Magnesium in PDB 3gj7: Crystal Structure of Human Rangdp-NUP153ZNF12 Complex

The structure of Crystal Structure of Human Rangdp-NUP153ZNF12 Complex, PDB code: 3gj7 was solved by J.R.Partridge, T.U.Schwartz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.523, 61.129, 80.215, 90.00, 93.71, 90.00
R / Rfree (%)	18.6 / 22.9

The structure of Crystal Structure of Human Rangdp-NUP153ZNF12 Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex (pdb code 3gj7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex, PDB code: 3gj7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex


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 Human Rangdp-NUP153ZNF12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:44.0 occ:1.00 O1B A:GDP302 2.2 36.2 1.0 O A:HOH240 2.2 35.2 1.0 OG1 A:THR24 2.2 34.7 1.0 O A:HOH241 2.3 35.5 1.0 O A:HOH242 2.3 40.7 1.0 O A:HOH239 2.3 38.5 1.0 CB A:THR24 3.3 35.9 1.0 PB A:GDP302 3.4 39.1 1.0 O2B A:GDP302 3.5 35.6 1.0 N A:THR24 4.1 32.2 1.0 O A:THR66 4.1 35.1 1.0 OG1 A:THR66 4.1 41.3 1.0 OD2 A:ASP65 4.2 36.4 1.0 CA A:THR24 4.3 33.1 1.0 O2A A:GDP302 4.3 36.5 1.0 OD1 A:ASP65 4.3 43.8 1.0 O3B A:GDP302 4.4 36.0 1.0 OE2 A:GLU70 4.4 40.4 1.0 CG2 A:THR24 4.4 33.2 1.0 O3A A:GDP302 4.5 33.9 1.0 CG A:ASP65 4.7 43.6 1.0 N A:GLY68 4.7 47.9 1.0 PA A:GDP302 4.8 39.1 1.0 C A:THR66 4.9 38.0 1.0 O1A A:GDP302 4.9 41.2 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex


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 Human Rangdp-NUP153ZNF12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:48.3 occ:1.00 O A:HOH279 2.6 48.4 1.0 O A:LEU31 2.8 28.7 1.0 MG C:MG303 3.1 58.0 1.0 C A:LEU31 3.7 31.2 1.0 CG A:GLU34 3.7 40.9 1.0 N A:SER35 3.8 36.4 1.0 CA A:LEU31 3.9 26.4 1.0 CB A:GLU34 3.9 37.2 1.0 CB A:SER35 4.0 42.2 1.0 CB A:LEU31 4.1 32.6 1.0 CD2 A:LEU31 4.1 33.4 1.0 ND1 C:HIS53 4.1 35.7 1.0 CA A:SER35 4.3 35.2 1.0 O C:HOH329 4.3 52.2 1.0 C A:GLU34 4.4 38.0 1.0 CE1 C:HIS53 4.5 39.1 1.0 O A:HOH293 4.5 43.4 1.0 O A:HOH329 4.5 57.1 1.0 O C:HOH358 4.6 48.8 1.0 OG A:SER35 4.6 41.8 1.0 CA A:GLU34 4.7 33.4 1.0 CG A:LEU31 4.7 35.5 1.0 N A:THR32 4.9 28.0 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex


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 Human Rangdp-NUP153ZNF12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:43.7 occ:1.00 O A:HOH221 3.0 37.1 1.0 MG C:MG305 3.0 40.5 1.0 N A:ALA181 3.2 32.0 1.0 O A:HOH238 3.2 44.7 1.0 O C:HOH381 3.5 54.1 1.0 CA A:PRO180 3.7 41.0 1.0 CB A:PRO180 3.7 44.1 1.0 C A:PRO180 3.9 36.4 1.0 CB A:ALA181 4.0 32.2 1.0 CA A:ALA181 4.2 33.5 1.0 OG1 A:THR32 4.2 43.6 1.0 CE1 A:HIS30 4.2 38.8 1.0 CB C:ALA181 4.3 27.9 1.0 NE2 A:HIS30 4.4 29.5 1.0 O A:ALA181 4.5 28.7 1.0 OG1 C:THR32 4.7 36.7 1.0 CG1 A:VAL51 4.8 52.6 1.0 CB A:THR32 4.8 42.3 1.0 C A:ALA181 4.8 31.1 1.0 N C:ALA181 4.8 32.6 1.0 O A:VAL51 4.9 33.8 1.0 O C:HOH244 5.0 37.3 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex


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 Human Rangdp-NUP153ZNF12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:34.2 occ:1.00 O1B C:GDP302 2.1 27.6 1.0 O C:HOH238 2.2 29.0 1.0 O C:HOH235 2.3 31.2 1.0 OG1 C:THR24 2.3 31.7 1.0 O C:HOH236 2.3 28.8 1.0 O C:HOH237 2.4 34.1 1.0 PB C:GDP302 3.3 33.1 1.0 CB C:THR24 3.3 38.6 1.0 O2B C:GDP302 3.4 33.8 1.0 N C:THR24 4.0 32.7 1.0 O2A C:GDP302 4.1 35.1 1.0 OG1 C:THR66 4.2 33.3 1.0 CA C:THR24 4.2 30.4 1.0 O3B C:GDP302 4.3 31.8 1.0 O C:THR66 4.3 36.3 1.0 OD1 C:ASP65 4.3 35.6 1.0 OD2 C:ASP65 4.3 32.8 1.0 OE2 C:GLU70 4.3 31.3 1.0 O3A C:GDP302 4.4 34.0 1.0 CG2 C:THR24 4.4 40.3 1.0 O C:HOH279 4.5 57.1 1.0 PA C:GDP302 4.6 34.8 1.0 O1A C:GDP302 4.7 33.4 1.0 CG C:ASP65 4.7 36.1 1.0 N C:GLY68 4.8 36.3 1.0 O C:HOH362 4.8 49.0 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Rangdp-NUP153ZNF12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:58.0 occ:1.00 ND1 C:HIS53 2.7 35.7 1.0 O C:HOH358 2.8 48.8 1.0 MG A:MG304 3.1 48.3 1.0 N C:PRO58 3.4 38.1 1.0 CG C:HIS53 3.5 32.9 1.0 CB C:HIS53 3.5 36.8 1.0 CG C:PRO58 3.6 45.7 1.0 CD C:PRO58 3.7 46.7 1.0 C C:GLY57 3.7 40.6 1.0 CE1 C:HIS53 3.7 39.1 1.0 CA C:PRO58 3.9 35.9 1.0 CA C:HIS53 4.0 30.6 1.0 CB C:PRO58 4.0 41.8 1.0 CA C:GLY57 4.0 41.9 1.0 O C:GLY57 4.4 35.3 1.0 O C:HOH329 4.5 52.2 1.0 N C:THR54 4.6 28.5 1.0 CB A:SER35 4.6 42.2 1.0 C C:HIS53 4.6 32.5 1.0 O C:THR54 4.7 35.2 1.0 CD2 C:HIS53 4.7 31.6 1.0 O A:HOH279 4.7 48.4 1.0 O A:LEU31 4.8 28.7 1.0 NE2 C:HIS53 4.8 39.0 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Human Rangdp-NUP153ZNF12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Rangdp-NUP153ZNF12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg305 b:40.5 occ:1.00 O C:HOH244 2.8 37.3 1.0 MG A:MG306 3.0 43.7 1.0 N C:ALA181 3.2 32.6 1.0 O C:HOH268 3.3 42.2 1.0 CA C:PRO180 3.7 39.7 1.0 CB C:PRO180 3.9 40.1 1.0 C C:PRO180 3.9 31.1 1.0 CB C:ALA181 4.0 27.9 1.0 OG1 C:THR32 4.1 36.7 1.0 CA C:ALA181 4.2 34.6 1.0 O C:HOH381 4.2 54.1 1.0 CB A:ALA181 4.2 32.2 1.0 CE1 C:HIS30 4.3 33.4 1.0 NE2 C:HIS30 4.6 27.7 1.0 O C:ALA181 4.6 26.6 1.0 N A:ALA181 4.7 32.0 1.0 CB C:THR32 4.7 40.7 1.0 OG1 A:THR32 4.7 43.6 1.0 C C:ALA181 4.9 34.9 1.0 O C:VAL51 5.0 25.9 1.0 O A:HOH221 5.0 37.1 1.0

J.R.Partridge, T.U.Schwartz. Crystallographic and Biochemical Analysis of the Ran-Binding Zinc Finger Domain. J.Mol.Biol. V. 391 375 2009.
ISSN: ISSN 0022-2836
PubMed: 19505478
DOI: 10.1016/J.JMB.2009.06.011