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Calcium in PDB 2i52: Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372

Protein crystallography data

The structure of Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372, PDB code: 2i52 was solved by U.A.Ramagopal, J.Gilmore, R.Toro, K.T.Bain, C.Mckenzie, C.Reyes, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.20 / 2.08
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 90.764, 143.485, 129.799, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.5

Other elements in 2i52:

The structure of Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 (pdb code 2i52). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372, PDB code: 2i52:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 2i52

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Calcium binding site 1 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


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 Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca807

b:48.2
occ:1.00
 O D:HOH905 2.2 7.9 0.4
O D:HOH930 2.4 31.2 1.0
O B:HOH898 2.6 25.9 1.0
O C:HOH907 2.6 25.8 1.0
O A:HOH907 2.6 13.4 0.5
O A:THR33 2.7 17.2 1.0
OG1 A:THR33 3.1 18.7 1.0
O D:THR33 3.3 16.7 1.0
O D:HOH905 3.4 14.4 0.5
C A:THR33 3.5 17.4 1.0
O A:HIS30 3.7 18.2 1.0
CB A:THR33 4.0 17.3 1.0
OG1 D:THR33 4.0 17.7 1.0
C D:THR33 4.0 17.2 1.0
CA A:THR33 4.2 17.4 1.0
N A:GLY34 4.3 17.4 1.0
O D:HIS30 4.4 15.9 1.0
CA A:GLY34 4.5 17.2 1.0
N A:THR33 4.6 17.0 1.0
CA D:GLY34 4.6 17.4 1.0
OE1 C:GLN31 4.6 15.1 1.0
OE1 B:GLN31 4.6 14.2 1.0
N D:GLY34 4.7 17.3 1.0
NE2 C:GLN31 4.7 13.1 1.0
C A:HIS30 4.7 16.6 1.0
CB D:THR33 4.8 17.2 1.0
CA D:THR33 4.9 17.3 1.0

Calcium binding site 2 out of 13 in 2i52

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Calcium binding site 2 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


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 Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:29.1
occ:1.00
 O B:HOH818 2.4 22.4 1.0
O F:HOH908 2.4 18.5 1.0
OE1 B:GLU46 2.5 23.5 1.0
OE1 F:GLU46 2.5 18.2 1.0
O B:HOH842 2.5 32.4 1.0
O F:HOH933 3.0 28.4 1.0
CD F:GLU46 3.5 18.5 1.0
CD B:GLU46 3.6 23.1 1.0
O F:HOH928 3.7 31.0 1.0
CB B:GLU46 3.9 23.1 1.0
OE2 F:GLU46 4.2 19.2 1.0
O F:HOH927 4.2 28.2 1.0
CB F:GLU46 4.2 18.4 1.0
CG B:GLU46 4.4 22.6 1.0
NH2 B:ARG63 4.4 24.5 1.0
NH1 F:ARG63 4.4 34.9 1.0
OE2 B:GLU46 4.4 23.0 1.0
CG F:GLU46 4.5 18.4 1.0
O F:ILE64 4.5 21.4 1.0
O B:ILE64 4.6 26.8 1.0
O B:SER43 4.8 25.3 1.0
OE2 B:GLU50 4.8 20.7 1.0
OG B:SER43 4.9 25.6 1.0
O F:HOH980 4.9 52.5 1.0
OG F:SER43 4.9 19.7 1.0

Calcium binding site 3 out of 13 in 2i52

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Calcium binding site 3 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


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 Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:26.2
occ:0.50
 CA B:CA802 0.0 26.2 0.5
CA B:CA802 2.2 16.4 0.3
O B:HOH824 2.3 32.8 1.0
O D:HOH911 2.4 25.3 1.0
O C:THR33 2.5 16.3 1.0
O A:HOH838 2.6 26.0 1.0
OG1 C:THR33 2.9 16.3 1.0
O C:HOH841 3.3 36.3 1.0
O C:HIS30 3.3 19.2 1.0
C C:THR33 3.4 16.6 1.0
CB C:THR33 3.9 16.5 1.0
O B:THR33 3.9 16.2 1.0
CA C:THR33 4.0 16.6 1.0
N C:THR33 4.2 16.5 1.0
C C:HIS30 4.3 17.7 1.0
N C:GLY34 4.4 16.8 1.0
O B:HIS30 4.5 18.5 1.0
NE2 A:GLN31 4.5 13.9 1.0
OG1 B:THR33 4.5 18.8 1.0
OE1 A:GLN31 4.6 15.2 1.0
O C:GLN31 4.7 16.7 1.0
CA C:GLY34 4.7 16.7 1.0
C B:THR33 4.8 17.2 1.0
OE1 D:GLN31 4.8 16.4 1.0
C C:GLN31 4.8 16.9 1.0
O C:PHE29 4.9 16.8 1.0
CA C:HIS30 4.9 17.2 1.0
CD A:GLN31 5.0 13.6 1.0

Calcium binding site 4 out of 13 in 2i52

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Calcium binding site 4 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


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 Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:16.4
occ:0.30
 CA B:CA802 0.0 16.4 0.3
CA B:CA802 2.2 26.2 0.5
O A:HOH838 2.3 26.0 1.0
O B:THR33 2.5 16.2 1.0
O B:HOH824 2.6 32.8 1.0
O B:HIS30 2.9 18.5 1.0
O D:HOH911 3.1 25.3 1.0
OG1 B:THR33 3.1 18.8 1.0
C B:THR33 3.4 17.2 1.0
C B:HIS30 3.9 17.6 1.0
O C:HOH841 3.9 36.3 1.0
CA B:THR33 4.0 17.4 1.0
NE2 D:GLN31 4.0 12.8 1.0
CB B:THR33 4.0 17.4 1.0
N B:THR33 4.1 17.2 1.0
O B:GLN31 4.3 16.3 1.0
O C:THR33 4.3 16.3 1.0
C B:GLN31 4.4 16.3 1.0
N B:GLY34 4.4 17.4 1.0
OE1 D:GLN31 4.5 16.4 1.0
CA B:HIS30 4.6 17.3 1.0
O C:HIS30 4.7 19.2 1.0
OG1 C:THR33 4.7 16.3 1.0
O B:PHE29 4.7 17.8 1.0
CD D:GLN31 4.7 15.5 1.0
C B:TYR32 4.7 17.1 1.0
N B:TYR32 4.8 16.4 1.0
N B:GLN31 4.8 17.0 1.0
CA B:GLY34 4.8 18.8 1.0
CA B:GLN31 4.9 16.1 1.0
OE1 A:GLN31 4.9 15.2 1.0
O D:HOH905 5.0 14.4 0.5

Calcium binding site 5 out of 13 in 2i52

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Calcium binding site 5 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


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 Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca810

b:25.2
occ:0.40
 O B:HOH860 2.2 39.0 1.0
O D:HOH904 2.4 15.3 0.4
O B:HOH851 2.5 39.7 1.0
O B:MET54 2.6 24.2 1.0
O D:HOH993 3.0 32.1 0.5
C B:MET54 3.6 23.9 1.0
CA B:ILE55 3.9 24.1 1.0
N B:ILE55 4.2 24.1 1.0
C B:ILE55 4.4 24.5 1.0
OE1 D:GLU40 4.4 29.5 1.0
OE2 D:GLU40 4.5 29.0 1.0
O B:ILE55 4.6 24.2 1.0
O D:HOH993 4.6 40.5 0.5
O B:VAL59 4.8 24.6 1.0
CA B:MET54 4.8 23.7 1.0
O B:GLN56 4.8 24.3 1.0
CE B:MET54 4.9 28.2 1.0
CD D:GLU40 5.0 24.9 1.0
CB B:MET54 5.0 23.9 1.0

Calcium binding site 6 out of 13 in 2i52

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Calcium binding site 6 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


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 Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca803

b:23.6
occ:0.60
 O C:HOH819 2.3 23.9 1.0
O C:HOH869 2.3 38.8 1.0
O C:HOH812 2.4 26.5 0.5
OE1 C:GLU46 2.4 18.1 1.0
OE2 C:GLU46 2.4 19.2 1.0
O C:HOH861 2.6 39.5 1.0
CD C:GLU46 2.8 18.0 1.0
CG C:GLU46 4.3 16.7 1.0
OG C:SER43 4.8 22.2 1.0
O C:ILE64 4.8 16.4 1.0
N C:ILE66 4.8 19.5 1.0
CA C:SER65 4.9 17.9 1.0
O C:ILE66 4.9 22.1 1.0

Calcium binding site 7 out of 13 in 2i52

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Calcium binding site 7 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca811

b:19.1
occ:0.50
 OD1 C:ASN61 2.3 18.6 0.5
ND2 C:ASN61 2.3 18.8 0.5
O C:HOH898 2.5 20.6 0.5
O C:HOH844 2.7 31.7 1.0
CG C:ASN61 3.2 18.5 0.5
ND2 C:ASN61 3.5 18.7 0.5
CG C:ASN61 3.5 18.9 0.5
O C:HOH816 4.1 23.5 1.0
OD1 C:ASN61 4.1 19.2 0.5
O C:VAL62 4.3 16.6 1.0
CB C:ASN61 4.6 18.3 0.5
CB C:ASN61 4.6 18.4 0.5
O C:HOH848 4.8 32.4 1.0
N C:VAL62 4.8 18.1 1.0
CA C:ASN61 4.9 18.4 0.5
CA C:ASN61 4.9 18.5 0.5

Calcium binding site 8 out of 13 in 2i52

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Calcium binding site 8 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca804

b:20.4
occ:0.60
 O D:HOH964 2.3 41.9 1.0
O D:HOH974 2.3 47.5 1.0
O D:HOH925 2.3 30.2 1.0
O D:HOH915 2.3 26.7 1.0
OE2 D:GLU50 2.4 22.5 1.0
O D:HOH948 2.4 37.0 1.0
OE1 D:GLU50 2.6 25.0 1.0
CD D:GLU50 2.9 23.0 1.0
O D:HOH949 4.2 37.4 1.0
OE1 D:GLU47 4.3 30.0 1.0
CG D:GLU50 4.4 22.1 1.0
O D:HOH912 4.6 24.8 1.0
O D:HOH928 4.6 27.7 1.0
O D:ILE64 4.6 23.1 1.0
N D:ILE64 4.9 23.8 1.0

Calcium binding site 9 out of 13 in 2i52

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Calcium binding site 9 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca805

b:29.5
occ:0.40
 O E:HOH851 2.2 29.7 1.0
O E:HOH898 2.4 14.1 0.4
OE2 E:GLU46 2.4 15.1 1.0
OE1 E:GLU46 2.4 13.6 1.0
O E:HOH843 2.5 29.1 1.0
O E:HOH834 2.5 25.8 1.0
O E:HOH926 2.8 23.1 0.4
CD E:GLU46 2.8 16.4 1.0
CA E:CA806 3.7 33.4 0.6
CG E:GLU46 4.3 14.6 1.0
OG E:SER43 4.6 21.7 1.0
N E:ILE66 4.7 21.1 1.0
O E:ILE66 4.8 24.1 1.0
CA E:SER65 4.9 19.4 1.0
O E:ILE64 4.9 15.4 1.0
OG E:SER65 4.9 22.4 1.0

Calcium binding site 10 out of 13 in 2i52

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Calcium binding site 10 out of 13 in the Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Protein PTO0218 From Picrophilus Torridus, Pfam DUF372 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca806

b:33.4
occ:0.60
 O E:HOH830 2.3 25.8 1.0
OG E:SER65 2.3 22.4 1.0
O E:HOH853 2.4 29.1 1.0
O E:HOH851 2.5 29.7 1.0
O E:HOH843 2.5 29.1 1.0
CB E:SER65 3.3 19.4 1.0
CA E:CA805 3.7 29.5 0.4
CA E:CA812 3.7 43.9 0.4
CA E:SER65 4.0 19.4 1.0
O E:HOH826 4.1 24.6 1.0
O E:HOH898 4.4 14.1 0.4
OE2 E:GLU46 4.6 15.1 1.0
O E:ILE64 4.7 15.4 1.0
ND2 E:ASN67 4.8 26.7 1.0
N E:SER65 4.9 17.3 1.0
OE1 E:GLU46 4.9 13.6 1.0
O E:HOH856 5.0 31.1 1.0

Reference:

U.A.Ramagopal, J.Gilmore, R.Toro, K.T.Bain, C.Mckenzie, C.Reyes, J.M.Sauder, S.K.Burley, S.C.Almo. Structure of Hypothetical Protein PTO0218 From Picrophilus Torridus To Be Published.
Page generated: Tue Jul 8 06:08:45 2025

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