Magnesium in PDB 5ioo: Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold

The structure of Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold, PDB code: 5ioo was solved by S.Handa, B.Paul, J.Miller, D.Valentine, P.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.00 / 2.52
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	143.998, 143.998, 59.261, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 25

The binding sites of Magnesium atom in the Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold (pdb code 5ioo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold, PDB code: 5ioo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:46.6 occ:1.00 O A:HOH460 2.5 31.6 1.0 OD1 A:ASP15 2.7 32.1 1.0 O A:HOH429 3.0 29.0 1.0 O A:GLY201 3.4 33.9 1.0 CG A:ASP15 3.8 36.1 1.0 O A:HOH408 4.0 29.1 1.0 CB A:ASP15 4.2 35.1 1.0 C A:GLY201 4.4 36.1 1.0 CA A:ASP15 4.4 35.2 1.0 OD1 A:ASN202 4.5 34.5 1.0 O A:SER14 4.8 30.9 1.0 O A:HOH407 4.8 42.4 1.0 OD2 A:ASP15 4.9 36.7 1.0

Magnesium binding site 2 out of 4 in the Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:43.5 occ:1.00 OE1 A:GLU178 2.4 30.5 1.0 O A:MSE98 2.8 32.0 1.0 CD A:GLU178 3.4 36.5 1.0 CG1 A:VAL97 3.5 32.0 1.0 CD A:PRO179 3.7 27.9 1.0 C A:MSE98 3.8 29.7 1.0 OE2 A:GLU178 3.9 39.4 1.0 CA A:PRO99 4.1 29.0 1.0 N A:VAL100 4.3 29.1 1.0 CB A:GLU178 4.3 32.9 1.0 N A:PRO99 4.3 31.0 1.0 CG A:GLU178 4.4 37.3 1.0 CG A:PRO179 4.5 29.1 1.0 C A:PRO99 4.5 26.9 1.0 N A:MSE98 4.6 32.1 1.0 N A:PRO179 4.8 29.1 1.0 CA A:MSE98 4.8 28.9 1.0 CA A:GLU178 4.9 32.3 1.0 CG2 A:VAL100 4.9 34.9 1.0

Magnesium binding site 3 out of 4 in the Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:72.8 occ:1.00 O B:HOH424 1.9 54.6 1.0 CD1 B:LEU48 3.0 67.1 1.0 NE2 B:GLN7 3.5 80.6 1.0 CG B:LEU48 4.4 50.7 1.0 OE2 B:GLU10 4.4 65.0 1.0 CB B:SER47 4.5 55.2 1.0 CD2 B:LEU48 4.6 43.5 1.0 CD B:GLN7 4.7 82.7 1.0 OG B:SER46 4.8 57.7 1.0 CG B:GLN7 4.9 81.0 1.0 OG B:SER47 4.9 56.9 1.0 N B:LEU48 5.0 56.5 1.0

Magnesium binding site 4 out of 4 in the Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Accommodation of Massive Sequence Variation in Nanoarchaeota By the C- Type Lectin Fold within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:52.5 occ:1.00 O B:HOH407 2.3 59.2 1.0 CE1 B:TYR198 3.5 61.4 1.0 OD1 B:ASN191 3.7 66.4 1.0 ND2 B:ASN197 3.7 49.0 1.0 CD2 B:TRP170 3.9 40.6 1.0 OD1 B:ASN197 3.9 46.6 1.0 CG B:TRP170 4.1 38.0 1.0 CE2 B:TRP170 4.1 38.0 1.0 OH B:TYR198 4.2 59.7 1.0 CE3 B:TRP170 4.2 37.6 1.0 CG B:ASN197 4.2 48.3 1.0 CZ B:TYR198 4.3 60.3 1.0 CD1 B:TRP170 4.3 37.3 1.0 NE1 B:TRP170 4.4 36.0 1.0 CD1 B:TYR198 4.4 59.5 1.0 CG B:ASN191 4.5 66.4 1.0 CZ2 B:TRP170 4.6 35.6 1.0 CB B:TRP170 4.6 41.1 1.0 CZ3 B:TRP170 4.6 35.9 1.0 ND2 B:ASN191 4.6 73.7 1.0 CG1 B:ILE195 4.7 39.8 1.0 CG2 B:ILE195 4.8 42.6 1.0 CH2 B:TRP170 4.8 35.1 1.0

S.Handa, B.G.Paul, J.F.Miller, D.L.Valentine, P.Ghosh. Conservation of the C-Type Lectin Fold For Accommodating Massive Sequence Variation in Archaeal Diversity-Generating Retroelements. Bmc Struct.Biol. V. 16 13 2016.
ISSN: ESSN 1472-6807
PubMed: 27578274
DOI: 10.1186/S12900-016-0064-6