Chlorine in PDB 5okl: Human Afamin Monoclinic Crystal Form

The structure of Human Afamin Monoclinic Crystal Form, PDB code: 5okl was solved by B.Rupp, A.Naschberger, M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	109.04 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.915, 112.872, 109.228, 90.00, 93.39, 90.00
R / Rfree (%)	19.9 / 23.7

The binding sites of Chlorine atom in the Human Afamin Monoclinic Crystal Form (pdb code 5okl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Afamin Monoclinic Crystal Form, PDB code: 5okl:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Afamin Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Afamin Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:72.4 occ:1.00 N A:GLY290 3.1 53.3 1.0 NE A:ARG289 3.3 67.2 1.0 O A:HOH974 3.4 58.0 1.0 NH2 A:ARG289 3.6 75.0 1.0 CA A:GLY290 3.6 55.8 1.0 CG A:MET264 3.8 56.1 1.0 CB A:ARG289 3.9 63.8 1.0 CZ A:ARG289 3.9 73.8 1.0 CA A:PRO287 4.0 76.1 1.0 CB A:MET264 4.0 56.4 1.0 O A:PRO287 4.0 75.8 1.0 CG1 A:ILE286 4.2 0.0 1.0 C A:ARG289 4.2 56.7 1.0 CA A:ILE286 4.2 85.0 1.0 C A:PRO287 4.2 75.6 1.0 CG A:ARG289 4.3 68.5 1.0 CA A:ARG289 4.4 67.6 1.0 CD A:ARG289 4.4 70.5 1.0 CG2 A:ILE286 4.5 91.6 1.0 CB A:ILE286 4.5 91.8 1.0 N A:ARG289 4.5 70.4 1.0 CA A:SER261 4.6 55.0 1.0 OG A:SER261 4.7 70.5 1.0 CB A:PRO287 4.9 77.1 1.0 O A:LYS285 4.9 69.2 1.0 N A:ILE286 4.9 78.9 1.0 N A:SER261 4.9 51.4 1.0 C A:GLY290 5.0 56.8 1.0 CG2 A:THR260 5.0 49.9 1.0 O A:THR260 5.0 52.4 1.0

Chlorine binding site 2 out of 3 in the Human Afamin Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Afamin Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:43.8 occ:1.00 N A:PHE151 3.2 39.7 1.0 O A:HOH984 3.2 60.4 1.0 C A:ASN149 3.4 43.4 1.0 N A:VAL152 3.5 44.6 1.0 CA A:ASN149 3.5 45.8 1.0 N A:PRO150 3.6 42.5 1.0 CB A:PHE151 3.6 42.6 1.0 CA A:PHE151 3.7 41.7 1.0 CB A:ASN149 3.7 46.4 1.0 CD A:PRO150 3.8 44.3 1.0 O A:ASN149 3.8 39.8 1.0 CD A:LYS200 3.9 48.6 1.0 C A:PHE151 3.9 44.9 1.0 CE A:LYS200 4.0 50.7 1.0 CD2 A:PHE151 4.0 46.2 1.0 NZ A:LYS200 4.1 59.5 1.0 CB A:SER196 4.2 45.5 1.0 C A:PRO150 4.3 41.3 1.0 CG A:PHE151 4.3 42.9 1.0 CG A:LYS200 4.3 43.4 1.0 OD1 A:ASN149 4.4 49.8 1.0 CA A:VAL152 4.4 43.2 1.0 CB A:VAL152 4.4 43.5 1.0 CA A:PRO150 4.5 41.7 1.0 CG A:ASN149 4.6 49.6 1.0 CG A:PRO150 4.6 43.2 1.0 OG A:SER196 4.6 55.3 1.0 CG1 A:VAL152 4.8 44.7 1.0 O A:HOH951 4.8 51.8 1.0 N A:ASN149 4.9 50.3 1.0 O A:PHE151 5.0 47.5 1.0

Chlorine binding site 3 out of 3 in the Human Afamin Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Afamin Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:55.3 occ:1.00 NE B:ARG289 3.2 56.4 1.0 N B:GLY290 3.2 45.6 1.0 NH2 B:ARG289 3.4 55.1 1.0 CZ B:ARG289 3.7 55.9 1.0 CA B:GLY290 3.7 46.1 1.0 O B:HOH1038 3.8 70.1 1.0 CB B:ARG289 3.8 54.6 1.0 O B:HOH913 3.9 37.8 1.0 CA B:PRO287 3.9 63.8 1.0 CG B:MET264 3.9 43.7 1.0 O B:PRO287 4.0 57.4 1.0 CG1 B:ILE286 4.0 74.9 1.0 CA B:ILE286 4.0 66.5 1.0 CB B:MET264 4.0 45.1 1.0 C B:PRO287 4.1 60.3 1.0 C B:ARG289 4.2 48.1 1.0 CG B:ARG289 4.3 58.2 1.0 CD B:ARG289 4.3 59.4 1.0 CA B:ARG289 4.4 51.8 1.0 CB B:ILE286 4.4 68.3 1.0 N B:ARG289 4.4 47.5 1.0 CG2 B:ILE286 4.5 72.5 1.0 CA B:SER261 4.6 42.7 1.0 O B:LYS285 4.6 53.6 1.0 OG B:SER261 4.7 57.8 1.0 CB B:PRO287 4.8 61.0 1.0 N B:ILE286 4.8 58.8 1.0 N B:PRO287 4.9 65.4 1.0 N B:GLU288 5.0 58.2 1.0

A.Naschberger, A.Orry, S.Lechner, M.W.Bowler, D.Nurizzo, M.Novokmet, M.A.Keller, G.Oemer, D.Seppi, M.Haslbeck, K.Pansi, H.Dieplinger, B.Rupp. Structural Evidence For A Role of the Multi-Functional Human Glycoprotein Afamin in Wnt Transport. Structure V. 25 1907 2017.
ISSN: ISSN 1878-4186
PubMed: 29153507
DOI: 10.1016/J.STR.2017.10.006