Magnesium in PDB 5wk4: Crystal Structure of An Anti-Idiotype Vlr

The structure of Crystal Structure of An Anti-Idiotype Vlr, PDB code: 5wk4 was solved by B.C.Collins, H.Nakahara, M.D.Cooper, B.R.Herrin, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.72 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.415, 61.382, 80.562, 110.09, 99.79, 93.52
R / Rfree (%)	19.3 / 22.3

The binding sites of Magnesium atom in the Crystal Structure of An Anti-Idiotype Vlr (pdb code 5wk4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of An Anti-Idiotype Vlr, PDB code: 5wk4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of An Anti-Idiotype Vlr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Anti-Idiotype Vlr within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg300 b:36.5 occ:1.00 O D:HOH410 2.0 28.8 1.0 O D:HOH434 2.1 28.6 1.0 O D:HOH520 2.1 33.1 1.0 O D:HOH417 2.2 27.5 1.0 OD2 D:ASP118 4.1 25.9 1.0 O D:GLY139 4.1 15.3 1.0 O D:HOH407 4.2 29.2 1.0 O D:ARG138 4.3 22.3 1.0 OD1 D:ASP118 4.4 28.3 1.0 C D:GLY139 4.6 18.6 1.0 OD2 D:ASP142 4.6 26.7 1.0 CG D:ASP118 4.7 24.5 1.0 CA D:GLY139 4.7 19.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of An Anti-Idiotype Vlr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Anti-Idiotype Vlr within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:35.6 occ:1.00 O A:HOH430 1.9 26.9 1.0 O B:HOH446 2.2 36.5 1.0 O A:HOH434 2.3 30.9 1.0 O B:HOH449 2.3 32.6 1.0 O A:HOH499 2.9 36.0 1.0 O A:GLY139 4.0 16.4 1.0 OD2 A:ASP142 4.0 23.7 1.0 O A:HOH453 4.3 20.9 1.0 OD2 A:ASP118 4.3 29.5 1.0 O A:ARG138 4.4 19.5 1.0 C A:GLY139 4.4 15.2 1.0 OD1 A:ASP118 4.4 27.8 1.0 O A:HOH516 4.5 22.8 1.0 CA A:GLY139 4.6 17.5 1.0 CB B:SER176 4.7 25.7 1.0 CG A:ASP118 4.8 27.8 1.0 O B:SER176 4.8 24.4 1.0 CG A:ASP142 4.9 21.6 1.0 CA B:SER176 4.9 23.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of An Anti-Idiotype Vlr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of An Anti-Idiotype Vlr within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg300 b:31.4 occ:1.00 O E:HOH540 2.0 29.9 1.0 O E:HOH433 2.0 29.9 1.0 O E:HOH468 2.1 33.2 1.0 O E:HOH442 2.2 31.6 1.0 O E:HOH518 2.2 30.9 1.0 O E:HOH520 2.3 35.8 1.0 OD2 E:ASP118 3.8 39.8 1.0 O E:GLY139 4.2 23.6 1.0 O E:ARG138 4.3 24.3 1.0 C E:GLY139 4.5 24.5 1.0 OD1 E:ASP118 4.6 34.8 1.0 CG E:ASP118 4.6 30.1 1.0 N E:GLY115 4.7 36.6 1.0 CA E:GLY139 4.8 23.6 1.0 CA E:GLY115 4.9 30.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of An Anti-Idiotype Vlr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of An Anti-Idiotype Vlr within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg300 b:46.3 occ:1.00 O F:HOH434 2.1 35.7 1.0 O F:HOH513 2.3 37.8 1.0 O F:HOH405 2.3 40.4 1.0 O F:HOH500 2.4 39.0 1.0 O F:HOH402 3.0 38.8 1.0 OD2 F:ASP118 3.9 37.0 1.0 O F:GLY139 4.1 28.7 1.0 O F:HOH518 4.1 41.2 1.0 O F:HOH502 4.2 39.1 1.0 O F:HOH403 4.3 35.2 1.0 OD1 F:ASP118 4.4 35.1 1.0 O F:ARG138 4.5 26.3 1.0 C F:GLY139 4.5 29.0 1.0 CG F:ASP118 4.6 33.1 1.0 CA F:GLY139 4.8 26.9 1.0 OD2 F:ASP142 4.9 38.7 1.0

B.C.Collins, H.Nakahara, S.Acharya, M.D.Cooper, B.R.Herrin, I.A.Wilson. Crystal Structure of An Anti-Idiotype Variable Lymphocyte Receptor. Acta Crystallogr F Struct V. 73 682 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29199989
DOI: 10.1107/S2053230X1701620X