Manganese in PDB 6x7u: Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad

All present enzymatic activity of Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad:
3.6.1.62; 3.6.1.64;

The structure of Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad, PDB code: 6x7u was solved by K.Hamilton, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.47 / 2.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	64.721, 64.721, 77.751, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 23.1

The binding sites of Manganese atom in the Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad (pdb code 6x7u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad, PDB code: 6x7u:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:75.0 occ:1.00 O1A A:FAD201 2.1 76.7 1.0 OE2 A:GLU80 2.2 60.8 1.0 O A:GLY59 2.3 43.4 1.0 CD A:GLU80 3.0 55.3 1.0 OE1 A:GLU80 3.2 54.6 1.0 PA A:FAD201 3.3 70.7 1.0 C A:GLY59 3.5 39.8 1.0 O2A A:FAD201 3.8 67.4 1.0 O3P A:FAD201 3.9 79.4 1.0 MN A:MN203 3.9 89.1 1.0 NE2 A:GLN48 4.1 44.8 1.0 CA A:GLY60 4.1 43.9 1.0 N A:GLY60 4.2 41.6 1.0 N A:GLY59 4.4 39.7 1.0 NE2 A:HIS24 4.4 49.5 1.0 CG A:GLU80 4.4 56.1 1.0 CA A:GLY59 4.5 39.4 1.0 O5B A:FAD201 4.6 63.8 1.0 CD2 A:HIS24 4.7 52.2 1.0 NH1 A:ARG50 4.7 50.4 1.0 O A:HOH304 4.8 60.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:89.1 occ:1.00 OE2 A:GLU76 3.3 47.0 1.0 O2A A:FAD201 3.3 67.4 1.0 OE1 A:GLU76 3.4 44.1 1.0 CD A:GLU76 3.5 48.1 1.0 MN A:MN202 3.9 75.0 1.0 OE2 A:GLU80 4.1 60.8 1.0 N A:PHE61 4.1 44.1 1.0 O1A A:FAD201 4.1 76.7 1.0 CA A:GLY60 4.2 43.9 1.0 O A:GLY59 4.2 43.4 1.0 PA A:FAD201 4.3 70.7 1.0 O3' A:FAD201 4.4 0.3 1.0 C A:GLY60 4.6 43.8 1.0 CG A:GLU76 4.7 50.8 1.0 C A:GLY59 4.9 39.8 1.0 N A:GLY60 4.9 41.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:64.1 occ:1.00 NE2 A:HIS99 2.4 87.7 1.0 OE2 A:GLU173 2.6 62.9 1.0 OE1 A:GLU173 2.7 58.4 1.0 CD A:GLU173 2.8 61.7 1.0 CD2 A:HIS99 3.2 90.8 1.0 CE1 A:HIS99 3.4 85.0 1.0 CG A:GLU173 4.2 57.1 1.0 CG A:HIS99 4.3 82.8 1.0 ND1 A:HIS99 4.4 82.6 1.0 CB A:GLU169 4.5 67.2 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Human Nudix Hydrolase NUDT16 in Complex with Fad within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn202 b:69.9 occ:1.00 O C:GLY59 2.0 48.9 1.0 O2P C:AMP201 2.3 53.8 1.0 OE2 C:GLU80 2.3 80.6 1.0 C C:GLY59 3.2 50.4 1.0 P C:AMP201 3.2 54.5 1.0 CD C:GLU80 3.2 74.0 1.0 OE1 C:GLU80 3.4 69.5 1.0 CA C:GLY60 3.6 48.8 1.0 O3P C:AMP201 3.6 46.4 1.0 O1P C:AMP201 3.7 57.4 1.0 N C:GLY60 3.8 48.4 1.0 NE2 C:HIS24 4.3 42.1 1.0 OE1 C:GLU76 4.3 62.5 1.0 N C:GLY59 4.4 49.1 1.0 CA C:GLY59 4.4 50.1 1.0 CG C:GLU80 4.6 70.9 1.0 O5' C:AMP201 4.6 46.3 1.0 CD2 C:HIS24 4.8 43.0 1.0 O C:HOH301 4.9 48.5 1.0

S.Sharma, E.Grudzien-Nogalska, K.Hamilton, X.Jiao, J.Yang, L.Tong, M.Kiledjian. Mammalian Nudix Proteins Cleave Nucleotide Metabolite Caps on Rnas. Nucleic Acids Res. V. 48 6788 2020.
ISSN: ESSN 1362-4962
PubMed: 32432673
DOI: 10.1093/NAR/GKAA402