Calcium in PDB 5gqq: Structure of Alg-2/HEBP2 Complex

The structure of Structure of Alg-2/HEBP2 Complex, PDB code: 5gqq was solved by X.Liu, J.Ma, H.Zhang, Y.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.94 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.279, 78.124, 87.171, 113.71, 105.64, 93.95
R / Rfree (%)	19.4 / 22.5

The structure of Structure of Alg-2/HEBP2 Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Structure of Alg-2/HEBP2 Complex (pdb code 5gqq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Alg-2/HEBP2 Complex, PDB code: 5gqq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Alg-2/HEBP2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Alg-2/HEBP2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:16.9 occ:1.00 O C:VAL42 2.2 18.9 1.0 OD1 C:ASP36 2.3 21.0 1.0 CL C:CL204 2.4 41.2 1.0 OD2 C:ASP38 2.4 20.7 1.0 OE2 C:GLU47 2.4 17.8 1.0 OE1 C:GLU47 2.4 16.9 1.0 OG C:SER40 2.7 18.7 1.0 CD C:GLU47 2.8 20.0 1.0 CG C:ASP38 3.3 30.6 1.0 C C:VAL42 3.4 21.3 1.0 CG C:ASP36 3.5 22.1 1.0 OD1 C:ASP38 3.6 24.2 1.0 CB C:SER40 3.7 22.3 1.0 N C:SER40 4.0 20.1 1.0 CA C:ILE43 4.2 16.5 1.0 N C:VAL42 4.3 16.5 1.0 N C:ILE43 4.3 17.2 1.0 CA C:ASP36 4.3 17.6 1.0 CG C:GLU47 4.3 15.4 1.0 OD2 C:ASP36 4.3 18.4 1.0 CA C:SER40 4.4 24.7 1.0 CB C:ASP36 4.4 20.7 1.0 OE2 B:GLU153 4.4 20.4 1.0 CA C:VAL42 4.5 11.4 1.0 N C:SER44 4.5 14.4 1.0 N C:ASP38 4.5 19.6 1.0 C C:ASP36 4.5 24.4 1.0 O C:HOH344 4.5 30.6 1.0 OE1 B:GLU153 4.5 24.3 1.0 CB C:ASP38 4.6 26.6 1.0 N C:ARG39 4.7 24.0 1.0 N C:LYS37 4.8 21.9 1.0 N C:GLY41 4.8 18.3 1.0 C C:SER40 4.8 23.5 1.0 C C:ASP38 4.9 25.4 1.0 C C:ILE43 4.9 18.5 1.0 CA C:ASP38 4.9 25.5 1.0 CD B:GLU153 4.9 25.8 1.0 O C:ASP36 5.0 18.9 1.0

Calcium binding site 2 out of 6 in the Structure of Alg-2/HEBP2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Alg-2/HEBP2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:40.9 occ:1.00 O C:MET109 2.3 37.9 1.0 OE1 C:GLU114 2.3 41.0 1.0 OD1 C:ASP103 2.4 38.9 1.0 OG C:SER107 2.4 39.5 1.0 OD2 C:ASP105 2.4 47.6 1.0 OE2 C:GLU114 2.5 39.9 1.0 CD C:GLU114 2.7 43.3 1.0 CG C:ASP105 3.2 48.1 1.0 OD1 C:ASP105 3.3 44.3 1.0 CB C:SER107 3.4 40.8 1.0 C C:MET109 3.5 39.7 1.0 CG C:ASP103 3.6 35.8 1.0 OD2 C:ASP111 4.1 52.0 1.0 N C:SER107 4.1 37.9 1.0 CG C:GLU114 4.3 38.9 1.0 N C:MET109 4.3 34.4 1.0 CA C:SER107 4.3 38.8 1.0 CA C:ILE110 4.3 39.5 1.0 OD2 C:ASP103 4.4 36.3 1.0 N C:ILE110 4.4 36.7 1.0 CA C:ASP103 4.4 38.1 1.0 N C:ASP111 4.4 45.9 1.0 CA C:MET109 4.5 37.9 1.0 CB C:ASP103 4.5 31.4 1.0 N C:ASP105 4.6 44.9 1.0 CB C:ASP105 4.7 41.6 1.0 C C:ASP103 4.7 40.5 1.0 N C:GLY108 4.7 47.6 1.0 CG C:ASP111 4.7 48.3 1.0 N C:ARG104 4.7 61.0 1.0 C C:ILE110 4.8 45.5 1.0 C C:SER107 4.9 40.4 1.0 OE1 C:GLN145 4.9 57.0 1.0 CB C:MET109 5.0 40.1 1.0

Calcium binding site 3 out of 6 in the Structure of Alg-2/HEBP2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Alg-2/HEBP2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:0.3 occ:1.00 OD1 C:ASP173 2.5 84.8 1.0 OD1 C:ASP169 2.6 70.8 1.0 O C:TRP175 2.8 51.5 1.0 OD1 C:ASP171 2.8 73.2 1.0 O C:HOH360 3.1 58.0 1.0 O C:HOH343 3.1 58.3 1.0 CG C:ASP173 3.4 83.7 1.0 CG C:ASP171 3.6 75.3 1.0 OD2 C:ASP171 3.7 77.2 1.0 CG C:ASP169 3.8 69.4 1.0 OD2 C:ASP173 3.9 85.6 1.0 C C:TRP175 3.9 48.1 1.0 CA C:ASP169 4.4 66.7 1.0 OD2 C:ASP169 4.6 66.7 1.0 CB C:ASP173 4.6 80.5 1.0 N C:THR170 4.6 89.2 1.0 CB C:ASP169 4.7 63.0 1.0 C C:ASP169 4.7 70.4 1.0 CA C:ILE176 4.7 59.1 1.0 CA C:TRP175 4.8 48.1 1.0 N C:TRP175 4.8 51.2 1.0 N C:ILE176 4.8 56.0 1.0 CB C:TRP175 4.9 45.6 1.0 N C:ASP173 4.9 80.8 1.0 OG1 C:THR170 5.0 87.7 1.0

Calcium binding site 4 out of 6 in the Structure of Alg-2/HEBP2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Alg-2/HEBP2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:18.3 occ:1.00 OD1 D:ASP36 2.2 20.8 1.0 O D:VAL42 2.3 18.1 1.0 OD2 D:ASP38 2.3 24.0 1.0 CL D:CL204 2.4 46.0 1.0 OE1 D:GLU47 2.5 15.6 1.0 OE2 D:GLU47 2.5 15.6 1.0 OG D:SER40 2.7 15.1 1.0 CD D:GLU47 2.8 19.1 1.0 CG D:ASP38 3.3 31.4 1.0 C D:VAL42 3.4 22.5 1.0 CG D:ASP36 3.4 22.9 1.0 OD1 D:ASP38 3.6 24.4 1.0 CB D:SER40 3.7 22.7 1.0 N D:SER40 4.0 25.1 1.0 N D:VAL42 4.2 15.4 1.0 OD2 D:ASP36 4.2 17.8 1.0 N D:ILE43 4.3 15.7 1.0 CA D:ASP36 4.3 17.1 1.0 CA D:ILE43 4.3 17.5 1.0 CG D:GLU47 4.3 17.2 1.0 CA D:SER40 4.3 24.4 1.0 OE2 A:GLU153 4.3 26.2 1.0 CB D:ASP36 4.4 19.1 1.0 CA D:VAL42 4.4 14.8 1.0 OE1 A:GLU153 4.5 23.6 1.0 N D:ASP38 4.5 24.4 1.0 C D:ASP36 4.5 22.8 1.0 N D:SER44 4.5 8.7 1.0 O D:HOH313 4.6 31.0 1.0 CB D:ASP38 4.6 28.7 1.0 N D:ARG39 4.7 32.1 1.0 N D:GLY41 4.7 23.5 1.0 N D:LYS37 4.8 21.4 1.0 C D:SER40 4.8 22.2 1.0 CD A:GLU153 4.9 28.0 1.0 C D:ASP38 4.9 31.4 1.0 CA D:ASP38 4.9 29.6 1.0 C D:ILE43 4.9 16.2 1.0 O D:ASP36 4.9 20.6 1.0

Calcium binding site 5 out of 6 in the Structure of Alg-2/HEBP2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Alg-2/HEBP2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:47.4 occ:1.00 OD1 D:ASP103 2.3 47.1 1.0 OD2 D:ASP105 2.3 50.1 1.0 OE1 D:GLU114 2.4 44.9 1.0 O D:MET109 2.4 44.2 1.0 OG D:SER107 2.4 55.2 1.0 OE2 D:GLU114 2.6 46.1 1.0 CD D:GLU114 2.8 46.7 1.0 CG D:ASP105 3.2 48.9 1.0 OD1 D:ASP105 3.3 53.5 1.0 CB D:SER107 3.5 53.6 1.0 CG D:ASP103 3.5 45.2 1.0 C D:MET109 3.6 45.5 1.0 N D:SER107 4.1 51.4 1.0 OD2 D:ASP111 4.2 57.0 1.0 OD2 D:ASP103 4.3 45.1 1.0 CA D:ILE110 4.3 37.6 1.0 CG D:GLU114 4.3 40.8 1.0 CA D:SER107 4.4 48.0 1.0 N D:MET109 4.4 48.3 1.0 N D:ILE110 4.4 36.8 1.0 CA D:ASP103 4.4 43.4 1.0 N D:ASP111 4.5 54.0 1.0 CB D:ASP103 4.5 38.6 1.0 CA D:MET109 4.5 46.2 1.0 CB D:ASP105 4.6 48.5 1.0 C D:ASP103 4.7 47.7 1.0 N D:ASP105 4.7 51.6 1.0 C D:ILE110 4.9 41.1 1.0 N D:GLY108 4.9 41.7 1.0 N D:ARG104 4.9 66.1 1.0 C D:SER107 4.9 51.8 1.0 N D:ASN106 5.0 56.5 1.0 CB D:MET109 5.0 48.5 1.0

Calcium binding site 6 out of 6 in the Structure of Alg-2/HEBP2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Alg-2/HEBP2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca203 b:0.2 occ:1.00 O D:TRP175 2.4 64.3 1.0 OD1 D:ASP171 2.4 97.1 1.0 CG D:ASP171 2.7 95.5 1.0 CB D:ASP173 2.9 81.6 1.0 OD2 D:ASP171 3.0 91.2 1.0 OD1 D:ASP169 3.1 97.0 1.0 OD1 D:ASP173 3.2 78.1 1.0 C D:TRP175 3.4 60.1 1.0 CG D:ASP173 3.5 78.6 1.0 CB D:ASP171 3.6 96.5 1.0 CG D:ASP169 3.6 91.4 1.0 OD2 D:ASP169 3.6 94.4 1.0 N D:TRP175 3.8 63.2 1.0 CA D:TRP175 4.0 60.6 1.0 CA D:ASP173 4.0 83.0 1.0 CB D:TRP175 4.2 62.8 1.0 C D:ASP173 4.3 84.9 1.0 N D:ASP173 4.3 84.4 1.0 N D:GLY174 4.5 66.7 1.0 N D:ILE176 4.5 53.4 1.0 OD2 D:ASP173 4.6 76.4 1.0 CB D:ASP169 4.8 88.7 1.0 CA D:ILE176 4.8 48.0 1.0 CA D:ASP171 4.9 97.8 1.0 CA D:ASP169 4.9 87.8 1.0 O D:ASP173 4.9 84.9 1.0 N D:ASP171 5.0 97.9 1.0 C D:GLY174 5.0 57.9 1.0

J.Ma, X.Zhang, Y.Feng, H.Zhang, X.Wang, Y.Zheng, W.Qiao, X.Liu. Structural and Functional Study of Apoptosis-Linked Gene-2HEME-Binding Protein 2 Interactions in Hiv-1 Production. J. Biol. Chem. V. 291 26670 2016.
ISSN: ESSN 1083-351X
PubMed: 27784779
DOI: 10.1074/JBC.M116.752444