Calcium in PDB 2f8p: Crystal Structure of Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State

The structure of Crystal Structure of Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State, PDB code: 2f8p was solved by Z.J.Liu, G.A.Stepanyuk, E.S.Vysotski, J.Lee, B.C.Wang, Southeastcollaboratory For Structural Genomics (Secsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.74 / 1.93
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	64.260, 64.260, 63.049, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23

The binding sites of Calcium atom in the Crystal Structure of Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State (pdb code 2f8p). 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 Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State, PDB code: 2f8p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State


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 Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:24.3 occ:1.00 OD1 A:ASP30 2.1 24.7 1.0 O A:LYS36 2.3 25.2 1.0 O A:HOH1609 2.3 22.7 1.0 OD1 A:ASN34 2.5 28.1 1.0 OD1 A:ASN32 2.5 27.3 1.0 OE2 A:GLU41 2.6 24.8 1.0 OE1 A:GLU41 2.6 22.9 1.0 CD A:GLU41 2.9 22.6 1.0 CG A:ASP30 3.3 27.1 1.0 C A:LYS36 3.5 25.6 1.0 CG A:ASN32 3.5 29.9 1.0 CG A:ASN34 3.5 31.9 1.0 ND2 A:ASN32 3.9 30.6 1.0 ND2 A:ASN34 4.1 30.6 1.0 OD2 A:ASP30 4.1 32.1 1.0 N A:LYS36 4.2 26.8 1.0 CA A:ASP30 4.3 24.4 1.0 CB A:ASP30 4.3 24.9 1.0 N A:ASN34 4.3 30.9 1.0 N A:ASN32 4.4 28.4 1.0 N A:ILE37 4.4 24.2 1.0 CA A:LYS36 4.4 26.7 1.0 OE2 A:GLU82 4.4 41.7 1.0 CG A:GLU41 4.4 18.5 1.0 N A:GLY33 4.4 31.4 1.0 CA A:ILE37 4.4 23.2 1.0 C A:ASP30 4.5 25.0 1.0 N A:ILE31 4.6 25.5 1.0 CB A:ASN34 4.6 30.3 1.0 CB A:ASN32 4.7 28.9 1.0 O A:HOH1637 4.7 43.3 1.0 C A:ASN32 4.8 31.0 1.0 CA A:ASN32 4.8 29.6 1.0 CA A:ASN34 4.9 30.7 1.0 CB A:LYS36 4.9 27.2 1.0 N A:GLY35 4.9 30.0 1.0 O A:ASP30 5.0 25.1 1.0 O A:HOH1615 5.0 30.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State


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 Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:30.3 occ:1.00 OE1 A:GLU134 2.3 29.7 1.0 OD1 A:ASP123 2.4 26.0 1.0 OD1 A:ASP125 2.4 36.6 1.0 O A:HOH1592 2.4 34.9 1.0 OG A:SER127 2.4 31.6 1.0 O A:THR129 2.5 28.8 1.0 OE2 A:GLU134 2.6 25.3 1.0 CD A:GLU134 2.8 31.0 1.0 CG A:ASP123 3.5 27.1 1.0 CG A:ASP125 3.5 35.3 1.0 CB A:SER127 3.5 30.7 1.0 C A:THR129 3.6 28.7 1.0 OD2 A:ASP125 3.9 37.7 1.0 CA A:ASP123 4.0 25.5 1.0 N A:SER127 4.0 30.4 1.0 CG2 A:THR129 4.1 30.9 1.0 CB A:ASP123 4.2 24.3 1.0 CG A:GLU134 4.3 30.0 1.0 CA A:SER127 4.3 30.8 1.0 OD2 A:ASP123 4.3 27.4 1.0 C A:ASP123 4.4 26.4 1.0 CA A:ILE130 4.4 26.9 1.0 N A:THR129 4.4 28.8 1.0 N A:ILE130 4.5 27.8 1.0 N A:ASP125 4.5 30.6 1.0 CA A:THR129 4.5 30.0 1.0 N A:LYS124 4.5 27.3 1.0 N A:THR131 4.6 27.5 1.0 CB A:ASP125 4.8 32.6 1.0 OG1 A:THR131 4.8 30.8 1.0 N A:GLY126 4.8 30.9 1.0 C A:SER127 4.9 31.0 1.0 CB A:THR129 4.9 30.7 1.0 N A:GLY128 4.9 30.1 1.0 O A:HOH1594 4.9 37.8 1.0 CA A:ASP125 5.0 32.2 1.0 O A:ASP123 5.0 26.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State


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 Obelin Following CA2+ Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:28.6 occ:1.00 O A:HOH1642 2.2 28.3 1.0 O A:ASP165 2.4 30.5 1.0 OD1 A:ASP159 2.4 35.1 1.0 OG A:SER163 2.4 35.0 1.0 OD1 A:ASP161 2.5 34.6 1.0 OE2 A:GLU170 2.5 27.5 1.0 OE1 A:GLU170 2.5 24.3 1.0 CD A:GLU170 2.8 25.1 1.0 CG A:ASP161 3.4 36.0 1.0 CG A:ASP159 3.5 35.4 1.0 C A:ASP165 3.6 31.2 1.0 CB A:SER163 3.6 36.4 1.0 OD2 A:ASP161 3.7 35.4 1.0 N A:SER163 4.0 38.2 1.0 OD1 A:ASP165 4.1 38.8 1.0 CA A:ASP159 4.1 35.1 1.0 CA A:LEU166 4.3 27.0 1.0 CB A:ASP159 4.3 35.1 1.0 CG A:GLU170 4.3 22.0 1.0 OD2 A:ASP167 4.4 27.3 1.0 CA A:SER163 4.4 36.6 1.0 N A:ASP161 4.4 35.6 1.0 N A:ASP165 4.4 33.7 1.0 N A:LEU166 4.4 28.8 1.0 OD2 A:ASP159 4.4 36.3 1.0 C A:ASP159 4.4 34.5 1.0 N A:LEU160 4.5 34.3 1.0 N A:ASP167 4.5 24.1 1.0 CA A:ASP165 4.6 32.1 1.0 CB A:ASP161 4.6 36.5 1.0 N A:ASN162 4.7 38.8 1.0 C A:LEU166 4.8 25.4 1.0 CA A:ASP161 4.8 36.8 1.0 C A:ASP161 4.8 38.1 1.0 C A:SER163 4.9 36.5 1.0 N A:GLY164 4.9 35.9 1.0 NZ A:LYS4 5.0 32.8 1.0

Z.J.Liu, G.A.Stepanyuk, E.S.Vysotski, J.Lee, S.V.Markova, N.P.Malikova, B.C.Wang. Crystal Structure of Obelin After CA2+-Triggered Bioluminescence Suggests Neutral Coelenteramide As the Primary Excited State. Proc.Natl.Acad.Sci.Usa V. 103 2570 2006.
ISSN: ISSN 0027-8424
PubMed: 16467137
DOI: 10.1073/PNAS.0511142103