Calcium in PDB 6k67: Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH)

The structure of Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH), PDB code: 6k67 was solved by J.O.Lee, M.S.Jin, J.W.Kim, S.Kim, H.Lee, G.Y.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.38 / 1.95
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.298, 115.298, 93.275, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.7

The binding sites of Calcium atom in the Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH) (pdb code 6k67). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH), PDB code: 6k67:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:43.0 occ:1.00 OD1 B:ASP63 2.2 43.1 1.0 O B:THR69 2.3 34.0 1.0 OD1 B:ASN67 2.3 50.4 1.0 OD1 B:ASP65 2.5 56.3 1.0 OE2 B:GLU74 2.6 46.2 1.0 OE1 B:GLU74 2.6 41.7 1.0 CD B:GLU74 3.0 44.6 1.0 CG B:ASP65 3.3 62.1 1.0 CG B:ASP63 3.4 48.6 1.0 CG B:ASN67 3.4 45.9 1.0 OD2 B:ASP65 3.4 65.0 1.0 C B:THR69 3.5 44.8 1.0 ND2 B:ASN67 4.1 44.0 1.0 OD2 B:ASP63 4.2 46.1 1.0 N B:THR69 4.2 41.2 1.0 N B:ASN67 4.2 46.6 1.0 CA B:ASP63 4.3 43.8 1.0 N B:ILE70 4.4 37.7 1.0 CB B:ASP63 4.4 41.2 1.0 CA B:THR69 4.4 42.6 1.0 CA B:ILE70 4.5 35.8 1.0 CG B:GLU74 4.5 44.4 1.0 N B:ASP71 4.5 42.9 1.0 CB B:ASN67 4.6 46.3 1.0 N B:ASP65 4.6 53.6 1.0 N B:GLY66 4.6 57.2 1.0 CB B:ASP65 4.6 57.6 1.0 N B:GLY68 4.7 41.1 1.0 OG1 B:THR69 4.7 52.6 1.0 N B:ALA64 4.7 52.3 1.0 C B:ASP63 4.7 54.3 1.0 CA B:ASN67 4.8 43.1 1.0 C B:ILE70 4.8 38.5 1.0 CG B:ASP71 4.8 43.5 1.0 C B:ASN67 4.9 44.7 1.0 OD1 B:ASP71 4.9 46.4 1.0 OD2 B:ASP71 5.0 51.8 1.0 CA B:ASP65 5.0 57.7 1.0

Calcium binding site 2 out of 4 in the Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:37.9 occ:1.00 O B:THR33 2.3 35.0 1.0 OE1 B:GLU38 2.4 33.3 1.0 OE2 B:GLU38 2.4 35.5 1.0 OD1 B:ASP27 2.5 44.8 1.0 OD1 B:ASP31 2.5 57.5 1.0 O B:HOH208 2.5 37.8 1.0 CD B:GLU38 2.8 30.2 1.0 CB B:ASP29 3.0 62.9 1.0 CG B:ASP31 3.3 53.1 1.0 C B:THR33 3.5 33.5 1.0 CG B:ASP27 3.5 46.7 1.0 OD2 B:ASP29 3.6 65.2 1.0 CG B:ASP29 3.9 64.4 1.0 OD2 B:ASP31 3.9 54.2 1.0 OG1 B:THR33 4.1 48.6 1.0 CA B:ASP27 4.1 41.8 1.0 N B:THR33 4.2 42.7 1.0 CA B:ASP29 4.2 62.1 1.0 N B:ASP31 4.2 48.2 1.0 N B:ASP29 4.3 55.5 1.0 CB B:ASP27 4.3 45.5 1.0 CG B:GLU38 4.3 30.7 1.0 CB B:ASP31 4.3 53.2 1.0 CA B:THR33 4.4 39.9 1.0 C B:ASP27 4.4 43.0 1.0 OD2 B:ASP27 4.4 47.0 1.0 N B:ILE34 4.4 33.3 1.0 CA B:ILE34 4.6 29.6 1.0 N B:GLY30 4.6 61.2 1.0 CA B:ASP31 4.7 46.5 1.0 CG2 B:THR35 4.8 38.6 1.0 O B:ASP27 4.8 41.6 1.0 N B:GLY32 4.8 45.4 1.0 N B:LYS28 4.8 41.1 1.0 C B:ASP29 4.9 64.4 1.0 N B:THR35 4.9 29.4 1.0 CB B:THR33 4.9 47.2 1.0 C B:ASP31 5.0 45.0 1.0

Calcium binding site 3 out of 4 in the Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:59.5 occ:1.00 OD1 D:ASN67 1.9 66.2 1.0 OD1 D:ASP63 2.4 62.2 1.0 OE1 D:GLU74 2.4 57.2 1.0 OE2 D:GLU74 2.5 55.2 1.0 OD1 D:ASP65 2.6 73.2 1.0 O D:THR69 2.6 50.4 1.0 CD D:GLU74 2.8 60.0 1.0 CG D:ASN67 3.1 66.3 1.0 CG D:ASP65 3.3 66.4 1.0 OD2 D:ASP65 3.5 71.4 1.0 CG D:ASP63 3.6 60.0 1.0 C D:THR69 3.7 54.6 1.0 CB D:ASN67 4.0 67.6 1.0 ND2 D:ASN67 4.0 72.6 1.0 N D:ASN67 4.1 60.3 1.0 CG D:GLU74 4.3 52.8 1.0 N D:THR69 4.3 64.4 1.0 OD2 D:ASP63 4.4 53.3 1.0 OG1 D:THR69 4.4 62.2 1.0 CA D:ASP63 4.4 59.2 1.0 N D:ASP65 4.4 56.0 1.0 CA D:ASN67 4.5 63.2 1.0 N D:ASP71 4.5 53.9 1.0 N D:ILE70 4.5 51.4 1.0 CB D:ASP65 4.5 64.8 1.0 CA D:ILE70 4.6 55.7 1.0 CB D:ASP63 4.6 60.7 1.0 CA D:THR69 4.6 57.5 1.0 N D:ALA64 4.6 73.0 1.0 N D:GLY66 4.7 62.1 1.0 N D:GLY68 4.7 65.7 1.0 C D:ASP63 4.7 69.9 1.0 OD1 D:ASP71 4.7 61.4 1.0 CG D:ASP71 4.8 62.3 1.0 C D:ASN67 4.8 64.8 1.0 CA D:ASP65 4.9 60.6 1.0 C D:ILE70 4.9 56.8 1.0 OD2 D:ASP71 5.0 66.7 1.0

Calcium binding site 4 out of 4 in the Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Application of Anti-Helix Antibodies in Protein Structure Determination (9011-3LRH) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:49.4 occ:1.00 O D:THR33 2.2 46.9 1.0 OD1 D:ASP27 2.3 47.9 1.0 OE1 D:GLU38 2.4 48.4 1.0 OE2 D:GLU38 2.5 43.4 1.0 O D:HOH221 2.6 59.5 1.0 OD1 D:ASP29 2.6 66.2 1.0 CD D:GLU38 2.8 43.2 1.0 CB D:ASP31 3.3 78.3 1.0 C D:THR33 3.4 52.2 1.0 CG D:ASP29 3.4 69.6 1.0 CG D:ASP27 3.5 53.8 1.0 OD2 D:ASP29 3.8 69.2 1.0 OG1 D:THR33 4.0 69.0 1.0 OD2 D:ASP31 4.1 90.8 1.0 N D:ASP31 4.2 64.6 1.0 CA D:ASP27 4.2 53.5 1.0 CG D:ASP31 4.2 88.1 1.0 CG D:GLU38 4.3 42.5 1.0 N D:THR33 4.3 54.4 1.0 CA D:ASP31 4.3 72.0 1.0 CB D:ASP27 4.3 55.4 1.0 N D:ILE34 4.3 45.8 1.0 OD2 D:ASP27 4.3 56.3 1.0 CA D:THR33 4.4 59.5 1.0 CA D:ILE34 4.5 42.2 1.0 C D:ASP27 4.5 56.1 1.0 N D:ASP29 4.6 65.6 1.0 CB D:ASP29 4.7 65.3 1.0 CG2 D:THR35 4.7 47.3 1.0 N D:LYS28 4.8 58.6 1.0 N D:THR35 4.8 38.8 1.0 CB D:THR33 4.9 63.2 1.0 N D:GLY30 4.9 65.9 1.0 N D:GLY32 4.9 59.5 1.0 C D:ASP31 4.9 65.8 1.0 O D:ASP27 4.9 57.5 1.0 CA D:ASP29 5.0 67.6 1.0 C D:ASP29 5.0 67.4 1.0 O D:HOH208 5.0 58.7 1.0

J.W.Kim, S.Kim, H.Lee, G.Cho, S.C.Kim, H.Lee, M.S.Jin, J.O.Lee. Application of Antihelix Antibodies in Protein Structure Determination. Proc.Natl.Acad.Sci.Usa V. 116 17786 2019.
ISSN: ESSN 1091-6490
PubMed: 31371498
DOI: 10.1073/PNAS.1910080116