Magnesium in PDB 4p3e: Structure of the Human Srp S Domain

The structure of Structure of the Human Srp S Domain, PDB code: 4p3e was solved by J.T.Grotwinkel, K.Wild, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.09 / 3.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.649, 70.530, 106.493, 90.00, 100.46, 90.00
R / Rfree (%)	24.4 / 28.5

The binding sites of Magnesium atom in the Structure of the Human Srp S Domain (pdb code 4p3e). 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 the Human Srp S Domain, PDB code: 4p3e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Human Srp S Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Human Srp S Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:7.7 occ:1.00 N6 A:A157 2.6 24.3 1.0 N4 A:C140 3.7 32.1 1.0 N6 A:A139 3.8 24.6 1.0 C6 A:A157 4.0 27.6 1.0 N4 A:C158 4.3 25.1 1.0 O6 A:G156 4.3 35.9 1.0 N1 A:A157 4.7 27.5 1.0 C4 A:C140 4.9 29.1 1.0 C5 A:A157 4.9 29.5 1.0

Magnesium binding site 2 out of 4 in the Structure of the Human Srp S Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Human Srp S Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:19.3 occ:1.00 N6 A:A127 2.8 55.3 1.0 N4 A:C126 2.9 61.5 1.0 C6 A:A127 3.9 56.1 1.0 C4 A:C126 4.1 69.0 1.0 C5 A:C126 4.5 70.8 1.0 C5 A:A127 4.6 59.5 1.0 N7 A:A127 4.6 61.1 1.0 N1 A:A127 4.8 51.5 1.0 O4 A:U223 5.0 50.7 1.0

Magnesium binding site 3 out of 4 in the Structure of the Human Srp S Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Human Srp S Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:26.7 occ:1.00 OP2 A:A163 2.8 21.6 1.0 O6 A:G164 3.2 36.2 1.0 N7 A:A163 3.5 26.1 1.0 C6 A:G164 3.9 37.0 1.0 C8 A:A163 4.0 25.6 1.0 P A:A163 4.2 27.1 1.0 N7 A:G164 4.3 32.3 1.0 C5 A:G164 4.4 35.0 1.0 O5' A:A163 4.5 26.6 1.0 O5' A:C162 4.6 27.2 1.0 C3' A:C162 4.6 33.2 1.0 C5 A:A163 4.8 27.9 1.0 N3 A:A176 4.8 47.1 1.0 OP2 A:C162 4.9 20.4 1.0 O3' A:C162 4.9 39.6 1.0 N1 A:G164 5.0 40.0 1.0

Magnesium binding site 4 out of 4 in the Structure of the Human Srp S Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Human Srp S Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:55.7 occ:1.00 N4 A:C145 3.1 31.8 1.0 CE B:LYS102 3.9 51.0 1.0 CD B:ARG34 4.0 26.6 1.0 NZ B:LYS102 4.2 43.2 1.0 C4 A:C145 4.3 38.8 1.0 NE B:ARG34 4.3 24.2 1.0 O6 A:G146 4.7 30.2 1.0 O6 A:G147 4.9 42.9 1.0 C5 A:C145 4.9 38.3 1.0

J.T.Grotwinkel, K.Wild, B.Segnitz, I.Sinning. Srp Rna Remodeling By SRP68 Explains Its Role in Protein Translocation. Science V. 344 101 2014.
ISSN: ESSN 1095-9203
PubMed: 24700861
DOI: 10.1126/SCIENCE.1249094