Magnesium in PDB 1d4r: 29-Mer Fragment of Human Srp Rna Helix 6

The structure of 29-Mer Fragment of Human Srp Rna Helix 6, PDB code: 1d4r was solved by K.Wild, O.Weichenrieder, G.A.Leonard, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.57 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	42.980, 42.980, 231.420, 90.00, 90.00, 120.00
R / Rfree (%)	26.4 / 28.8

The binding sites of Magnesium atom in the 29-Mer Fragment of Human Srp Rna Helix 6 (pdb code 1d4r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the 29-Mer Fragment of Human Srp Rna Helix 6, PDB code: 1d4r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the 29-Mer Fragment of Human Srp Rna Helix 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 29-Mer Fragment of Human Srp Rna Helix 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:78.1 occ:1.00 O A:HOH318 2.1 78.6 1.0 O A:HOH317 2.1 74.8 1.0 O A:HOH319 2.1 82.1 1.0 N7 A:GDP1 2.9 51.4 1.0 C5 A:GDP1 3.7 50.5 1.0 O6 A:GDP1 3.8 47.8 1.0 C8 A:GDP1 3.8 47.2 1.0 C6 A:GDP1 4.1 47.6 1.0 O A:HOH321 4.4 71.2 1.0 O1A A:GDP1 4.7 72.1 1.0 C4 A:GDP1 4.9 51.0 1.0 N9 A:GDP1 4.9 53.6 1.0

Magnesium binding site 2 out of 5 in the 29-Mer Fragment of Human Srp Rna Helix 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 29-Mer Fragment of Human Srp Rna Helix 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:76.5 occ:1.00 O A:HOH320 2.1 73.0 1.0 O A:HOH322 2.1 78.0 1.0 O A:HOH321 2.1 71.2 1.0 O A:HOH318 4.6 78.6 1.0

Magnesium binding site 3 out of 5 in the 29-Mer Fragment of Human Srp Rna Helix 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 29-Mer Fragment of Human Srp Rna Helix 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:63.8 occ:1.00 O B:HOH313 2.1 67.4 1.0 O B:HOH310 2.1 67.6 1.0 O B:HOH312 2.1 66.7 1.0 O B:HOH311 2.1 64.6 1.0 N7 B:G19 2.9 69.3 1.0 O6 B:G19 3.4 60.2 1.0 C5 B:G19 3.7 64.0 1.0 C6 B:G19 3.9 61.2 1.0 C8 B:G19 3.9 71.4 1.0 N7 B:G18 4.0 68.7 1.0 C5 B:G18 4.3 70.2 1.0 O6 B:G18 4.3 71.4 1.0 C6 B:G18 4.5 71.0 1.0 O6 B:G20 4.5 62.2 1.0 N7 B:G20 4.5 62.5 1.0 C8 B:G18 4.7 68.5 1.0 O B:HOH179 4.9 51.1 1.0 C4 B:G19 4.9 62.6 1.0

Magnesium binding site 4 out of 5 in the 29-Mer Fragment of Human Srp Rna Helix 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 29-Mer Fragment of Human Srp Rna Helix 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:65.4 occ:1.00 O B:HOH314 2.1 65.7 1.0 O A:HOH316 2.1 60.8 1.0 O A:HOH315 2.1 63.1 1.0 O A:HOH161 3.8 51.5 1.0 OP2 B:A15 3.8 67.8 1.0 OP1 B:G14 4.1 60.1 1.0 OP2 B:G14 4.3 65.2 1.0 O6 A:G12 4.5 61.7 1.0 N4 A:C11 4.6 53.5 1.0 P B:G14 4.6 62.0 1.0 O B:HOH106 4.8 74.2 1.0 O5' B:G14 4.9 61.4 1.0 P B:A15 5.0 66.7 1.0

Magnesium binding site 5 out of 5 in the 29-Mer Fragment of Human Srp Rna Helix 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 29-Mer Fragment of Human Srp Rna Helix 6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:61.1 occ:1.00 O C:HOH306 2.1 55.6 1.0 O C:HOH307 2.1 61.8 1.0 O C:HOH309 2.1 57.6 1.0 O C:HOH308 2.1 58.0 1.0

K.Wild, O.Weichenrieder, G.A.Leonard, S.Cusack. The 2 A Structure of Helix 6 of the Human Signal Recognition Particle Rna Structure Fold.Des. V. 7 1345 1999.
ISSN: ISSN 0969-2126
PubMed: 10574798
DOI: 10.1016/S0969-2126(00)80024-6