Magnesium in PDB 4nkt: Structure of CID1 in Complex with the Utp Analog Umpnpp

The structure of Structure of CID1 in Complex with the Utp Analog Umpnpp, PDB code: 4nkt was solved by P.Munoz-Tello, C.Gabus, S.Thore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.770, 77.320, 82.110, 90.00, 90.86, 90.00
R / Rfree (%)	17.9 / 21.2

The structure of Structure of CID1 in Complex with the Utp Analog Umpnpp also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Magnesium atom in the Structure of CID1 in Complex with the Utp Analog Umpnpp (pdb code 4nkt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of CID1 in Complex with the Utp Analog Umpnpp, PDB code: 4nkt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of CID1 in Complex with the Utp Analog Umpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of CID1 in Complex with the Utp Analog Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:27.6 occ:1.00 ND2 A:ASN165 3.3 28.1 1.0 O A:HOH705 3.5 33.4 1.0 N1 A:2KH401 3.6 16.5 1.0 O A:HOH583 3.6 26.2 1.0 C2 A:2KH401 3.7 18.2 1.0 O2 A:2KH401 3.8 16.9 1.0 C1' A:2KH401 3.9 18.2 1.0 O A:HOH763 4.0 35.1 1.0 N3 A:2KH401 4.2 18.6 1.0 O4' A:2KH401 4.2 18.6 1.0 C6 A:2KH401 4.2 18.2 1.0 CG A:ASN165 4.4 24.1 1.0 CB A:ALA168 4.6 14.0 1.0 OD1 A:ASN165 4.6 23.1 1.0 C4 A:2KH401 4.6 21.4 1.0 C5 A:2KH401 4.7 19.1 1.0 O A:HOH745 4.7 33.9 1.0 O A:HOH754 4.9 33.6 1.0 O A:HOH760 4.9 26.9 1.0 CE2 A:PHE88 5.0 13.5 1.0

Magnesium binding site 2 out of 4 in the Structure of CID1 in Complex with the Utp Analog Umpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of CID1 in Complex with the Utp Analog Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:27.4 occ:1.00 OD1 B:ASN362 2.9 33.6 1.0 O B:HOH567 3.2 37.4 1.0 ND2 B:ASN362 3.4 39.7 1.0 CG B:ASN362 3.6 40.6 1.0 NE B:ARG277 4.3 34.8 1.0 CD B:ARG277 4.3 32.0 1.0 CE1 B:HIS273 4.3 30.3 1.0 O B:HOH601 4.7 34.0 1.0 NE2 B:HIS273 4.7 31.9 1.0 CZ B:ARG277 4.8 38.8 1.0 O B:HOH634 4.9 26.9 1.0

Magnesium binding site 3 out of 4 in the Structure of CID1 in Complex with the Utp Analog Umpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of CID1 in Complex with the Utp Analog Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:31.5 occ:1.00 ND2 B:ASN165 3.4 29.5 1.0 N1 B:2KH401 3.6 19.4 1.0 C2 B:2KH401 3.7 21.3 1.0 C1' B:2KH401 3.8 22.4 1.0 O B:HOH573 3.8 28.6 1.0 O2 B:2KH401 3.9 23.7 1.0 O4' B:2KH401 4.0 19.8 1.0 C6 B:2KH401 4.2 23.2 1.0 N3 B:2KH401 4.3 23.8 1.0 CB B:ALA168 4.4 19.1 1.0 CG B:ASN165 4.4 30.9 1.0 OD1 B:ASN165 4.6 27.3 1.0 O B:HOH696 4.7 42.8 1.0 C5 B:2KH401 4.7 22.4 1.0 C4 B:2KH401 4.8 22.7 1.0 CE2 B:PHE88 4.8 20.4 1.0

Magnesium binding site 4 out of 4 in the Structure of CID1 in Complex with the Utp Analog Umpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of CID1 in Complex with the Utp Analog Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:14.2 occ:1.00 O B:HOH516 3.4 16.4 1.0 CG2 B:THR45 3.7 15.0 1.0 CE2 B:TYR49 4.2 11.9 1.0 O B:HOH530 4.4 21.8 1.0 CB B:THR45 4.8 14.9 1.0 CD2 B:TYR49 4.9 10.3 1.0 CB B:SER267 4.9 15.6 1.0 OH B:TYR49 5.0 10.7 1.0

P.Munoz-Tello, C.Gabus, S.Thore. A Critical Switch in the Enzymatic Properties of the CID1 Protein Deciphered From Its Product-Bound Crystal Structure. Nucleic Acids Res. V. 42 3372 2014.
ISSN: ISSN 0305-1048
PubMed: 24322298
DOI: 10.1093/NAR/GKT1278