Calcium in PDB 4n1g: Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution

The structure of Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution, PDB code: 4n1g was solved by P.V.Natashin, S.V.Markova, J.Lee, E.S.Vysotski, Z.J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.54 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.920, 85.127, 90.088, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.9

The binding sites of Calcium atom in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution (pdb code 4n1g). 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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution, PDB code: 4n1g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:16.2 occ:1.00 OD1 A:ASP30 2.3 19.4 1.0 O A:HOH376 2.3 16.6 1.0 O A:LYS36 2.3 17.4 1.0 OD1 A:ASN32 2.4 20.9 1.0 OE2 A:GLU41 2.4 18.9 1.0 OD1 A:ASN34 2.5 19.7 1.0 OE1 A:GLU41 2.6 16.1 1.0 CD A:GLU41 2.9 16.1 1.0 CG A:ASN32 3.3 21.4 1.0 CG A:ASN34 3.4 20.6 1.0 CG A:ASP30 3.4 19.3 1.0 C A:LYS36 3.6 15.0 1.0 ND2 A:ASN32 3.7 20.7 1.0 ND2 A:ASN34 3.8 26.0 1.0 N A:ASN34 4.2 20.5 1.0 CA A:ASP30 4.2 17.5 1.0 N A:LYS36 4.3 16.9 1.0 OD2 A:ASP30 4.3 20.6 1.0 N A:ASN32 4.3 22.3 1.0 CB A:ASP30 4.3 18.8 1.0 CG A:GLU41 4.3 11.7 1.0 CA A:LYS36 4.4 16.6 1.0 CA A:ILE37 4.4 14.8 1.0 N A:ILE37 4.4 13.8 1.0 C A:ASP30 4.5 19.0 1.0 CB A:ASN34 4.5 22.9 1.0 N A:GLY33 4.6 24.9 1.0 CB A:ASN32 4.6 24.5 1.0 OE1 A:GLU82 4.6 35.9 1.0 N A:ILE31 4.7 22.4 1.0 CA A:ASN34 4.7 20.2 1.0 CB A:LYS36 4.7 17.5 1.0 CA A:ASN32 4.8 22.1 1.0 C A:ASN32 4.8 23.6 1.0 N A:GLY35 4.9 18.4 1.0 O A:HOH341 4.9 19.5 1.0 O A:ASP30 5.0 21.7 1.0 C A:ASN34 5.0 22.1 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:16.4 occ:1.00 OD1 A:ASP123 2.3 15.7 1.0 O A:THR129 2.3 17.2 1.0 OD1 A:ASP125 2.3 19.5 1.0 O A:HOH312 2.4 19.7 1.0 OE1 A:GLU134 2.4 13.8 1.0 OG A:SER127 2.5 18.8 1.0 OE2 A:GLU134 2.6 15.4 1.0 CD A:GLU134 2.9 14.6 1.0 CG A:ASP125 3.3 23.5 1.0 CG A:ASP123 3.4 15.7 1.0 C A:THR129 3.6 14.6 1.0 CB A:SER127 3.6 20.0 1.0 OD2 A:ASP125 3.6 29.0 1.0 N A:SER127 4.0 23.9 1.0 O A:HOH422 4.2 31.6 1.0 CA A:ASP123 4.2 12.2 1.0 OD2 A:ASP123 4.3 20.3 1.0 CA A:ILE130 4.3 12.7 0.4 CA A:SER127 4.3 21.7 1.0 CB A:ASP123 4.4 13.0 1.0 N A:THR129 4.4 18.9 1.0 N A:ILE130 4.4 12.0 0.4 CA A:ILE130 4.4 12.9 0.6 N A:ILE130 4.4 11.4 0.6 N A:ASP125 4.4 20.9 1.0 CG A:GLU134 4.4 15.1 1.0 C A:ASP123 4.5 12.4 1.0 N A:THR131 4.5 10.5 1.0 OG1 A:THR131 4.6 17.1 1.0 CB A:ASP125 4.6 21.0 1.0 CA A:THR129 4.6 12.5 1.0 N A:GLY126 4.7 19.8 1.0 N A:GLY128 4.7 16.2 1.0 N A:LYS124 4.7 13.1 1.0 CA A:ASP125 4.9 20.4 1.0 C A:SER127 4.9 19.8 1.0 CD1 A:ILE130 4.9 13.0 0.6 OG1 A:THR129 4.9 23.4 1.0 C A:ILE130 4.9 11.9 0.4 C A:ASP125 4.9 20.9 1.0 O A:HOH326 4.9 22.6 1.0 C A:ILE130 4.9 11.5 0.6

Calcium binding site 3 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:12.1 occ:1.00 O A:HOH336 2.3 21.1 1.0 OD1 A:ASP159 2.4 14.6 1.0 OG A:SER163 2.4 13.2 1.0 OD1 A:ASP161 2.4 12.9 1.0 O A:ASP165 2.4 12.5 1.0 OE2 A:GLU170 2.5 13.1 1.0 OE1 A:GLU170 2.6 12.3 1.0 CD A:GLU170 2.9 11.3 1.0 CG A:ASP161 3.4 20.8 1.0 CB A:SER163 3.5 13.6 1.0 CG A:ASP159 3.5 12.9 1.0 C A:ASP165 3.7 11.6 1.0 OD2 A:ASP161 3.8 22.9 1.0 N A:SER163 4.0 14.1 1.0 OD1 A:ASP165 4.1 19.6 1.0 OD2 A:ASP159 4.3 14.6 1.0 CA A:ASP159 4.3 10.7 1.0 CA A:LEU166 4.3 11.4 1.0 CA A:SER163 4.3 13.0 1.0 O A:HOH552 4.4 49.2 1.0 CG A:GLU170 4.4 9.5 1.0 CB A:ASP159 4.4 12.3 1.0 N A:ASP165 4.5 12.0 1.0 N A:LEU166 4.5 11.2 1.0 N A:ASP161 4.5 15.0 1.0 OD2 A:ASP167 4.6 22.0 1.0 N A:ASP167 4.6 11.1 1.0 C A:ASP159 4.6 11.1 1.0 CB A:ASP161 4.6 17.5 1.0 CA A:ASP165 4.7 14.5 1.0 O A:HOH458 4.7 22.6 1.0 N A:ASN162 4.8 13.4 1.0 N A:LEU160 4.8 12.1 1.0 N A:GLY164 4.8 13.6 1.0 C A:LEU166 4.9 11.0 1.0 CA A:ASP161 4.9 15.9 1.0 C A:ASP161 4.9 16.1 1.0 C A:SER163 5.0 14.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:14.2 occ:1.00 OD1 B:ASP159 2.3 14.0 1.0 O B:HOH313 2.3 17.9 1.0 O B:ASP165 2.4 14.8 1.0 OD1 B:ASP161 2.4 15.0 1.0 OG B:SER163 2.5 14.9 1.0 OE1 B:GLU170 2.5 12.6 1.0 OE2 B:GLU170 2.5 14.3 1.0 CD B:GLU170 2.9 12.9 1.0 CG B:ASP161 3.3 19.9 1.0 CG B:ASP159 3.5 17.4 1.0 CB B:SER163 3.6 18.4 1.0 C B:ASP165 3.6 15.8 1.0 OD2 B:ASP161 3.8 23.3 1.0 N B:SER163 4.0 18.1 1.0 OD1 B:ASP165 4.1 25.3 1.0 CA B:LEU166 4.3 11.7 1.0 CA B:ASP159 4.3 14.2 1.0 OD2 B:ASP159 4.3 19.1 1.0 CG B:GLU170 4.3 12.5 1.0 CA B:SER163 4.4 20.0 1.0 N B:ASP161 4.4 18.4 1.0 OD2 B:ASP167 4.4 22.0 1.0 N B:ASP165 4.4 15.3 1.0 CB B:ASP159 4.4 14.1 1.0 O B:HOH354 4.4 29.2 1.0 N B:LEU166 4.4 12.5 1.0 N B:ASP167 4.5 14.3 1.0 C B:ASP159 4.6 13.2 1.0 CB B:ASP161 4.6 18.2 1.0 CA B:ASP165 4.6 14.3 1.0 O B:HOH523 4.6 50.6 1.0 O B:HOH428 4.7 31.0 1.0 N B:LEU160 4.7 15.0 1.0 N B:ASN162 4.7 17.3 1.0 CA B:ASP161 4.8 20.1 1.0 C B:LEU166 4.8 13.4 1.0 N B:GLY164 4.8 16.3 1.0 C B:ASP161 4.8 18.6 1.0 C B:SER163 4.9 15.7 1.0 CD2 B:LEU166 5.0 15.7 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:19.3 occ:1.00 OD1 B:ASP123 2.3 18.7 1.0 O B:HOH317 2.3 24.4 1.0 O B:THR129 2.3 19.0 1.0 OD1 B:ASP125 2.4 20.7 1.0 OG B:SER127 2.4 23.1 1.0 OE1 B:GLU134 2.5 17.4 1.0 OE2 B:GLU134 2.6 20.1 1.0 CD B:GLU134 2.9 18.0 1.0 CG B:ASP125 3.3 31.0 1.0 CG B:ASP123 3.4 15.2 1.0 CB B:SER127 3.5 24.8 1.0 C B:THR129 3.5 16.7 1.0 OD2 B:ASP125 3.6 35.9 1.0 N B:SER127 4.0 22.4 1.0 CA B:ASP123 4.2 16.9 1.0 CB B:ASP123 4.3 13.5 1.0 OD2 B:ASP123 4.3 18.4 1.0 CA B:SER127 4.3 20.9 1.0 OG1 B:THR129 4.3 26.6 1.0 N B:THR129 4.4 19.9 1.0 CA B:ILE130 4.4 12.4 1.0 CG B:GLU134 4.4 20.0 1.0 N B:ILE130 4.4 14.7 1.0 N B:ASP125 4.4 21.4 1.0 C B:ASP123 4.5 19.3 1.0 CA B:THR129 4.5 15.7 1.0 CB B:ASP125 4.6 25.0 1.0 N B:THR131 4.6 13.1 1.0 N B:GLY126 4.6 20.4 1.0 N B:LYS124 4.7 16.6 1.0 N B:GLY128 4.8 20.2 1.0 OG1 B:THR131 4.8 25.2 1.0 CA B:ASP125 4.9 24.6 1.0 O B:HOH329 4.9 21.9 1.0 C B:ASP125 4.9 26.7 1.0 C B:SER127 4.9 21.7 1.0 CG2 B:THR131 5.0 19.6 1.0 C B:ILE130 5.0 14.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution


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 Ca(2+)- Discharged F88Y Obelin Mutant From Obelia Longissima at 1.50 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:20.7 occ:1.00 O B:HOH330 2.3 25.6 1.0 OD1 B:ASP30 2.3 25.3 1.0 O B:LYS36 2.3 20.7 1.0 OD1 B:ASN32 2.4 28.2 1.0 OD1 B:ASN34 2.4 25.4 1.0 OE2 B:GLU41 2.6 24.2 1.0 OE1 B:GLU41 2.6 21.2 1.0 CD B:GLU41 2.9 24.3 1.0 CG B:ASN32 3.4 31.4 1.0 CG B:ASN34 3.4 27.2 1.0 CG B:ASP30 3.4 25.7 1.0 C B:LYS36 3.5 17.1 1.0 ND2 B:ASN32 3.8 33.3 1.0 ND2 B:ASN34 3.9 29.5 1.0 OD2 B:ASP30 4.2 25.5 1.0 CA B:ASP30 4.3 23.6 1.0 N B:ASN34 4.3 28.9 1.0 N B:LYS36 4.3 20.5 1.0 CB B:ASP30 4.4 24.2 1.0 N B:ILE37 4.4 13.7 1.0 N B:ASN32 4.4 24.1 1.0 CA B:ILE37 4.4 15.4 1.0 CA B:LYS36 4.4 16.5 1.0 C B:ASP30 4.5 25.1 1.0 CG B:GLU41 4.5 15.2 1.0 OE2 B:GLU82 4.5 44.4 1.0 CB B:ASN34 4.5 26.4 1.0 N B:ILE31 4.6 25.1 1.0 CB B:ASN32 4.6 26.1 1.0 N B:GLY33 4.6 32.0 1.0 CB B:LYS36 4.7 22.2 1.0 O B:HOH388 4.7 36.4 1.0 O B:HOH384 4.7 28.6 1.0 CA B:ASN34 4.8 27.6 1.0 CA B:ASN32 4.8 27.8 1.0 C B:ASN32 4.9 34.7 1.0 N B:GLY35 4.9 24.6 1.0

P.V.Natashin, S.V.Markova, J.Lee, E.S.Vysotski, Z.J.Liu. Crystal Structures of the F88Y Obelin Mutant Before and After Bioluminescence Provide Molecular Insight Into Spectral Tuning Among Hydromedusan Photoproteins Febs J. V. 281 1432 2014.
ISSN: ISSN 1742-464X
PubMed: 24418253
DOI: 10.1111/FEBS.12715