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Calcium in PDB 2hq8: Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form

Protein crystallography data

The structure of Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form, PDB code: 2hq8 was solved by G.Stepanyuk, Z.J.Liu, E.S.Vysotski, J.Lee, J.P.Rose, B.C.Wang, Southeast Collaboratory For Structural Genomics (Secsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 78.414, 78.414, 125.001, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form (pdb code 2hq8). 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 Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form, PDB code: 2hq8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2hq8

Go back to Calcium Binding Sites List in 2hq8
Calcium binding site 1 out of 6 in the Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form


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 Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:16.4
occ:1.00
 OD1 A:ASN150 2.3 18.6 1.0
O A:GLN154 2.3 15.9 1.0
OD1 A:ASP148 2.4 17.0 1.0
O A:HOH466 2.4 15.2 1.0
OD1 A:ASN152 2.4 17.5 1.0
OE1 A:GLU159 2.5 13.9 1.0
OE2 A:GLU159 2.6 14.5 1.0
CD A:GLU159 2.9 13.9 1.0
CG A:ASN152 3.3 17.7 1.0
CG A:ASN150 3.4 22.3 1.0
CG A:ASP148 3.5 17.7 1.0
C A:GLN154 3.5 17.9 1.0
ND2 A:ASN150 3.9 21.5 1.0
ND2 A:ASN152 3.9 20.2 1.0
CA A:ASP148 4.2 18.0 1.0
N A:ASN152 4.2 19.5 1.0
N A:GLN154 4.3 18.3 1.0
N A:ASN150 4.3 19.6 1.0
CG A:GLU159 4.4 16.4 1.0
OD2 A:ASP148 4.4 18.8 1.0
CB A:ASP148 4.4 17.6 1.0
C A:ASP148 4.4 18.5 1.0
CB A:ASN152 4.4 19.9 1.0
CA A:ILE155 4.4 16.6 1.0
N A:ILE155 4.4 17.7 1.0
N A:SER156 4.4 16.5 1.0
CA A:GLN154 4.5 19.5 1.0
OG A:SER156 4.5 18.3 1.0
N A:PHE149 4.6 19.0 1.0
N A:LYS151 4.6 20.3 1.0
CB A:ASN150 4.6 19.3 1.0
CA A:ASN152 4.7 19.3 1.0
CA A:ASN150 4.7 20.4 1.0
O A:HOH485 4.8 21.4 1.0
C A:ASN150 4.8 20.1 1.0
C A:ILE155 4.9 16.9 1.0
N A:GLY153 4.9 18.6 1.0
O A:ASP148 5.0 17.9 1.0

Calcium binding site 2 out of 6 in 2hq8

Go back to Calcium Binding Sites List in 2hq8
Calcium binding site 2 out of 6 in the Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form


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 Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:15.0
occ:1.00
 O A:PHE30 2.3 16.2 1.0
OD1 A:ASP24 2.4 16.1 1.0
O A:HOH439 2.4 16.4 1.0
OG1 A:THR26 2.4 17.7 1.0
OD1 A:ASP28 2.4 14.9 1.0
OD2 A:ASP35 2.5 14.1 1.0
OD1 A:ASP35 2.5 13.5 1.0
CG A:ASP35 2.8 12.9 1.0
CG A:ASP24 3.3 13.5 1.0
C A:PHE30 3.4 15.9 1.0
CG A:ASP28 3.4 18.3 1.0
CB A:THR26 3.7 18.6 1.0
OD2 A:ASP28 3.8 17.7 1.0
N A:THR26 4.1 17.9 1.0
CA A:ASP24 4.1 15.2 1.0
CB A:ASP24 4.1 15.5 1.0
OD2 A:ASP24 4.1 19.1 1.0
CG2 A:THR26 4.2 19.1 1.0
CA A:THR26 4.2 18.6 1.0
N A:PHE30 4.3 15.8 1.0
N A:ILE31 4.3 16.2 1.0
CB A:ASP35 4.3 13.2 1.0
CA A:PHE30 4.3 16.0 1.0
O A:HOH719 4.3 26.5 1.0
N A:GLY27 4.3 19.0 1.0
CA A:ILE31 4.4 16.8 1.0
N A:ASP28 4.4 19.8 1.0
OG A:SER32 4.5 16.4 1.0
C A:ASP24 4.5 15.4 1.0
C A:THR26 4.6 18.7 1.0
N A:SER32 4.6 15.3 1.0
CB A:PHE30 4.6 15.0 1.0
CB A:ASP28 4.7 18.6 1.0
N A:VAL25 4.8 15.4 1.0
C A:ILE31 4.9 15.5 1.0
N A:GLY29 5.0 16.7 1.0
CA A:ASP28 5.0 18.6 1.0

Calcium binding site 3 out of 6 in 2hq8

Go back to Calcium Binding Sites List in 2hq8
Calcium binding site 3 out of 6 in the Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form


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 Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:21.4
occ:1.00
 OD1 A:ASP112 2.2 20.2 1.0
O A:TYR118 2.3 19.2 1.0
OE1 A:GLU123 2.4 17.4 1.0
OD1 A:ASP114 2.5 21.9 1.0
OD1 A:ASP116 2.5 22.0 1.0
OE2 A:GLU123 2.5 17.3 1.0
O A:HOH639 2.7 35.3 1.0
CD A:GLU123 2.8 14.9 1.0
CG A:ASP112 3.3 19.3 1.0
CG A:ASP116 3.4 24.7 1.0
CG A:ASP114 3.4 24.1 1.0
C A:TYR118 3.5 20.1 1.0
OD2 A:ASP114 3.9 25.2 1.0
OD2 A:ASP116 3.9 25.3 1.0
OD2 A:ASP112 4.1 22.5 1.0
CA A:ASP112 4.1 17.9 1.0
CB A:ASP112 4.2 17.5 1.0
N A:TYR118 4.2 20.9 1.0
N A:ASP116 4.2 25.9 1.0
CG A:GLU123 4.3 14.9 1.0
CA A:TYR118 4.3 20.6 1.0
N A:VAL119 4.4 18.2 1.0
N A:ASP114 4.4 22.0 1.0
N A:SER120 4.4 17.2 1.0
CA A:VAL119 4.4 16.9 1.0
CB A:ASP116 4.4 25.6 1.0
C A:ASP112 4.5 18.2 1.0
N A:LYS115 4.5 24.7 1.0
CB A:ASP114 4.6 23.6 1.0
N A:THR113 4.7 18.5 1.0
CB A:TYR118 4.7 22.9 1.0
N A:GLY117 4.7 24.5 1.0
CA A:ASP114 4.7 23.8 1.0
CA A:ASP116 4.8 25.5 1.0
C A:ASP114 4.8 24.8 1.0
C A:VAL119 4.9 16.8 1.0
OG A:SER120 5.0 17.4 1.0
CB A:SER120 5.0 18.3 1.0

Calcium binding site 4 out of 6 in 2hq8

Go back to Calcium Binding Sites List in 2hq8
Calcium binding site 4 out of 6 in the Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form


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 Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:17.2
occ:1.00
 OD2 B:ASP148 2.3 17.8 1.0
O B:GLN154 2.3 17.1 1.0
OD1 B:ASN150 2.3 20.0 1.0
O B:HOH616 2.5 21.4 1.0
OD1 B:ASN152 2.5 19.2 1.0
OE2 B:GLU159 2.5 17.5 1.0
OE1 B:GLU159 2.5 14.9 1.0
CD B:GLU159 2.9 15.2 1.0
CG B:ASN150 3.4 23.7 1.0
CG B:ASN152 3.4 20.0 1.0
CG B:ASP148 3.4 17.8 1.0
C B:GLN154 3.5 17.9 1.0
ND2 B:ASN150 3.9 25.0 1.0
ND2 B:ASN152 4.0 21.4 1.0
CA B:ASP148 4.1 18.5 1.0
N B:ASN152 4.2 19.7 1.0
OD1 B:ASP148 4.2 17.9 1.0
N B:ASN150 4.2 21.1 1.0
N B:GLN154 4.2 18.6 1.0
CB B:ASP148 4.3 17.7 1.0
C B:ASP148 4.3 18.6 1.0
CG B:GLU159 4.4 15.8 1.0
CA B:ILE155 4.4 16.5 1.0
N B:ILE155 4.4 17.5 1.0
CB B:ASN152 4.5 20.6 1.0
CA B:GLN154 4.5 18.8 1.0
N B:PHE149 4.5 19.5 1.0
N B:SER156 4.5 15.8 1.0
N B:LYS151 4.6 21.5 1.0
CB B:ASN150 4.6 21.3 1.0
O B:HOH618 4.6 24.1 1.0
OG B:SER156 4.7 18.4 1.0
CA B:ASN150 4.7 22.0 1.0
CA B:ASN152 4.7 20.3 1.0
CG B:GLN154 4.8 23.4 1.0
N B:GLY153 4.8 20.2 1.0
C B:ASN150 4.8 22.3 1.0
O B:ASP148 4.9 18.4 1.0
C B:ILE155 4.9 15.7 1.0
C B:ASN152 5.0 19.9 1.0

Calcium binding site 5 out of 6 in 2hq8

Go back to Calcium Binding Sites List in 2hq8
Calcium binding site 5 out of 6 in the Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form


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 Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:16.8
occ:1.00
 O B:PHE30 2.3 16.7 1.0
O B:HOH449 2.4 16.1 1.0
OD1 B:ASP24 2.4 13.6 1.0
OD1 B:ASP28 2.4 15.2 1.0
OD1 B:ASP35 2.4 15.1 1.0
OG1 B:THR26 2.5 16.9 1.0
OD2 B:ASP35 2.5 14.7 1.0
CG B:ASP35 2.8 14.2 1.0
CG B:ASP24 3.4 14.0 1.0
C B:PHE30 3.4 15.2 1.0
CG B:ASP28 3.4 18.3 1.0
CB B:THR26 3.8 17.8 1.0
OD2 B:ASP28 3.9 19.3 1.0
N B:THR26 4.1 16.7 1.0
CA B:ASP24 4.1 14.5 1.0
CB B:ASP24 4.1 13.8 1.0
CG2 B:THR26 4.2 19.8 1.0
OD2 B:ASP24 4.3 15.4 1.0
N B:PHE30 4.3 15.6 1.0
N B:ASP28 4.3 18.7 1.0
O B:HOH638 4.3 29.6 1.0
CA B:PHE30 4.3 15.9 1.0
CB B:ASP35 4.3 15.1 1.0
CA B:THR26 4.4 18.4 1.0
N B:ILE31 4.4 15.3 1.0
N B:GLY27 4.4 18.4 1.0
CA B:ILE31 4.5 14.5 1.0
C B:ASP24 4.5 15.1 1.0
OG B:SER32 4.6 16.9 1.0
CB B:ASP28 4.6 17.4 1.0
C B:THR26 4.7 18.1 1.0
CB B:PHE30 4.7 15.5 1.0
N B:SER32 4.7 13.3 1.0
N B:VAL25 4.8 14.8 1.0
CA B:ASP28 4.9 17.4 1.0
N B:GLY29 4.9 16.1 1.0
C B:ILE31 5.0 13.5 1.0

Calcium binding site 6 out of 6 in 2hq8

Go back to Calcium Binding Sites List in 2hq8
Calcium binding site 6 out of 6 in the Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form


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 Coelenterazine-Binding Protein From Renilla Muelleri in the Ca Loaded Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:20.9
occ:1.00
 OD1 B:ASP112 2.2 21.0 1.0
O B:TYR118 2.3 19.3 1.0
OE2 B:GLU123 2.4 16.4 1.0
OD2 B:ASP116 2.5 23.3 1.0
OD1 B:ASP114 2.5 25.6 1.0
OE1 B:GLU123 2.6 17.7 1.0
CD B:GLU123 2.8 15.1 1.0
CG B:ASP112 3.3 20.9 1.0
CG B:ASP116 3.4 27.5 1.0
C B:TYR118 3.4 18.9 1.0
CG B:ASP114 3.4 25.3 1.0
OD2 B:ASP114 3.8 26.9 1.0
OD1 B:ASP116 3.9 27.8 1.0
OD2 B:ASP112 4.1 23.0 1.0
CB B:ASP112 4.1 19.8 1.0
CA B:ASP112 4.1 19.3 1.0
N B:TYR118 4.1 20.5 1.0
N B:ASP116 4.3 27.7 1.0
CA B:TYR118 4.3 19.6 1.0
N B:VAL119 4.3 17.6 1.0
N B:SER120 4.4 16.9 1.0
CA B:VAL119 4.4 16.6 1.0
CG B:GLU123 4.4 14.0 1.0
N B:ASP114 4.4 23.0 1.0
C B:ASP112 4.5 19.5 1.0
N B:LYS115 4.5 26.0 1.0
CB B:ASP116 4.5 26.8 1.0
CB B:ASP114 4.6 24.5 1.0
N B:THR113 4.7 19.6 1.0
CB B:TYR118 4.7 21.0 1.0
CA B:ASP114 4.8 25.1 1.0
N B:GLY117 4.8 25.0 1.0
C B:ASP114 4.8 25.8 1.0
CA B:ASP116 4.8 27.3 1.0
C B:VAL119 4.8 16.4 1.0
CB B:SER120 4.9 17.8 1.0

Reference:

G.A.Stepanyuk, Z.J.Liu, S.S.Markova, L.A.Frank, J.Lee, E.S.Vysotski, B.C.Wang. Crystal Structure of Coelenterazine-Binding Protein From Renilla Muelleri at 1.7 A: Why It Is Not A Calcium-Regulated Photoprotein. Photochem.Photobiol.Sci. V. 7 442 2008.
PubMed: 18385886
DOI: 10.1039/B716535H
Page generated: Fri Jul 12 12:48:23 2024

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