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Calcium in PDB 1qx2: X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution

Protein crystallography data

The structure of X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution, PDB code: 1qx2 was solved by C.G.Bunick, M.R.Nelson, S.Mangahas, L.S.Mizoue, G.J.Bunick, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.40 / 1.44
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 59.540, 62.174, 69.463, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.4

Other elements in 1qx2:

The structure of X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution (pdb code 1qx2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution, PDB code: 1qx2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1qx2

Go back to Calcium Binding Sites List in 1qx2
Calcium binding site 1 out of 4 in the X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:7.6
occ:1.00
OD1 A:ASP54 2.3 7.3 1.0
O A:GLU60 2.3 10.0 1.0
OD1 A:ASN56 2.3 9.1 1.0
OD1 A:ASP58 2.4 8.5 1.0
O A:HOH1017 2.4 12.9 1.0
OE1 A:GLU65 2.5 6.9 1.0
OE2 A:GLU65 2.6 6.9 1.0
CD A:GLU65 2.9 5.9 1.0
CG A:ASP58 3.3 10.2 1.0
CG A:ASP54 3.4 8.3 1.0
CG A:ASN56 3.5 10.5 1.0
C A:GLU60 3.5 9.8 1.0
OD2 A:ASP58 3.6 12.9 1.0
ND2 A:ASN56 4.1 13.1 1.0
OD2 A:ASP54 4.2 9.8 1.0
CA A:ASP54 4.2 9.1 1.0
CB A:ASP54 4.2 8.6 1.0
N A:ASP58 4.3 9.5 1.0
N A:GLU60 4.3 11.3 1.0
N A:VAL61 4.3 7.9 1.0
CA A:VAL61 4.3 7.4 1.0
N A:ASN56 4.3 10.0 1.0
CG A:GLU65 4.4 6.6 1.0
N A:SER62 4.5 6.7 1.0
C A:ASP54 4.5 9.1 1.0
CA A:GLU60 4.5 11.4 1.0
N A:GLY57 4.5 9.0 1.0
N A:LYS55 4.6 9.7 1.0
CB A:ASP58 4.6 9.5 1.0
CB A:ASN56 4.6 10.2 1.0
OE1 A:GLN22 4.6 13.8 1.0
O A:HOH1067 4.8 31.7 1.0
CA A:ASN56 4.8 9.8 1.0
CA A:ASP58 4.8 10.0 1.0
C A:VAL61 4.9 6.9 1.0
O A:HOH1008 4.9 13.9 1.0
N A:GLY59 4.9 10.7 1.0
C A:ASN56 4.9 9.4 1.0

Calcium binding site 2 out of 4 in 1qx2

Go back to Calcium Binding Sites List in 1qx2
Calcium binding site 2 out of 4 in the X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:6.8
occ:1.00
O A:ALA14 2.3 7.2 1.0
O A:ASP19 2.3 8.2 1.0
O A:GLN22 2.4 7.8 1.0
O A:GLU17 2.4 8.9 1.0
O A:HOH1010 2.4 10.9 1.0
OE1 A:GLU27 2.4 8.4 1.0
OE2 A:GLU27 2.6 9.0 1.0
CD A:GLU27 2.9 7.7 1.0
C A:ALA14 3.4 7.0 1.0
C A:ASP19 3.5 8.7 1.0
C A:GLN22 3.6 7.9 1.0
C A:GLU17 3.6 9.7 1.0
CA A:ALA14 3.9 6.1 1.0
N A:ASP19 3.9 8.5 1.0
C A:GLY18 4.1 9.2 1.0
CA A:ASP19 4.3 8.4 1.0
N A:GLU17 4.3 9.6 1.0
CG A:GLU27 4.4 8.8 1.0
N A:PRO20 4.4 9.1 1.0
N A:ILE23 4.4 7.2 1.0
CA A:ILE23 4.4 6.8 1.0
N A:GLN22 4.5 8.2 1.0
N A:SER24 4.5 7.1 1.0
N A:ALA15 4.5 7.4 1.0
CB A:ALA14 4.5 6.4 1.0
N A:GLY18 4.5 9.4 1.0
CA A:PRO20 4.5 9.4 1.0
CA A:GLY18 4.5 9.2 1.0
CA A:GLU17 4.5 10.3 1.0
O A:GLY18 4.5 9.8 1.0
CA A:GLN22 4.6 8.8 1.0
O A:HOH1045 4.6 19.9 1.0
OE2 A:GLU60 4.6 16.9 0.5
CB A:ASP19 4.7 8.5 1.0
C A:PRO20 4.7 9.7 1.0
CG A:GLU17 4.7 12.9 0.7
N A:LYS16 4.9 8.6 1.0
CA A:ALA15 4.9 7.9 1.0
O A:PHE13 4.9 8.6 1.0
C A:ILE23 4.9 7.1 1.0

Calcium binding site 3 out of 4 in 1qx2

Go back to Calcium Binding Sites List in 1qx2
Calcium binding site 3 out of 4 in the X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:7.1
occ:1.00
O B:GLU60 2.3 7.8 1.0
OD1 B:ASP54 2.3 8.1 1.0
OD1 B:ASN56 2.3 9.2 1.0
O B:HOH1016 2.4 9.2 1.0
OD1 B:ASP58 2.4 9.4 1.0
OE1 B:GLU65 2.4 7.4 1.0
OE2 B:GLU65 2.6 7.9 1.0
CD B:GLU65 2.9 7.3 1.0
CG B:ASN56 3.3 11.4 1.0
CG B:ASP58 3.3 10.0 1.0
CG B:ASP54 3.4 8.8 1.0
C B:GLU60 3.4 8.0 1.0
OD2 B:ASP58 3.6 12.1 1.0
ND2 B:ASN56 3.8 15.0 1.0
CA B:ASP54 4.2 10.0 1.0
CB B:ASP54 4.2 9.8 1.0
OD2 B:ASP54 4.2 9.3 1.0
N B:GLU60 4.2 9.2 1.0
N B:VAL61 4.2 7.2 1.0
N B:ASN56 4.3 11.4 1.0
N B:ASP58 4.3 10.8 1.0
CA B:VAL61 4.3 6.1 1.0
N B:SER62 4.3 6.6 1.0
CA B:GLU60 4.4 9.5 1.0
CG B:GLU65 4.4 7.0 1.0
C B:ASP54 4.5 10.7 1.0
N B:LYS55 4.5 11.3 1.0
N B:GLY57 4.5 11.4 1.0
CB B:ASN56 4.5 11.5 1.0
CB B:ASP58 4.6 10.6 1.0
OE1 B:GLN22 4.7 8.7 1.0
CA B:ASN56 4.7 11.6 1.0
C B:VAL61 4.8 6.0 1.0
CA B:ASP58 4.8 10.6 1.0
N B:GLY59 4.8 10.1 1.0
C B:ASN56 4.9 11.6 1.0
OG B:SER62 5.0 7.7 1.0
O B:HOH1022 5.0 14.1 1.0

Calcium binding site 4 out of 4 in 1qx2

Go back to Calcium Binding Sites List in 1qx2
Calcium binding site 4 out of 4 in the X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Calcium-Loaded Calbindomodulin (A Calbindin D9K Re- Engineered to Undergo A Conformational Opening) at 1.44 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1006

b:5.9
occ:1.00
O B:ALA14 2.3 7.2 1.0
O B:GLN22 2.3 6.3 1.0
O B:GLY18 2.3 7.1 1.0
O B:HOH1010 2.4 7.9 1.0
O B:ASP19 2.4 8.1 1.0
OE1 B:GLU27 2.4 5.7 1.0
OE2 B:GLU27 2.5 5.7 1.0
CD B:GLU27 2.8 5.8 1.0
C B:ASP19 3.3 8.7 1.0
C B:ALA14 3.4 6.8 1.0
C B:GLY18 3.5 6.9 1.0
C B:GLN22 3.5 6.6 1.0
CA B:ALA14 3.9 6.7 1.0
CB B:ASP19 3.9 8.8 1.0
CA B:ASP19 4.0 8.4 1.0
N B:ASP19 4.2 8.1 1.0
CB B:ALA14 4.3 7.3 1.0
N B:PRO20 4.3 8.8 1.0
CG B:GLU27 4.4 7.1 1.0
CA B:ILE23 4.4 6.5 1.0
O B:HOH1008 4.4 9.5 1.0
N B:ILE23 4.4 6.6 1.0
N B:SER24 4.5 6.6 1.0
N B:ALA15 4.5 6.5 1.0
N B:GLN22 4.5 6.8 1.0
CA B:GLN22 4.5 6.6 1.0
N B:GLY18 4.6 6.5 1.0
CA B:PRO20 4.6 9.6 1.0
CA B:GLY18 4.7 6.8 1.0
O B:HOH1020 4.7 12.0 1.0
C B:GLU17 4.7 6.5 1.0
CG B:ASP19 4.7 9.7 1.0
N B:GLU17 4.8 6.7 1.0
CA B:ALA15 4.9 6.9 1.0
O B:GLU17 4.9 6.5 1.0
CB B:GLN22 4.9 6.9 1.0
C B:ILE23 4.9 6.7 1.0

Reference:

C.G.Bunick, M.R.Nelson, S.Mangahas, M.J.Hunter, J.H.Sheehan, L.S.Mizoue, G.J.Bunick, W.J.Chazin. Designing Sequence to Control Protein Function in An Ef-Hand Protein J.Am.Chem.Soc. V. 126 5990 2004.
ISSN: ISSN 0002-7863
PubMed: 15137763
DOI: 10.1021/JA0397456
Page generated: Sat Dec 12 03:17:11 2020

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