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Calcium in PDB 8ted: Porx Primitive Orthorhombic Crystal Form

Protein crystallography data

The structure of Porx Primitive Orthorhombic Crystal Form, PDB code: 8ted 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) 42.40 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.696, 97.849, 133.2, 90, 90, 90
R / Rfree (%) 17.9 / 22.6

Other elements in 8ted:

The structure of Porx Primitive Orthorhombic Crystal Form also contains other interesting chemical elements:

Bromine (Br) 23 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Porx Primitive Orthorhombic Crystal Form (pdb code 8ted). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Porx Primitive Orthorhombic Crystal Form, PDB code: 8ted:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8ted

Go back to Calcium Binding Sites List in 8ted
Calcium binding site 1 out of 6 in the Porx Primitive Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Porx Primitive Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca613

b:57.9
occ:1.00
 OG1 A:THR271 2.2 29.4 1.0
OD2 A:ASP414 2.3 21.7 1.0
OD1 A:ASP237 2.4 32.6 1.0
NE2 A:HIS415 2.6 22.3 1.0
CG A:ASP237 3.0 31.1 1.0
OD2 A:ASP237 3.0 41.4 1.0
CG A:ASP414 3.0 23.9 1.0
CB A:THR271 3.2 31.3 1.0
OD1 A:ASP414 3.2 23.3 1.0
CD2 A:HIS415 3.4 22.5 1.0
CE1 A:HIS415 3.5 24.7 1.0
CG2 A:THR271 3.5 28.7 1.0
CA A:THR271 3.5 29.0 1.0
N A:THR271 3.7 26.8 1.0
N A:ASN238 4.0 25.6 1.0
O A:HOH756 4.1 45.8 1.0
CB A:ASP237 4.3 27.9 1.0
CG A:HIS415 4.4 21.4 1.0
ND1 A:HIS415 4.4 23.4 1.0
CB A:ASP414 4.5 23.1 1.0
O A:HOH880 4.5 31.6 1.0
CB A:ASN238 4.5 35.4 1.0
CA A:ASN238 4.5 31.2 1.0
CA A:ASP237 4.5 25.3 1.0
C A:ASP237 4.6 25.3 1.0
C A:ALA270 4.7 23.7 1.0
OD1 A:ASP360 4.7 55.2 1.0
NH1 A:ARG275 4.9 23.5 1.0
CG A:ASP360 4.9 48.1 1.0
OD2 A:ASP360 4.9 50.3 1.0
CD A:ARG275 5.0 22.3 1.0

Calcium binding site 2 out of 6 in 8ted

Go back to Calcium Binding Sites List in 8ted
Calcium binding site 2 out of 6 in the Porx Primitive Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Porx Primitive Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca614

b:36.9
occ:1.00
 O A:ASN56 2.2 36.9 1.0
OD2 A:ASP11 2.2 41.2 1.0
O A:HOH771 2.3 32.8 1.0
OD2 A:ASP54 2.3 31.5 1.0
O A:HOH971 2.5 40.6 1.0
O A:HOH912 2.5 31.9 1.0
CG A:ASP11 3.2 39.8 1.0
C A:ASN56 3.4 35.6 1.0
CG A:ASP54 3.4 31.4 1.0
OD1 A:ASP11 3.6 46.6 1.0
OD1 A:ASP54 3.9 31.8 1.0
O A:HOH725 4.1 36.3 1.0
OD1 A:ASP10 4.2 35.1 1.0
O A:HOH709 4.2 37.6 1.0
CA A:ASN56 4.3 38.0 1.0
N A:MET57 4.3 33.4 1.0
CG A:MET57 4.4 33.8 1.0
CB A:ASN56 4.5 41.8 1.0
CA A:MET57 4.5 34.5 1.0
CB A:ASP11 4.6 37.5 1.0
CB A:ASP54 4.6 31.6 1.0
N A:ASN56 4.6 37.1 1.0
O A:HOH785 4.6 41.5 1.0
OE1 A:GLU12 4.7 51.2 1.0
O A:HOH915 4.8 45.0 1.0
N A:ASP11 4.8 34.6 1.0
BR A:BR608 4.9 86.7 1.0
CD A:GLU12 5.0 54.4 1.0
O A:HOH977 5.0 25.4 1.0

Calcium binding site 3 out of 6 in 8ted

Go back to Calcium Binding Sites List in 8ted
Calcium binding site 3 out of 6 in the Porx Primitive Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Porx Primitive Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca613

b:36.4
occ:1.00
 OD1 B:ASN238 2.3 26.1 1.0
OG1 B:THR271 2.4 15.7 1.0
OD2 B:ASP414 2.4 16.2 1.0
OD1 B:ASP237 2.4 23.7 1.0
NE2 B:HIS415 2.6 15.4 1.0
CG B:ASP414 3.0 17.4 1.0
OD1 B:ASP414 3.0 17.9 1.0
CG B:ASP237 3.3 23.5 1.0
CB B:THR271 3.3 18.9 1.0
CD2 B:HIS415 3.4 14.7 1.0
CE1 B:HIS415 3.4 16.7 1.0
O B:HOH773 3.5 32.3 1.0
CG B:ASN238 3.5 25.0 1.0
CG2 B:THR271 3.6 19.5 1.0
OD2 B:ASP237 3.7 26.0 1.0
CA B:THR271 3.7 18.8 1.0
N B:ASN238 3.8 19.9 1.0
N B:THR271 3.9 18.0 1.0
CA B:ASN238 4.2 21.0 1.0
ND1 B:HIS415 4.4 17.2 1.0
CG B:HIS415 4.4 15.9 1.0
CB B:ASP237 4.4 22.5 1.0
ND2 B:ASN238 4.4 25.7 1.0
CA B:ASP237 4.4 22.6 1.0
CB B:ASN238 4.5 21.9 1.0
C B:ASP237 4.5 18.8 1.0
CB B:ASP414 4.5 19.0 1.0
O B:HOH852 4.7 37.9 1.0
C B:ALA270 4.8 18.0 1.0
NH1 B:ARG275 4.9 18.9 1.0
O B:HOH1026 4.9 29.6 1.0

Calcium binding site 4 out of 6 in 8ted

Go back to Calcium Binding Sites List in 8ted
Calcium binding site 4 out of 6 in the Porx Primitive Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Porx Primitive Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca614

b:32.1
occ:1.00
 OD2 B:ASP54 2.3 32.8 1.0
O B:ASN56 2.3 32.2 1.0
O B:HOH719 2.4 26.1 1.0
OD1 B:ASP11 2.4 37.8 1.0
O B:HOH874 2.5 47.3 1.0
O B:HOH870 2.6 36.5 1.0
CG B:ASP54 3.4 28.5 1.0
CG B:ASP11 3.4 33.6 1.0
C B:ASN56 3.5 33.0 1.0
OD2 B:ASP11 3.6 40.0 1.0
OD1 B:ASP54 3.9 35.6 1.0
OD1 B:ASP10 4.1 30.1 1.0
O B:HOH802 4.2 29.5 1.0
OE1 B:GLU12 4.4 45.5 1.0
CA B:ASN56 4.4 35.8 1.0
CG B:MET57 4.5 31.0 1.0
N B:MET57 4.5 30.7 1.0
CB B:ASP54 4.6 26.6 1.0
CA B:MET57 4.6 30.9 1.0
CD B:GLU12 4.6 41.0 1.0
CB B:ASN56 4.6 42.3 1.0
O B:HOH778 4.7 46.3 1.0
N B:ASN56 4.7 32.2 1.0
CB B:ASP11 4.8 31.4 1.0
N B:ASP11 4.8 28.7 1.0
CG B:GLU12 4.9 35.4 1.0
O B:HOH1044 4.9 26.7 1.0
CG B:ASP10 5.0 30.5 1.0

Calcium binding site 5 out of 6 in 8ted

Go back to Calcium Binding Sites List in 8ted
Calcium binding site 5 out of 6 in the Porx Primitive Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Porx Primitive Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca615

b:26.9
occ:1.00
 O B:MET467 2.3 25.6 1.0
O B:LYS455 2.4 28.4 1.0
O B:HOH984 2.5 21.0 1.0
O B:HOH731 2.5 20.2 1.0
O B:ACT601 2.5 35.2 1.0
OXT B:ACT601 2.8 40.2 1.0
C B:ACT601 3.0 43.9 1.0
C B:MET467 3.3 24.9 1.0
C B:LYS455 3.6 25.2 1.0
O B:SER469 4.0 22.9 1.0
CA B:MET467 4.0 29.8 1.0
N B:SER468 4.3 25.7 1.0
CA B:LYS455 4.3 25.1 1.0
CB B:LYS455 4.3 27.6 1.0
CA B:SER468 4.5 25.9 1.0
CH3 B:ACT601 4.5 44.7 1.0
CB B:MET467 4.6 34.0 1.0
OE2 B:GLU456 4.6 28.4 1.0
N B:GLU456 4.6 25.6 1.0
C B:SER468 4.6 23.8 1.0
O B:HOH1036 4.7 33.2 1.0
O B:HOH909 4.7 37.1 1.0
N B:SER469 4.7 23.5 1.0
CG B:GLU456 4.8 27.2 1.0
CA B:GLU456 4.8 22.3 1.0
BR B:BR602 4.8 37.5 1.0
C B:SER469 4.9 21.9 1.0

Calcium binding site 6 out of 6 in 8ted

Go back to Calcium Binding Sites List in 8ted
Calcium binding site 6 out of 6 in the Porx Primitive Orthorhombic Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Porx Primitive Orthorhombic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca616

b:51.7
occ:1.00
 O B:HOH837 2.3 35.1 1.0
O B:HOH799 2.5 48.2 1.0
OE1 B:GLU92 2.7 29.6 1.0
CD B:GLU92 3.6 27.7 1.0
OE2 B:GLU92 3.8 32.6 1.0
O B:HOH790 4.2 30.1 1.0
OE1 B:GLU86 4.5 53.9 0.5
OE2 B:GLU55 4.6 33.5 1.0
CD1 B:ILE89 4.6 34.5 1.0

Reference:

A.Saran, N.Zeytuni. Porx Primitive Orthorhombic Crystal Form To Be Published.
Page generated: Thu Jul 10 07:30:01 2025

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