Magnesium in PDB 7ndi: Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion

The structure of Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion, PDB code: 7ndi was solved by A.Garg, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.77 / 2.88
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.701, 114.701, 257.309, 90, 90, 120
R / Rfree (%)	19.2 / 21.5

The structure of Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion (pdb code 7ndi). 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 ZC3H12C Pin Domain with MG2+ Ion, PDB code: 7ndi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion


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 ZC3H12C Pin Domain with MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:54.8 occ:1.00 O A:HOH414 2.0 68.3 1.0 O A:HOH427 2.1 63.0 1.0 O A:HOH412 2.1 53.6 1.0 OD1 A:ASP226 2.2 82.0 1.0 O A:HOH455 2.3 54.6 1.0 O A:HOH420 2.5 61.5 1.0 OD2 A:ASP226 2.8 58.9 1.0 CG A:ASP226 2.8 73.7 1.0 OD2 A:ASP225 3.9 54.5 1.0 OD1 A:ASP225 3.9 62.1 1.0 OD2 A:ASP141 4.0 51.3 1.0 CG A:ASP225 4.3 62.6 1.0 CB A:ASP226 4.3 48.6 1.0 OD1 A:ASP141 4.3 69.3 1.0 OD2 A:ASP244 4.4 98.1 1.0 CG A:ASP141 4.6 51.8 1.0 N A:ASP226 4.8 48.7 1.0 CE1 A:TYR246 4.8 59.7 1.0 CE1 A:TYR224 4.8 102.7 1.0 CA A:ASP226 4.9 58.1 1.0 OH A:TYR224 5.0 115.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion


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 ZC3H12C Pin Domain with MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:67.6 occ:1.00 O B:HOH407 2.1 54.1 1.0 OD1 B:ASP226 2.4 91.5 1.0 O B:HOH402 2.5 55.2 1.0 O B:HOH453 2.5 58.7 1.0 O B:HOH405 2.9 53.7 1.0 OD1 B:ASP225 3.2 77.2 1.0 CG B:ASP226 3.3 75.6 1.0 OD2 B:ASP225 3.3 79.2 1.0 OD2 B:ASP226 3.5 54.3 1.0 CG B:ASP225 3.7 71.5 1.0 CB B:SER143 4.5 68.5 1.0 CB B:ASP226 4.7 73.2 1.0 OD1 B:ASP141 4.8 63.2 1.0 N B:ASP226 4.8 55.2 1.0 OD2 B:ASP141 4.9 52.4 1.0 O B:HOH401 4.9 58.9 1.0 OG B:SER143 4.9 64.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion


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 ZC3H12C Pin Domain with MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:58.2 occ:1.00 O C:HOH412 2.0 58.0 1.0 O C:HOH410 2.1 57.4 1.0 O C:HOH411 2.2 68.2 1.0 OD1 C:ASP226 2.3 81.7 1.0 O C:HOH421 2.4 59.1 1.0 O C:HOH438 2.6 56.9 1.0 OD2 C:ASP226 3.0 58.9 1.0 CG C:ASP226 3.0 62.3 1.0 OD1 C:ASP225 4.0 68.1 1.0 OD2 C:ASP225 4.0 59.9 1.0 OD2 C:ASP141 4.3 57.0 1.0 CG C:ASP225 4.4 62.2 1.0 OD2 C:ASP244 4.5 93.5 1.0 CB C:ASP226 4.5 60.1 1.0 O C:HOH402 4.5 62.6 1.0 OD1 C:ASP141 4.6 77.2 1.0 CG C:ASP141 4.9 57.1 1.0 N C:ASP226 5.0 61.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion


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 ZC3H12C Pin Domain with MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:55.5 occ:1.00 O D:HOH405 2.1 64.7 1.0 O D:HOH411 2.1 52.7 1.0 O D:HOH426 2.1 75.7 1.0 O D:HOH402 2.2 118.4 1.0 OD1 D:ASP226 2.7 87.0 1.0 OD2 D:ASP226 2.8 48.3 1.0 CG D:ASP226 3.1 71.4 1.0 O D:HOH441 3.1 84.0 1.0 OD2 D:ASP244 4.0 98.9 1.0 OD2 D:ASP141 4.3 54.5 1.0 OD1 D:ASP225 4.6 56.5 1.0 CB D:ASP226 4.6 48.0 1.0 OD2 D:ASP225 4.7 76.4 1.0 OD1 D:ASP141 4.8 64.2 1.0 CG D:ASP244 4.9 99.7 1.0

A.Garg, Y.Roske, S.Yamada, T.Uehata, O.Takeuchi, U.Heinemann. Pin and Ccch Zn-Finger Domains Coordinate Rna Targeting in ZC3H12 Family Endoribonucleases. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33950203
DOI: 10.1093/NAR/GKAB316