Atomistry » Calcium » PDB 2hih-2i52 » 2hq8
Atomistry »
  Calcium »
    PDB 2hih-2i52 »
      2hq8 »

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: Sat Dec 12 03:39:32 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy