.2 1.0
CB H:ASN215 4.5 47.2 1.0
CA H:TYR217 4.5 41.1 1.0
CA H:LYS218 4.5 48.8 1.0
CB H:ASP182 4.6 41.6 1.0
CA H:ASP182 4.6 38.1 1.0
N H:ASN215 4.7 44.2 1.0
CD H:LYS300 4.7 43.5 1.0
CE H:LYS300 4.7 44.7 1.0
CA H:GLY181 4.8 40.3 1.0
C H:GLY181 4.8 37.4 1.0
C H:ASP182 4.8 43.0 1.0
CA H:ASN215 4.9 45.3 1.0
N H:GLY216 5.0 44.6 1.0
C H:ASN215 5.0 43.8 1.0

Reference:

K.Nakata, T.Kashiwagi, E.Nango, H.Miyano, T.Mizukoshi, S.Iwata. Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate To Be Published.
Page generated: Sat Jul 10 11:15:42 2021

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