Magnesium in PDB 5l3s: Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy

The structure of Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy, PDB code: 5l3s was solved by G.Bange, K.Wild, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.87 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.196, 199.672, 124.869, 90.00, 92.95, 90.00
R / Rfree (%)	17.3 / 21.6

The binding sites of Magnesium atom in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy (pdb code 5l3s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy, PDB code: 5l3s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


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 Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:20.5 occ:1.00 O A:HOH439 2.1 17.3 1.0 O1B A:GNP301 2.1 20.2 1.0 O A:HOH429 2.1 20.6 1.0 OG1 A:THR110 2.1 17.4 1.0 O2G A:GNP301 2.1 18.3 1.0 O A:HOH472 2.1 21.6 1.0 CB A:THR110 3.2 17.8 1.0 PB A:GNP301 3.3 17.2 1.0 PG A:GNP301 3.3 19.2 1.0 N3B A:GNP301 3.4 13.6 1.0 N A:THR110 3.9 16.7 1.0 OD2 A:ASP133 4.1 18.7 1.0 OD2 A:ASP185 4.1 22.2 1.0 CA A:THR110 4.1 16.4 1.0 OD1 A:ASP185 4.2 19.2 1.0 O2B A:GNP301 4.3 18.4 1.0 CD A:ARG136 4.3 19.2 1.0 CG2 A:THR110 4.3 15.4 1.0 O1G A:GNP301 4.3 17.9 1.0 O1A A:GNP301 4.3 19.4 1.0 O A:HOH453 4.4 22.1 1.0 O3G A:GNP301 4.4 19.3 1.0 O A:HOH469 4.4 20.3 1.0 O3A A:GNP301 4.4 15.0 1.0 OE1 A:GLN142 4.5 18.8 1.0 CG A:ASP185 4.6 26.2 1.0 PA A:GNP301 4.7 20.2 1.0 CE A:LYS109 4.7 18.4 1.0 O2A A:GNP301 4.7 20.2 1.0 O A:THR186 4.7 19.2 1.0 NE A:ARG136 4.7 19.7 1.0 CB A:LYS109 4.8 18.2 1.0 NH1 A:ARG136 4.9 20.6 1.0 C A:LYS109 5.0 20.0 1.0

Magnesium binding site 2 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


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 Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:19.6 occ:1.00 O1G B:GNP401 1.9 20.0 1.0 O B:HOH527 2.1 19.3 1.0 O B:HOH532 2.1 18.4 1.0 O B:HOH547 2.1 16.3 1.0 O1B B:GNP401 2.1 16.2 1.0 OG1 B:THR187 2.1 18.0 1.0 PG B:GNP401 3.2 18.5 1.0 CB B:THR187 3.2 17.7 1.0 PB B:GNP401 3.3 18.9 1.0 N3B B:GNP401 3.4 15.3 1.0 NH1 B:ARG213 3.8 20.9 1.0 N B:THR187 3.9 19.6 1.0 OD2 B:ASP262 4.1 25.5 1.0 CA B:THR187 4.2 18.0 1.0 O2G B:GNP401 4.2 17.5 1.0 O2A B:GNP401 4.2 18.1 1.0 O2B B:GNP401 4.2 18.9 1.0 OD2 B:ASP210 4.2 24.7 1.0 OD1 B:ASP262 4.3 19.3 1.0 O3G B:GNP401 4.3 15.8 1.0 O B:HOH582 4.3 18.9 1.0 O3A B:GNP401 4.3 14.1 1.0 CG2 B:THR187 4.3 21.3 1.0 OE1 B:GLN219 4.4 17.2 1.0 O B:HOH553 4.4 19.0 1.0 CE B:LYS186 4.5 15.2 1.0 CG B:ASP262 4.6 24.5 1.0 PA B:GNP401 4.6 21.2 1.0 O B:THR263 4.6 22.1 1.0 O1A B:GNP401 4.7 23.6 1.0 CB B:LYS186 4.8 21.0 1.0 NZ B:LYS186 4.9 19.7 1.0 CZ B:ARG213 4.9 23.5 1.0

Magnesium binding site 3 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


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 Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:25.1 occ:1.00 O2G C:GNP301 2.1 27.3 1.0 O2B C:GNP301 2.1 23.9 1.0 O C:HOH447 2.1 22.3 1.0 O C:HOH452 2.1 23.0 1.0 OG1 C:THR110 2.1 22.5 1.0 O C:HOH456 2.1 22.9 1.0 PG C:GNP301 3.2 25.4 1.0 PB C:GNP301 3.3 21.8 1.0 CB C:THR110 3.3 24.0 1.0 N3B C:GNP301 3.4 18.2 1.0 N C:THR110 3.9 21.1 1.0 OD2 C:ASP133 4.1 22.7 1.0 OD2 C:ASP185 4.1 28.7 1.0 CA C:THR110 4.2 21.6 1.0 CD C:ARG136 4.2 26.1 1.0 O1B C:GNP301 4.3 24.3 1.0 O3G C:GNP301 4.3 27.4 1.0 OD1 C:ASP185 4.3 25.5 1.0 O1G C:GNP301 4.3 26.2 1.0 O3A C:GNP301 4.3 20.4 1.0 O C:HOH431 4.4 24.6 1.0 O C:HOH446 4.4 26.1 1.0 CG2 C:THR110 4.4 21.3 1.0 O1A C:GNP301 4.4 26.5 1.0 OE1 C:GLN142 4.5 24.1 1.0 PA C:GNP301 4.6 24.1 1.0 CE C:LYS109 4.6 23.1 1.0 NE C:ARG136 4.7 22.1 1.0 CG C:ASP185 4.7 27.3 1.0 CB C:LYS109 4.8 27.2 1.0 O2A C:GNP301 4.8 23.8 1.0 O C:THR186 4.8 23.9 1.0 NH1 C:ARG136 4.9 25.2 1.0 C C:LYS109 5.0 26.1 1.0 CZ C:ARG136 5.0 22.7 1.0

Magnesium binding site 4 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


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 Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:22.8 occ:1.00 O1G D:GNP401 1.9 23.6 1.0 O D:HOH516 2.0 23.1 1.0 O1B D:GNP401 2.1 22.3 1.0 O D:HOH580 2.1 18.7 1.0 OG1 D:THR187 2.1 22.6 1.0 O D:HOH512 2.1 22.6 1.0 PG D:GNP401 3.2 21.2 1.0 CB D:THR187 3.2 25.2 1.0 PB D:GNP401 3.2 22.7 1.0 N3B D:GNP401 3.4 18.7 1.0 NH1 D:ARG213 3.8 24.8 1.0 N D:THR187 4.0 24.1 1.0 OD2 D:ASP262 4.1 28.0 1.0 O2G D:GNP401 4.2 21.0 1.0 CA D:THR187 4.2 24.4 1.0 O2A D:GNP401 4.2 20.0 1.0 O3A D:GNP401 4.2 17.0 1.0 O D:HOH585 4.3 21.9 1.0 O3G D:GNP401 4.3 19.8 1.0 OD1 D:ASP262 4.3 28.3 1.0 O2B D:GNP401 4.3 19.5 1.0 CG2 D:THR187 4.3 26.0 1.0 OE1 D:GLN219 4.3 24.0 1.0 OD2 D:ASP210 4.4 26.3 1.0 O D:HOH514 4.5 22.9 1.0 PA D:GNP401 4.5 22.2 1.0 CE D:LYS186 4.6 21.1 1.0 O D:THR263 4.6 25.8 1.0 CG D:ASP262 4.6 35.6 1.0 O1A D:GNP401 4.7 25.0 1.0 CB D:LYS186 4.8 29.3 1.0 NZ D:LYS186 4.8 25.0 1.0 CZ D:ARG213 4.9 29.6 1.0

Magnesium binding site 5 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:25.1 occ:1.00 O2G E:GNP301 2.0 26.9 1.0 O1B E:GNP301 2.0 20.7 1.0 O E:HOH432 2.1 21.4 1.0 O E:HOH421 2.1 20.9 1.0 O E:HOH435 2.1 24.1 1.0 OG1 E:THR110 2.2 20.4 1.0 PG E:GNP301 3.2 23.4 1.0 PB E:GNP301 3.2 21.3 1.0 CB E:THR110 3.3 22.7 1.0 N3B E:GNP301 3.4 16.6 1.0 N E:THR110 4.0 22.8 1.0 OD2 E:ASP133 4.0 21.6 1.0 OD2 E:ASP185 4.2 26.0 1.0 CA E:THR110 4.2 22.5 1.0 CD E:ARG136 4.2 30.6 1.0 OD1 E:ASP185 4.2 21.7 1.0 O3G E:GNP301 4.3 21.4 1.0 O2B E:GNP301 4.3 19.4 1.0 O1G E:GNP301 4.3 22.9 1.0 O E:HOH420 4.3 22.2 1.0 O3A E:GNP301 4.3 17.6 1.0 O E:HOH450 4.4 19.0 1.0 O1A E:GNP301 4.4 22.3 1.0 OE1 E:GLN142 4.4 25.4 1.0 CG2 E:THR110 4.4 18.7 1.0 CE E:LYS109 4.5 24.4 1.0 O2A E:GNP301 4.6 24.9 1.0 PA E:GNP301 4.6 24.4 1.0 O E:THR186 4.6 20.3 1.0 CG E:ASP185 4.6 29.5 1.0 CB E:LYS109 4.7 17.7 1.0 NE E:ARG136 4.7 23.6 1.0 NZ E:LYS109 4.9 22.9 1.0 NH1 E:ARG136 4.9 24.0 1.0

Magnesium binding site 6 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:24.9 occ:1.00 O1G F:GNP401 2.0 25.8 1.0 O1B F:GNP401 2.1 21.5 1.0 O F:HOH528 2.1 27.0 1.0 O F:HOH523 2.1 21.6 1.0 O F:HOH536 2.1 29.5 1.0 OG1 F:THR187 2.1 24.9 1.0 PG F:GNP401 3.2 22.0 1.0 CB F:THR187 3.2 19.5 1.0 PB F:GNP401 3.3 22.1 1.0 N3B F:GNP401 3.4 19.8 1.0 NH1 F:ARG213 3.7 28.1 1.0 N F:THR187 4.0 24.2 1.0 OD2 F:ASP262 4.1 32.8 1.0 O2G F:GNP401 4.2 23.3 1.0 CA F:THR187 4.2 23.6 1.0 O2A F:GNP401 4.2 25.0 1.0 OD2 F:ASP210 4.2 29.5 1.0 O2B F:GNP401 4.3 20.7 1.0 O F:HOH543 4.3 25.8 1.0 OD1 F:ASP262 4.3 27.2 1.0 CG2 F:THR187 4.3 24.6 1.0 O3G F:GNP401 4.3 22.7 1.0 O3A F:GNP401 4.3 18.8 1.0 OE1 F:GLN219 4.4 25.1 1.0 O F:HOH551 4.5 23.5 1.0 CG F:ASP262 4.6 26.6 1.0 PA F:GNP401 4.6 24.1 1.0 CE F:LYS186 4.6 28.4 1.0 O F:THR263 4.6 23.8 1.0 O1A F:GNP401 4.7 24.7 1.0 CB F:LYS186 4.8 30.4 1.0 CZ F:ARG213 4.9 26.2 1.0 NZ F:LYS186 5.0 25.3 1.0

Magnesium binding site 7 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:22.3 occ:1.00 O2B G:GNP301 2.0 19.1 1.0 O2G G:GNP301 2.1 23.8 1.0 OG1 G:THR110 2.1 19.7 1.0 O G:HOH440 2.1 21.6 1.0 O G:HOH430 2.1 19.5 1.0 O G:HOH456 2.2 24.4 1.0 CB G:THR110 3.2 20.8 1.0 PB G:GNP301 3.3 19.4 1.0 PG G:GNP301 3.3 20.4 1.0 N3B G:GNP301 3.5 14.3 1.0 N G:THR110 3.9 16.1 1.0 OD2 G:ASP185 4.0 24.6 1.0 OD2 G:ASP133 4.1 19.4 1.0 CA G:THR110 4.1 16.6 1.0 O1B G:GNP301 4.2 20.7 1.0 CD G:ARG136 4.2 23.4 1.0 OD1 G:ASP185 4.2 21.2 1.0 O3A G:GNP301 4.3 18.4 1.0 CG2 G:THR110 4.3 15.5 1.0 O3G G:GNP301 4.4 21.1 1.0 O1G G:GNP301 4.4 23.7 1.0 O1A G:GNP301 4.4 21.8 1.0 O G:HOH478 4.4 22.1 1.0 O G:HOH424 4.4 22.1 1.0 OE1 G:GLN142 4.5 25.4 1.0 CG G:ASP185 4.6 28.3 1.0 PA G:GNP301 4.6 19.9 1.0 CB G:LYS109 4.6 21.4 1.0 O2A G:GNP301 4.7 18.8 1.0 O G:THR186 4.7 21.0 1.0 CE G:LYS109 4.7 23.6 1.0 NE G:ARG136 4.7 23.4 1.0 C G:LYS109 4.9 21.3 1.0

Magnesium binding site 8 out of 8 in the Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Gtpase Heterodimer of Crenarchaeal SRP54 and Ftsy within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg402 b:21.1 occ:1.00 O1G H:GNP401 2.0 24.0 1.0 O1B H:GNP401 2.1 20.0 1.0 O H:HOH549 2.1 19.2 1.0 O H:HOH533 2.1 18.9 1.0 OG1 H:THR187 2.1 19.7 1.0 O H:HOH571 2.1 16.8 1.0 CB H:THR187 3.2 18.4 1.0 PG H:GNP401 3.2 21.3 1.0 PB H:GNP401 3.2 20.9 1.0 N3B H:GNP401 3.3 21.2 1.0 NH1 H:ARG213 3.8 21.2 1.0 N H:THR187 3.9 18.5 1.0 CA H:THR187 4.1 16.8 1.0 OD2 H:ASP262 4.2 26.3 1.0 O2B H:GNP401 4.2 17.2 1.0 O2G H:GNP401 4.2 22.6 1.0 OD1 H:ASP262 4.2 23.6 1.0 CG2 H:THR187 4.2 23.4 1.0 O3A H:GNP401 4.3 17.0 1.0 O2A H:GNP401 4.3 19.2 1.0 O3G H:GNP401 4.3 22.5 1.0 O H:HOH596 4.4 19.9 1.0 OD2 H:ASP210 4.4 25.4 1.0 OE1 H:GLN219 4.4 22.9 1.0 O H:HOH524 4.5 23.2 1.0 CE H:LYS186 4.5 26.0 1.0 PA H:GNP401 4.6 20.3 1.0 O H:THR263 4.6 23.4 1.0 CG H:ASP262 4.6 24.9 1.0 CB H:LYS186 4.7 24.1 1.0 O1A H:GNP401 4.7 21.8 1.0 NZ H:LYS186 4.9 20.4 1.0 C H:LYS186 5.0 24.4 1.0 CZ H:ARG213 5.0 22.4 1.0

K.Wild, G.Bange, D.Motiejunas, J.Kribelbauer, A.Hendricks, B.Segnitz, R.C.Wade, I.Sinning. Structural Basis For Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex. J.Mol.Biol. V. 428 2880 2016.
ISSN: ESSN 1089-8638
PubMed: 27241309
DOI: 10.1016/J.JMB.2016.05.015