Calcium in PDB 8tff: Porx with BEF3 Phosphate Analog

Protein crystallography data

The structure of Porx with BEF3 Phosphate Analog, PDB code: 8tff was solved by A.Saran, N.Zeytuni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.81 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.32, 97.518, 131.258, 90, 90, 90
R / Rfree (%) 16.5 / 23.1

Other elements in 8tff:

The structure of Porx with BEF3 Phosphate Analog also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Porx with BEF3 Phosphate Analog (pdb code 8tff). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Porx with BEF3 Phosphate Analog, PDB code: 8tff:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 8tff

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Calcium binding site 1 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:21.9
occ:1.00
OD1 A:ASN238 2.1 21.2 1.0
OD2 A:ASP414 2.2 16.1 1.0
OG1 A:THR271 2.2 16.9 1.0
OD1 A:ASP237 2.2 24.5 1.0
NE2 A:HIS415 2.4 15.4 1.0
CG A:ASP414 2.9 20.3 1.0
OD1 A:ASP414 3.1 21.3 1.0
CG A:ASP237 3.1 23.6 1.0
CB A:THR271 3.2 19.8 1.0
CE1 A:HIS415 3.2 17.9 1.0
CD2 A:HIS415 3.2 16.0 1.0
O A:HOH703 3.3 32.2 1.0
CG A:ASN238 3.3 23.8 1.0
OD2 A:ASP237 3.6 25.9 1.0
CA A:THR271 3.6 20.9 1.0
CG2 A:THR271 3.6 21.2 1.0
N A:THR271 3.7 22.2 1.0
N A:ASN238 3.8 19.5 1.0
ND2 A:ASN238 4.2 23.3 1.0
ND1 A:HIS415 4.2 16.0 1.0
CG A:HIS415 4.2 16.1 1.0
CA A:ASN238 4.3 21.1 1.0
CB A:ASP237 4.3 22.5 1.0
CB A:ASN238 4.4 22.0 1.0
CB A:ASP414 4.4 20.5 1.0
CA A:ASP237 4.4 22.2 1.0
C A:ASP237 4.5 22.0 1.0
O A:HOH851 4.6 29.4 1.0
C A:ALA270 4.7 21.3 1.0
NH1 A:ARG275 4.7 24.1 1.0

Calcium binding site 2 out of 7 in 8tff

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Calcium binding site 2 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:35.2
occ:1.00
O A:MET467 2.3 28.6 1.0
O A:HOH876 2.3 38.1 1.0
O A:LYS455 2.3 34.1 1.0
O A:HOH748 2.4 29.2 1.0
OXT A:ACT604 2.6 34.6 1.0
O A:ACT604 2.9 36.3 1.0
C A:ACT604 3.1 44.2 1.0
C A:MET467 3.3 30.0 1.0
C A:LYS455 3.5 27.1 1.0
O A:SER469 4.0 29.4 1.0
CA A:MET467 4.1 36.1 1.0
CA A:LYS455 4.2 27.7 1.0
CB A:LYS455 4.2 35.2 1.0
OE2 A:GLU456 4.2 37.9 1.0
N A:SER468 4.3 29.3 1.0
CA A:SER468 4.4 30.8 1.0
N A:GLU456 4.5 25.8 1.0
C A:SER468 4.5 26.5 1.0
O A:HOH921 4.5 12.3 1.0
CH3 A:ACT604 4.6 41.2 1.0
CB A:MET467 4.7 42.5 1.0
CA A:GLU456 4.7 30.7 1.0
N A:SER469 4.7 24.1 1.0
CG A:GLU456 4.8 35.1 1.0
C A:SER469 4.9 24.8 1.0
CD A:GLU456 4.9 36.6 1.0
O A:SER468 5.0 28.7 1.0

Calcium binding site 3 out of 7 in 8tff

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Calcium binding site 3 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:40.2
occ:1.00
F3 A:BEF605 2.1 50.3 1.0
OD2 A:ASP54 2.3 35.6 1.0
O A:ASN56 2.3 34.6 0.5
O A:ASN56 2.4 34.1 0.5
O A:HOH728 2.4 34.0 1.0
OD1 A:ASP11 2.5 39.6 1.0
O A:HOH800 2.5 37.1 1.0
CG A:ASP11 3.3 33.7 1.0
CG A:ASP54 3.4 36.1 1.0
OD2 A:ASP11 3.4 36.1 1.0
BE A:BEF605 3.4 42.1 1.0
C A:ASN56 3.6 32.1 0.5
C A:ASN56 3.6 31.4 0.5
OD1 A:ASP54 3.9 37.7 1.0
OD1 A:ASP10 4.1 36.5 1.0
OE1 A:GLU12 4.2 47.3 1.0
F1 A:BEF605 4.4 39.1 1.0
CB A:ASN56 4.4 35.2 0.5
CG A:MET57 4.4 35.7 1.0
CA A:ASN56 4.4 33.0 0.5
N A:MET57 4.5 31.5 1.0
CA A:ASN56 4.5 31.7 0.5
CD A:GLU12 4.5 50.6 1.0
CB A:ASN56 4.6 33.0 0.5
CA A:MET57 4.6 31.9 1.0
F2 A:BEF605 4.6 46.6 1.0
CB A:ASP54 4.7 34.5 1.0
CG A:GLU12 4.7 44.8 1.0
CB A:ASP11 4.7 29.6 1.0
N A:ASN56 4.7 32.7 0.5
N A:ASN56 4.8 32.1 0.5
N A:ASP11 4.8 32.4 1.0
CG A:ASP10 4.9 36.9 1.0
CG A:ASN56 5.0 32.1 0.5

Calcium binding site 4 out of 7 in 8tff

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Calcium binding site 4 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:40.5
occ:1.00
F3 B:BEF605 2.0 40.5 1.0
O B:ASN56 2.3 35.3 1.0
OD1 B:ASP11 2.4 40.4 1.0
OD2 B:ASP54 2.4 42.0 1.0
O B:HOH705 2.5 32.0 1.0
O B:HOH811 2.5 45.5 1.0
O B:HOH756 3.0 48.1 1.0
CG B:ASP11 3.2 40.5 1.0
OD2 B:ASP11 3.3 62.3 1.0
CG B:ASP54 3.4 39.4 1.0
BE B:BEF605 3.5 40.9 1.0
C B:ASN56 3.5 36.6 1.0
OD1 B:ASP54 3.9 32.1 1.0
ND2 B:ASN56 4.1 37.5 0.5
OD1 B:ASP10 4.2 47.8 1.0
NZ B:LYS83 4.2 63.2 1.0
OE1 B:GLU12 4.3 48.9 1.0
F2 B:BEF605 4.4 48.9 1.0
CB B:ASN56 4.4 36.9 0.5
CA B:ASN56 4.4 36.2 0.5
CA B:ASN56 4.4 36.2 0.5
CG B:MET57 4.5 39.1 1.0
CB B:ASN56 4.5 36.9 0.5
N B:MET57 4.5 38.7 1.0
CB B:ASP11 4.6 35.8 1.0
CD B:GLU12 4.6 55.4 1.0
CA B:MET57 4.6 37.8 1.0
CG B:GLU12 4.6 46.2 1.0
CE B:LYS83 4.7 58.4 1.0
N B:ASN56 4.7 38.1 1.0
CB B:ASP54 4.7 38.7 1.0
N B:ASP11 4.7 32.9 1.0
CG B:ASN56 4.8 36.8 0.5
F1 B:BEF605 4.8 42.4 1.0
CG B:ASP10 4.9 40.5 1.0

Calcium binding site 5 out of 7 in 8tff

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Calcium binding site 5 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:32.5
occ:1.00
OD2 B:ASP414 2.1 28.7 1.0
OG1 B:THR271 2.2 32.8 1.0
OD2 B:ASP237 2.3 29.9 1.0
OD1 B:ASP237 2.3 28.4 1.0
NE2 B:HIS415 2.4 26.8 1.0
O B:HOH729 2.6 36.7 1.0
CG B:ASP237 2.6 29.1 1.0
CG B:ASP414 3.0 25.7 1.0
CB B:THR271 3.2 33.0 1.0
CE1 B:HIS415 3.2 27.5 1.0
OD1 B:ASP414 3.2 23.7 1.0
CD2 B:HIS415 3.2 30.4 1.0
CA B:THR271 3.5 32.2 1.0
CG2 B:THR271 3.5 29.1 1.0
N B:THR271 3.7 30.8 1.0
CB B:ASP237 4.1 25.8 1.0
F3 B:BEF606 4.1 51.1 1.0
ND1 B:HIS415 4.2 29.3 1.0
CG B:HIS415 4.2 28.9 1.0
N B:ASN238 4.3 25.2 1.0
CB B:ASP414 4.4 24.8 1.0
OD1 B:ASP360 4.5 43.2 1.0
CA B:ASP237 4.6 25.2 1.0
C B:ALA270 4.6 28.6 1.0
F2 B:BEF606 4.6 49.4 1.0
NH1 B:ARG275 4.8 25.6 1.0
CB B:ASN238 4.8 30.8 1.0
CA B:ASN238 4.8 29.1 1.0
C B:ASP237 4.8 26.1 1.0
BE B:BEF606 4.8 47.2 1.0

Calcium binding site 6 out of 7 in 8tff

Go back to Calcium Binding Sites List in 8tff
Calcium binding site 6 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:97.6
occ:1.00
NE2 B:HIS364 2.0 49.3 0.5
OD1 B:ASP360 2.8 43.2 1.0
CD2 B:HIS364 2.8 46.8 0.5
F1 B:BEF606 2.9 52.8 1.0
NE2 B:HIS499 2.9 45.3 1.0
CE1 B:HIS364 3.1 48.6 0.5
BE B:BEF606 3.2 47.2 1.0
O B:HOH729 3.2 36.7 1.0
OD2 B:ASP360 3.3 50.6 1.0
CG B:ASP360 3.4 38.9 1.0
CE1 B:HIS499 3.8 46.7 1.0
CD2 B:HIS499 3.8 34.1 1.0
F2 B:BEF606 3.9 49.4 1.0
CG B:HIS364 4.0 43.5 0.5
ND1 B:HIS364 4.1 45.9 0.5
F3 B:BEF606 4.1 51.1 1.0
ND2 B:ASN238 4.4 36.9 1.0
O B:HOH787 4.6 41.5 1.0
O B:ASP360 4.8 31.6 1.0
ND1 B:HIS364 4.8 48.0 0.5
CB B:ASP360 4.8 36.0 1.0
ND1 B:HIS499 4.9 44.6 1.0
CG B:HIS499 5.0 34.9 1.0
OG B:SER363 5.0 34.7 1.0

Calcium binding site 7 out of 7 in 8tff

Go back to Calcium Binding Sites List in 8tff
Calcium binding site 7 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Porx with BEF3 Phosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:94.5
occ:1.00
F3 B:BEF607 2.4 61.7 1.0
BE B:BEF607 3.1 58.1 1.0
F1 B:BEF607 3.3 64.2 1.0
OE2 B:GLU68 3.9 46.9 1.0
OE1 B:GLU68 4.0 41.5 1.0
CD B:GLU68 4.3 38.5 1.0
F2 B:BEF607 4.7 60.8 1.0

Reference:

A.Saran, N.Zeytuni. Porx with BEF3 Phosphate Analog To Be Published.
Page generated: Fri Jul 19 12:02:39 2024

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