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Magnesium in PDB 2xxa: The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr)

Enzymatic activity of The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr)

All present enzymatic activity of The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr):
3.6.5.4;

Protein crystallography data

The structure of The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr), PDB code: 2xxa was solved by S.F.Ataide, N.Schmitz, K.Shen, A.Ke, S.Shan, J.A.Doudna, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.30 / 3.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.100, 131.040, 266.040, 90.00, 90.00, 90.00
R / Rfree (%) 23.17 / 26.69

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr) (pdb code 2xxa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr), PDB code: 2xxa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2xxa

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Magnesium binding site 1 out of 4 in the The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.2
occ:1.00
 O1G A:GCP600 2.1 0.7 1.0
OG1 A:THR114 2.1 0.0 1.0
O A:HOH2001 2.1 0.5 1.0
O2B A:GCP600 2.1 0.7 1.0
O A:HOH2002 2.1 0.6 1.0
O A:HOH2003 2.1 0.3 1.0
PB A:GCP600 3.2 0.7 1.0
PG A:GCP600 3.3 0.7 1.0
CB A:THR114 3.4 0.7 1.0
C3B A:GCP600 3.5 0.7 1.0
N A:THR114 3.8 1.0 1.0
OD2 A:ASP138 3.9 0.2 1.0
OD2 A:ASP190 4.0 0.2 1.0
OD1 A:ASP190 4.1 0.5 1.0
O2G A:GCP600 4.1 0.7 1.0
NH1 A:ARG141 4.1 0.4 1.0
CA A:THR114 4.2 0.6 1.0
O1B A:GCP600 4.2 0.7 1.0
O3G A:GCP600 4.3 0.7 1.0
CG2 A:THR114 4.3 0.1 1.0
O2A A:GCP600 4.4 0.7 1.0
O3A A:GCP600 4.4 0.7 1.0
OE1 A:GLN147 4.5 0.7 1.0
CG A:ASP190 4.5 0.6 1.0
O A:THR191 4.5 0.9 1.0
CB A:LYS113 4.5 0.0 1.0
CE A:LYS113 4.6 0.8 1.0
PA A:GCP600 4.7 0.7 1.0
O1A A:GCP600 4.8 0.7 1.0
CG A:ASP138 4.9 0.3 1.0
C A:LYS113 4.9 0.4 1.0

Magnesium binding site 2 out of 4 in 2xxa

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Magnesium binding site 2 out of 4 in the The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:0.3
occ:1.00
 O2B B:GCP600 2.0 0.9 1.0
OG1 B:THR112 2.1 0.3 1.0
O B:HOH2003 2.1 0.2 1.0
O1G B:GCP600 2.1 0.9 1.0
O B:HOH2001 2.1 0.9 1.0
O B:HOH2002 2.1 0.7 1.0
PB B:GCP600 3.3 0.9 1.0
CB B:THR112 3.3 0.3 1.0
PG B:GCP600 3.3 0.9 1.0
C3B B:GCP600 3.6 0.9 1.0
NH1 B:ARG138 3.6 0.9 1.0
N B:THR112 3.8 0.8 1.0
OD2 B:ASP135 3.9 0.9 1.0
OD2 B:ASP187 3.9 0.2 1.0
CA B:THR112 4.1 1.0 1.0
OD1 B:ASP187 4.3 0.3 1.0
O1B B:GCP600 4.3 0.9 1.0
O2G B:GCP600 4.3 0.9 1.0
O3G B:GCP600 4.3 0.9 1.0
CG2 B:THR112 4.3 0.2 1.0
O2A B:GCP600 4.4 0.9 1.0
CB B:LYS111 4.4 0.8 1.0
O3A B:GCP600 4.4 0.9 1.0
OE1 B:GLN144 4.4 0.6 1.0
CG B:ASP187 4.5 0.4 1.0
O B:THR188 4.7 0.4 1.0
PA B:GCP600 4.7 0.9 1.0
CE B:LYS111 4.7 0.6 1.0
CG B:ASP135 4.8 0.7 1.0
CZ B:ARG138 4.9 0.2 1.0
C B:LYS111 4.9 0.7 1.0
CB B:ASP135 4.9 0.6 1.0
O1A B:GCP600 4.9 0.9 1.0
NE2 B:GLN144 5.0 1.0 1.0

Magnesium binding site 3 out of 4 in 2xxa

Go back to Magnesium Binding Sites List in 2xxa
Magnesium binding site 3 out of 4 in the The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:0.4
occ:1.00
 OG1 C:THR114 2.1 0.8 1.0
O1G C:GCP600 2.1 0.3 1.0
O C:HOH2001 2.1 0.2 1.0
O2B C:GCP600 2.1 0.3 1.0
O C:HOH2002 2.1 0.9 1.0
O C:HOH2003 2.1 0.4 1.0
PB C:GCP600 3.2 0.3 1.0
PG C:GCP600 3.3 0.3 1.0
CB C:THR114 3.4 0.0 1.0
C3B C:GCP600 3.5 0.3 1.0
N C:THR114 3.8 0.4 1.0
OD2 C:ASP190 4.0 0.9 1.0
OD1 C:ASP190 4.1 0.2 1.0
O2G C:GCP600 4.1 0.3 1.0
NH1 C:ARG141 4.2 0.2 1.0
CA C:THR114 4.2 0.6 1.0
OD2 C:ASP138 4.2 0.2 1.0
O1B C:GCP600 4.2 0.3 1.0
O3G C:GCP600 4.3 0.3 1.0
CG2 C:THR114 4.3 0.8 1.0
O2A C:GCP600 4.4 0.3 1.0
O3A C:GCP600 4.4 0.3 1.0
OE1 C:GLN147 4.5 0.6 1.0
CG C:ASP190 4.5 0.6 1.0
CB C:LYS113 4.5 0.2 1.0
O C:THR191 4.5 0.9 1.0
CE C:LYS113 4.6 0.0 1.0
PA C:GCP600 4.7 0.3 1.0
O1A C:GCP600 4.8 0.3 1.0
C C:LYS113 4.9 0.7 1.0

Magnesium binding site 4 out of 4 in 2xxa

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Magnesium binding site 4 out of 4 in the The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the Signal Recognition Particle (Srp) in Complex with Its Receptor(Sr) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:0.7
occ:1.00
 O2B D:GCP600 2.1 1.0 1.0
O D:HOH2002 2.1 0.2 1.0
OG1 D:THR112 2.1 0.9 1.0
O D:HOH2001 2.1 1.0 1.0
O1G D:GCP600 2.1 1.0 1.0
O D:HOH2003 2.1 0.1 1.0
PB D:GCP600 3.3 1.0 1.0
CB D:THR112 3.3 0.0 1.0
PG D:GCP600 3.3 1.0 1.0
C3B D:GCP600 3.6 1.0 1.0
NH1 D:ARG138 3.6 0.9 1.0
N D:THR112 3.8 0.4 1.0
OD2 D:ASP135 3.9 0.4 1.0
OD2 D:ASP187 3.9 0.1 1.0
CA D:THR112 4.2 0.8 1.0
O1B D:GCP600 4.3 1.0 1.0
OD1 D:ASP187 4.3 0.6 1.0
O2G D:GCP600 4.3 1.0 1.0
O3G D:GCP600 4.3 1.0 1.0
CG2 D:THR112 4.3 0.8 1.0
O2A D:GCP600 4.4 1.0 1.0
O3A D:GCP600 4.4 1.0 1.0
CB D:LYS111 4.4 0.5 1.0
OE1 D:GLN144 4.5 0.6 1.0
CG D:ASP187 4.5 0.9 1.0
O D:THR188 4.7 0.1 1.0
PA D:GCP600 4.7 1.0 1.0
CE D:LYS111 4.8 0.6 1.0
CG D:ASP135 4.8 0.5 1.0
CZ D:ARG138 4.9 0.8 1.0
CB D:ASP135 4.9 0.1 1.0
C D:LYS111 4.9 0.9 1.0
O1A D:GCP600 4.9 1.0 1.0
NE2 D:GLN144 5.0 0.7 1.0

Reference:

S.F.Ataide, N.Schmitz, K.Shen, A.Ke, S.Shan, J.A.Doudna, N.Ban. The Crystal Structure of the Signal Recognition Particle in Complex with Its Receptor. Science V. 331 881 2011.
ISSN: ISSN 0036-8075
PubMed: 21330537
DOI: 10.1126/SCIENCE.1196473
Page generated: Wed Aug 14 07:20:18 2024

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