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Calcium in PDB 5tea: Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae

Enzymatic activity of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae

All present enzymatic activity of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae, PDB code: 5tea was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.03 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.720, 65.650, 133.210, 90.00, 115.65, 90.00
R / Rfree (%) 17 / 20.9

Other elements in 5tea:

The structure of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae (pdb code 5tea). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae, PDB code: 5tea:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5tea

Go back to Calcium Binding Sites List in 5tea
Calcium binding site 1 out of 6 in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:36.7
occ:1.00
 O A:HOH303 2.1 32.3 1.0
OD1 A:ASP104 2.2 32.1 1.0
OD2 A:ASP65 2.4 35.6 1.0
OD2 A:ASP72 2.4 27.2 1.0
O A:HOH321 2.4 21.3 1.0
O A:GLU70 2.6 40.1 1.0
OD2 A:ASP69 2.7 56.9 1.0
CG A:ASP72 3.1 24.4 1.0
CG A:ASP65 3.3 40.0 1.0
CG A:ASP69 3.3 54.3 1.0
OD1 A:ASP72 3.4 29.3 1.0
CG A:ASP104 3.5 31.5 1.0
O A:HOH319 3.6 31.0 1.0
OD1 A:ASP65 3.7 37.0 1.0
CB A:ASP69 3.8 33.2 1.0
C A:GLU70 3.9 37.0 1.0
O A:HOH331 4.0 41.3 1.0
OD2 A:ASP104 4.2 34.8 1.0
OD1 A:ASP69 4.2 56.0 1.0
N A:ASP72 4.2 23.4 1.0
CB A:ASP72 4.3 23.6 1.0
CA A:ASP104 4.5 22.8 1.0
CB A:ASP104 4.5 31.0 1.0
CB A:ASP65 4.5 46.8 1.0
NZ A:LYS106 4.6 25.1 1.0
CA A:LEU71 4.6 23.6 1.0
C A:ASP69 4.6 41.9 1.0
N A:GLU70 4.6 36.1 1.0
O A:ASP105 4.7 20.9 1.0
N A:LEU71 4.7 33.7 1.0
O A:HOH326 4.7 34.8 1.0
C A:ASP104 4.8 21.5 1.0
CA A:ASP69 4.8 35.3 1.0
C A:LEU71 4.8 23.6 1.0
CA A:GLU70 4.9 39.2 1.0
O A:ASP69 4.9 41.9 1.0
CA A:ASP72 4.9 21.2 1.0
O A:ASP104 4.9 23.1 1.0

Calcium binding site 2 out of 6 in 5tea

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Calcium binding site 2 out of 6 in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:39.5
occ:1.00
 O B:HOH301 2.0 20.1 1.0
OD1 B:ASP104 2.3 30.3 1.0
OD2 B:ASP65 2.4 54.3 1.0
O B:HOH324 2.4 22.6 1.0
OD2 B:ASP72 2.7 23.0 1.0
OD2 B:ASP69 2.8 53.7 1.0
O B:GLU70 2.8 43.6 1.0
CG B:ASP69 3.2 58.1 1.0
CG B:ASP72 3.3 23.7 1.0
CG B:ASP65 3.4 53.5 1.0
OD1 B:ASP72 3.4 25.6 1.0
CG B:ASP104 3.5 31.8 1.0
CB B:ASP69 3.5 41.5 1.0
O B:HOH359 3.7 35.5 1.0
C B:GLU70 4.0 35.1 1.0
OD2 B:ASP104 4.0 32.7 1.0
OD1 B:ASP69 4.1 67.0 1.0
OD1 B:ASP65 4.1 49.7 1.0
N B:ASP72 4.2 22.1 1.0
CB B:ASP65 4.3 51.5 1.0
C B:ASP69 4.4 42.1 1.0
CB B:ASP72 4.4 18.2 1.0
CA B:LEU71 4.6 21.3 1.0
CA B:ASP69 4.6 42.2 1.0
N B:GLU70 4.6 42.5 1.0
CB B:ASP104 4.6 25.9 1.0
CA B:ASP104 4.7 22.8 1.0
O B:ASP69 4.7 40.9 1.0
N B:LEU71 4.7 30.3 1.0
O B:ASP105 4.8 22.4 1.0
NZ B:LYS106 4.8 21.8 1.0
C B:LEU71 4.8 19.3 1.0
O B:HOH322 4.8 35.5 1.0
CA B:ASP72 4.9 17.6 1.0
CA B:GLU70 4.9 49.9 1.0
C B:ASP104 4.9 19.0 1.0

Calcium binding site 3 out of 6 in 5tea

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Calcium binding site 3 out of 6 in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:32.5
occ:1.00
 OD2 C:ASP67 2.3 32.2 1.0
O C:HOH351 2.3 31.1 1.0
OD2 C:ASP72 2.4 21.2 1.0
O C:HOH377 2.4 29.0 1.0
OD1 C:ASP104 2.5 35.1 1.0
OD1 C:ASP72 2.8 24.2 1.0
OD2 C:ASP104 2.8 33.6 1.0
CG C:ASP72 2.9 19.4 1.0
O C:HOH327 2.9 28.8 1.0
CG C:ASP104 3.0 29.5 1.0
CG C:ASP67 3.4 43.6 1.0
OD1 C:ASP67 3.9 40.1 1.0
O C:HOH317 3.9 20.9 1.0
OH C:TYR57 4.3 20.6 1.0
CB C:ASP72 4.4 20.4 1.0
NZ C:LYS106 4.5 18.9 1.0
O C:HOH347 4.5 34.2 1.0
CB C:ASP104 4.5 25.7 1.0
O C:GLU70 4.5 31.4 1.0
O C:HOH313 4.5 31.5 1.0
CB C:ASP67 4.6 47.4 1.0
O C:HOH374 4.7 34.8 1.0
OD2 C:ASP69 4.8 46.4 1.0
CB C:ASP69 4.8 40.5 1.0
O C:HOH417 4.8 38.0 1.0
O C:HOH305 5.0 27.3 1.0
N C:ASP72 5.0 18.6 1.0

Calcium binding site 4 out of 6 in 5tea

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Calcium binding site 4 out of 6 in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:42.9
occ:1.00
 OD2 D:ASP72 2.4 28.6 1.0
O D:HOH392 2.4 41.4 1.0
OD2 D:ASP67 2.5 50.0 1.0
O D:HOH323 2.5 39.5 1.0
OD1 D:ASP104 2.6 41.4 1.0
OD2 D:ASP104 2.7 45.2 1.0
OD1 D:ASP72 2.8 25.6 1.0
O D:HOH316 2.9 33.5 1.0
CG D:ASP72 2.9 28.8 1.0
CG D:ASP104 3.0 41.1 1.0
CG D:ASP67 3.6 58.0 1.0
O D:HOH302 3.9 28.9 1.0
OD1 D:ASP67 4.0 57.1 1.0
OH D:TYR57 4.3 23.6 1.0
NZ D:LYS106 4.4 27.6 1.0
CB D:ASP72 4.4 27.5 1.0
O D:GLU70 4.5 34.7 1.0
CB D:ASP104 4.5 35.2 1.0
O D:HOH356 4.7 33.5 1.0
CB D:ASP69 4.7 49.5 1.0
CB D:ASP67 4.8 61.1 1.0
O D:HOH306 4.9 34.5 1.0

Calcium binding site 5 out of 6 in 5tea

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Calcium binding site 5 out of 6 in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:34.8
occ:1.00
 O E:HOH395 2.4 33.3 1.0
OD2 E:ASP72 2.5 26.5 1.0
O E:HOH357 2.5 26.2 1.0
OD2 E:ASP67 2.6 45.9 1.0
OD1 E:ASP104 2.7 37.5 1.0
O E:HOH363 2.7 31.5 1.0
OD1 E:ASP72 2.7 27.3 1.0
OD2 E:ASP104 2.7 36.6 1.0
CG E:ASP72 2.9 28.7 1.0
CG E:ASP104 3.1 37.0 1.0
CG E:ASP67 3.6 49.9 1.0
OD1 E:ASP67 4.0 48.7 1.0
O E:HOH301 4.1 27.2 1.0
OH E:TYR57 4.3 24.9 1.0
O E:HOH343 4.4 31.8 1.0
CB E:ASP72 4.4 23.2 1.0
O E:HOH316 4.5 40.2 1.0
NZ E:LYS106 4.5 23.6 1.0
O E:GLU70 4.5 33.3 1.0
CB E:ASP104 4.6 36.1 1.0
O E:HOH364 4.7 34.3 1.0
O E:HOH315 4.7 26.5 1.0
CB E:ASP69 4.8 46.9 1.0
O E:HOH319 4.9 40.8 1.0
CB E:ASP67 4.9 57.2 1.0
OD2 E:ASP69 4.9 60.0 1.0

Calcium binding site 6 out of 6 in 5tea

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Calcium binding site 6 out of 6 in the Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Inorganic Pyrophosphatase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:45.6
occ:1.00
 O F:HOH384 2.3 41.0 1.0
O F:HOH322 2.4 44.4 1.0
OD2 F:ASP72 2.4 34.4 1.0
OD2 F:ASP67 2.6 52.0 1.0
OD1 F:ASP104 2.7 44.5 1.0
OD1 F:ASP72 2.7 29.9 1.0
O F:HOH343 2.9 35.8 1.0
OD2 F:ASP104 2.9 49.4 1.0
CG F:ASP72 2.9 30.6 1.0
CG F:ASP104 3.1 47.5 1.0
CG F:ASP67 3.6 57.6 1.0
O F:HOH313 3.9 33.5 1.0
OD1 F:ASP67 4.0 52.8 1.0
OH F:TYR57 4.2 35.6 1.0
O F:GLU70 4.4 47.8 1.0
CB F:ASP72 4.4 26.6 1.0
NZ F:LYS106 4.4 30.7 1.0
CB F:ASP69 4.6 59.4 1.0
CB F:ASP104 4.6 43.9 1.0
O F:HOH355 4.7 41.8 1.0
O F:HOH347 4.7 35.7 1.0
O F:HOH369 4.8 43.4 1.0
OD2 F:ASP69 4.8 59.6 1.0
CB F:ASP67 4.9 58.7 1.0

Reference:

T.E.Edwards, P.S.Horanyi, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of An Inorganic Pyrophosphatase From To Be Published.
Page generated: Mon Jul 15 11:11:59 2024

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