Calcium in PDB 5xtw: Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH

The structure of Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH, PDB code: 5xtw was solved by Y.He, Z.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.94 / 3.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.819, 164.768, 164.596, 91.11, 97.56, 97.50
R / Rfree (%)	21.1 / 24.8

The binding sites of Calcium atom in the Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH (pdb code 5xtw). 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 the Cysr-CTLD2 Fragment of Human Mr at Acidic pH, PDB code: 5xtw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH


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 the Cysr-CTLD2 Fragment of Human Mr at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:38.5 occ:1.00 OE1 A:GLU461 2.4 27.6 1.0 O A:ASP475 2.5 19.4 1.0 OG A:SER454 2.6 25.7 1.0 OE1 A:GLU452 2.6 26.8 1.0 OD1 A:ASP475 2.8 24.0 1.0 OE2 A:GLU452 3.2 22.7 1.0 CD A:GLU452 3.3 21.0 1.0 CD A:GLU461 3.4 29.7 1.0 C A:ASP475 3.6 17.5 1.0 OE2 A:GLU461 3.8 44.2 1.0 CB A:SER454 3.8 25.0 1.0 CG A:ASP475 4.0 21.4 1.0 N A:ASP475 4.3 13.5 1.0 N A:SER454 4.4 18.5 1.0 CA A:ASP475 4.4 16.4 1.0 N A:ARG476 4.6 16.6 1.0 CA A:SER454 4.7 21.8 1.0 N A:HIS455 4.7 29.0 1.0 CG A:GLU461 4.7 26.9 1.0 CA A:ARG476 4.8 21.6 1.0 CG A:GLU452 4.8 14.2 1.0 CB A:ASP475 4.8 18.1 1.0 OD2 A:ASP475 4.8 20.9 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH


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 the Cysr-CTLD2 Fragment of Human Mr at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:38.8 occ:1.00 OE1 C:GLU452 2.5 15.3 1.0 O C:ASP475 2.5 19.1 1.0 OE1 C:GLU461 2.5 34.3 1.0 OG C:SER454 2.6 46.3 1.0 OD1 C:ASP475 2.8 21.7 1.0 CD C:GLU452 3.3 13.6 1.0 OE2 C:GLU452 3.4 15.9 1.0 CD C:GLU461 3.6 30.0 1.0 C C:ASP475 3.7 17.1 1.0 CB C:SER454 3.9 28.5 1.0 OE2 C:GLU461 3.9 46.5 1.0 CG C:ASP475 4.0 21.6 1.0 N C:ASP475 4.3 13.9 1.0 N C:SER454 4.3 17.1 1.0 CA C:ASP475 4.5 16.2 1.0 N C:HIS455 4.6 30.4 1.0 N C:ARG476 4.7 16.2 1.0 CA C:SER454 4.7 21.3 1.0 CG C:GLU452 4.7 12.3 1.0 CA C:ARG476 4.8 20.7 1.0 CG C:GLU461 4.8 22.8 1.0 CB C:ASP475 4.8 18.4 1.0 OD2 C:ASP475 4.9 23.8 1.0 CB C:ALA474 5.0 11.3 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH


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 the Cysr-CTLD2 Fragment of Human Mr at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:38.3 occ:1.00 OE1 D:GLU452 2.4 20.0 1.0 OG D:SER454 2.5 43.8 1.0 O D:ASP475 2.5 22.0 1.0 OE1 D:GLU461 2.6 26.6 1.0 OD1 D:ASP475 2.7 28.6 1.0 OE2 D:GLU452 2.9 20.6 1.0 CD D:GLU452 3.0 18.4 1.0 CD D:GLU461 3.6 28.8 1.0 CB D:SER454 3.7 27.7 1.0 C D:ASP475 3.7 21.3 1.0 CG D:ASP475 3.9 29.3 1.0 N D:ASP475 4.0 14.0 1.0 OE2 D:GLU461 4.0 33.7 1.0 N D:SER454 4.2 18.8 1.0 CA D:ASP475 4.3 19.4 1.0 CA D:SER454 4.5 22.1 1.0 CG D:GLU452 4.5 15.6 1.0 CB D:ALA474 4.7 11.3 1.0 N D:HIS455 4.7 25.0 1.0 CB D:ASP475 4.8 23.4 1.0 N D:ARG476 4.8 22.9 1.0 OD2 D:ASP475 4.8 23.8 1.0 CG D:GLU461 4.9 28.0 1.0 C D:ALA474 4.9 13.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH


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 the Cysr-CTLD2 Fragment of Human Mr at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:38.6 occ:1.00 OE1 E:GLU452 2.3 22.7 1.0 O E:ASP475 2.4 15.8 1.0 OE1 E:GLU461 2.6 22.3 1.0 OG E:SER454 2.7 19.2 1.0 OD1 E:ASP475 2.9 17.9 1.0 CD E:GLU452 3.0 23.4 1.0 OE2 E:GLU452 3.0 20.5 1.0 C E:ASP475 3.6 16.6 1.0 CD E:GLU461 3.6 18.5 1.0 CB E:SER454 3.9 24.1 1.0 N E:ASP475 4.0 9.9 1.0 OE2 E:GLU461 4.1 19.7 1.0 CG E:ASP475 4.1 14.7 1.0 CA E:ASP475 4.3 14.2 1.0 N E:SER454 4.3 14.5 1.0 CG E:GLU452 4.5 17.1 1.0 CB E:ALA474 4.5 12.6 1.0 N E:ARG476 4.6 13.9 1.0 CA E:SER454 4.7 17.1 1.0 CA E:ARG476 4.8 20.0 1.0 CG E:GLU461 4.8 19.9 1.0 CB E:ASP475 4.8 14.2 1.0 C E:ALA474 4.9 10.8 1.0 CB E:ARG476 4.9 26.8 1.0 N E:HIS455 4.9 18.8 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH


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 the Cysr-CTLD2 Fragment of Human Mr at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca502 b:44.7 occ:1.00 OG F:SER454 2.5 27.4 1.0 OE1 F:GLU461 2.7 28.8 1.0 O F:ASP475 3.1 23.8 1.0 OE2 F:GLU452 3.2 17.4 1.0 OE1 F:GLU452 3.2 23.6 1.0 CD F:GLU461 3.4 35.1 1.0 OE2 F:GLU461 3.4 53.8 1.0 OD1 F:ASP475 3.5 21.4 1.0 CD F:GLU452 3.6 16.7 1.0 CB F:SER454 3.7 24.3 1.0 C F:ASP475 4.3 21.1 1.0 CG F:ASP475 4.7 20.1 1.0 N F:SER454 4.7 17.1 1.0 CA F:SER454 4.8 19.4 1.0 CG F:GLU461 4.8 28.9 1.0 N F:ASP475 4.9 13.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the Cysr-CTLD2 Fragment of Human Mr at Acidic pH


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 the Cysr-CTLD2 Fragment of Human Mr at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca502 b:40.8 occ:1.00 O H:ASP475 2.4 19.5 1.0 OE1 H:GLU452 2.4 16.0 1.0 OE1 H:GLU461 2.4 28.3 1.0 OG H:SER454 2.5 54.6 1.0 OD1 H:ASP475 2.6 24.0 1.0 CD H:GLU452 3.2 13.7 1.0 OE2 H:GLU452 3.3 18.2 1.0 CD H:GLU461 3.5 30.6 1.0 C H:ASP475 3.5 18.9 1.0 CB H:SER454 3.8 29.7 1.0 CG H:ASP475 3.8 21.3 1.0 N H:ASP475 3.9 15.4 1.0 OE2 H:GLU461 3.9 47.7 1.0 N H:SER454 4.1 16.9 1.0 CA H:ASP475 4.2 18.6 1.0 N H:HIS455 4.5 28.3 1.0 CA H:SER454 4.5 23.2 1.0 N H:ARG476 4.6 20.2 1.0 CB H:ASP475 4.6 20.4 1.0 CB H:ALA474 4.6 12.1 1.0 CG H:GLU452 4.6 11.7 1.0 OD2 H:ASP475 4.7 24.1 1.0 CG H:GLU461 4.8 26.3 1.0 CA H:ARG476 4.8 24.4 1.0 C H:ALA474 4.9 13.8 1.0

Z.Hu, X.Shi, B.Yu, N.Li, Y.Huang, Y.He. Structural Insights Into the pH-Dependent Conformational Change and Collagen Recognition of the Human Mannose Receptor Structure V. 26 60 2018.
ISSN: ISSN 1878-4186
PubMed: 29225077
DOI: 10.1016/J.STR.2017.11.006