Calcium in PDB 4mry: Crystal Structure of Ca(2+)- Discharged Y138F Obelin Mutant From Obelia Longissima at 1.30 Angstrom Resolution

The structure of Crystal Structure of Ca(2+)- Discharged Y138F Obelin Mutant From Obelia Longissima at 1.30 Angstrom Resolution, PDB code: 4mry was solved by P.V.Natashin, W.Ding, E.V.Eremeeva, 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)	34.66 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.614, 57.112, 68.258, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.3

The binding sites of Calcium atom in the Crystal Structure of Ca(2+)- Discharged Y138F Obelin Mutant From Obelia Longissima at 1.30 Angstrom Resolution (pdb code 4mry). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Ca(2+)- Discharged Y138F Obelin Mutant From Obelia Longissima at 1.30 Angstrom Resolution, PDB code: 4mry:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Ca(2+)- Discharged Y138F Obelin Mutant From Obelia Longissima at 1.30 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 Y138F Obelin Mutant From Obelia Longissima at 1.30 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:7.2 occ:1.00 OD1 A:ASP30 2.3 8.2 1.0 O A:LYS36 2.4 5.3 1.0 OD1 A:ASN32 2.5 9.4 1.0 OD1 A:ASN34 2.6 8.9 1.0 OE2 A:GLU41 2.6 8.0 1.0 O A:HOH370 2.6 12.9 1.0 OE1 A:GLU41 2.6 9.1 1.0 CD A:GLU41 3.0 7.5 1.0 CG A:ASP30 3.4 7.1 1.0 CG A:ASN32 3.5 10.9 1.0 CG A:ASN34 3.6 9.7 1.0 C A:LYS36 3.6 8.1 1.0 ND2 A:ASN32 4.0 17.2 1.0 ND2 A:ASN34 4.2 14.5 1.0 OD2 A:ASP30 4.2 7.5 1.0 N A:ASN34 4.3 7.8 1.0 N A:LYS36 4.3 7.2 1.0 CA A:ASP30 4.3 6.2 1.0 N A:ASN32 4.3 7.7 1.0 CB A:ASP30 4.3 8.1 1.0 CG A:GLU41 4.4 7.5 1.0 CA A:LYS36 4.5 7.8 1.0 C A:ASP30 4.5 6.1 1.0 CA A:ILE37 4.5 6.7 0.7 CA A:ILE37 4.5 8.0 0.3 N A:ILE37 4.5 5.5 0.7 N A:ILE37 4.6 7.9 0.3 CB A:ASN34 4.6 11.6 1.0 N A:GLY33 4.6 7.5 1.0 N A:ILE31 4.6 7.1 1.0 OE2 A:GLU82 4.6 14.2 1.0 CB A:LYS36 4.7 11.0 1.0 CB A:ASN32 4.7 9.0 1.0 CA A:ASN32 4.8 8.5 1.0 CA A:ASN34 4.8 8.8 1.0 N A:GLY35 4.9 7.5 1.0 C A:ASN32 4.9 8.6 1.0 O A:ASP30 5.0 7.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Ca(2+)- Discharged Y138F Obelin Mutant From Obelia Longissima at 1.30 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 Y138F Obelin Mutant From Obelia Longissima at 1.30 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:11.2 occ:1.00 O A:HOH418 2.2 30.7 1.0 OD1 A:ASP159 2.5 9.6 1.0 OD1 A:ASP161 2.6 14.9 1.0 O A:ASP165 2.6 13.0 1.0 OE1 A:GLU170 2.6 12.6 1.0 OE2 A:GLU170 2.7 12.2 1.0 OG A:SER163 2.7 14.8 1.0 CD A:GLU170 3.0 11.7 1.0 CG A:ASP159 3.6 8.6 1.0 CG A:ASP161 3.6 16.0 1.0 CB A:SER163 3.6 15.0 1.0 C A:ASP165 3.8 12.5 1.0 OD2 A:ASP161 4.0 20.0 1.0 OD1 A:ASP165 4.0 21.2 1.0 N A:SER163 4.0 11.0 1.0 CA A:ASP159 4.3 7.9 1.0 CA A:LEU166 4.3 10.6 1.0 OD2 A:ASP159 4.3 9.8 1.0 CA A:SER163 4.4 12.5 1.0 CG A:GLU170 4.4 9.0 1.0 N A:ASP161 4.4 11.7 1.0 CB A:ASP159 4.5 8.5 1.0 O A:HOH429 4.5 20.2 1.0 N A:ASP165 4.5 11.5 1.0 N A:LEU166 4.5 11.1 1.0 C A:ASP159 4.5 8.0 1.0 N A:LEU160 4.7 10.1 1.0 N A:ASP167 4.8 11.0 1.0 N A:ASN162 4.8 9.5 1.0 CA A:ASP165 4.8 12.8 1.0 CB A:ASP161 4.8 16.9 1.0 N A:GLY164 4.9 12.8 1.0 C A:LEU166 4.9 9.1 1.0 CA A:ASP161 4.9 11.9 1.0 O A:HOH575 5.0 31.3 1.0 CD2 A:LEU166 5.0 12.1 1.0 C A:ASP161 5.0 10.9 1.0 C A:SER163 5.0 14.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Ca(2+)- Discharged Y138F Obelin Mutant From Obelia Longissima at 1.30 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 Y138F Obelin Mutant From Obelia Longissima at 1.30 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:9.3 occ:1.00 OD1 A:ASP125 2.3 25.2 0.5 OD1 A:ASP123 2.4 8.9 1.0 O A:HOH481 2.4 24.4 1.0 OD1 A:ASP125 2.5 25.2 0.5 OG A:SER127 2.5 11.8 1.0 O A:THR129 2.5 9.9 1.0 OE1 A:GLU134 2.6 11.2 1.0 OE2 A:GLU134 2.6 11.0 1.0 CD A:GLU134 3.0 9.9 1.0 CG A:ASP125 3.2 21.1 0.5 CB A:SER127 3.5 10.7 1.0 CG A:ASP125 3.5 21.1 0.5 CG A:ASP123 3.5 11.3 1.0 OD2 A:ASP125 3.6 18.2 0.5 C A:THR129 3.7 9.3 1.0 OD2 A:ASP125 3.9 18.2 0.5 N A:SER127 4.1 12.1 1.0 OG1 A:THR129 4.1 15.4 1.0 N A:ASP125 4.2 14.2 0.5 CA A:ASP123 4.2 10.0 1.0 CA A:SER127 4.3 15.2 1.0 N A:THR129 4.3 8.9 1.0 CB A:ASP123 4.3 9.0 1.0 OD2 A:ASP123 4.4 13.3 1.0 N A:GLY126 4.4 15.2 0.5 CG A:GLU134 4.4 10.7 1.0 CA A:ILE130 4.4 11.4 1.0 CB A:ASP125 4.5 20.7 0.5 O A:HOH475 4.5 32.0 1.0 C A:ASP123 4.5 11.1 1.0 N A:ILE130 4.5 9.8 1.0 CA A:THR129 4.6 10.1 1.0 OG1 A:THR131 4.6 9.6 1.0 C A:ASP125 4.6 16.6 0.5 N A:LYS124 4.6 10.9 0.4 CA A:ASP125 4.7 17.0 0.5 N A:ASP125 4.7 14.2 0.5 N A:THR131 4.7 9.7 1.0 CB A:ASP125 4.7 20.7 0.5 N A:GLY128 4.8 11.6 1.0 N A:LYS124 4.8 10.7 0.6 C A:SER127 4.8 11.5 1.0 N A:GLY126 4.9 15.2 0.5 C A:GLY126 4.9 14.6 0.5

P.V.Natashin, W.Ding, E.V.Eremeeva, S.V.Markova, J.Lee, E.S.Vysotski, Z.J.Liu. Structures of the CA2+-Regulated Photoprotein Obelin Y138F Mutant Before and After Bioluminescence Support the Catalytic Function of A Water Molecule in the Reaction Acta Crystallogr.,Sect.D V. 70 720 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004713032434