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Magnesium in PDB 1rlo: Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12

Protein crystallography data

The structure of Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12, PDB code: 1rlo was solved by A.Roberts, S.Y.Lee, E.Mccullagh, R.E.Silversmith, D.E.Wemmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.85 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.276, 91.195, 176.415, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.1

Other elements in 1rlo:

The structure of Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12 also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12 (pdb code 1rlo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12, PDB code: 1rlo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1rlo

Go back to Magnesium Binding Sites List in 1rlo
Magnesium binding site 1 out of 4 in the Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:11.3
occ:1.00
 OD2 A:BFD9 2.0 10.4 1.0
OD1 A:ASP215 2.0 12.1 1.0
O A:ASP11 2.0 13.7 1.0
F2 A:BFD9 2.1 11.1 1.0
O A:HOH927 2.1 10.8 1.0
O A:HOH802 2.2 13.7 1.0
CG A:BFD9 2.9 10.6 1.0
CG A:ASP215 3.0 15.4 1.0
BE A:BFD9 3.1 12.9 1.0
C A:ASP11 3.2 13.3 1.0
OD1 A:BFD9 3.3 12.0 1.0
OD2 A:ASP215 3.3 14.4 1.0
CA A:ASP11 4.0 13.1 1.0
OG1 A:THR13 4.0 13.9 1.0
OD2 A:ASP219 4.0 12.4 1.0
O A:GLY179 4.1 16.6 1.0
F1 A:BFD9 4.1 12.8 1.0
N A:ASP11 4.1 10.2 1.0
OG A:SER216 4.1 25.4 1.0
CB A:ASP11 4.1 13.7 1.0
CB A:BFD9 4.2 9.5 1.0
F3 A:BFD9 4.2 12.5 1.0
N A:GLY12 4.3 13.8 1.0
CB A:ASP215 4.4 15.3 1.0
CA A:GLY179 4.4 16.9 1.0
CA A:GLY12 4.5 14.0 1.0
N A:SER216 4.5 17.7 1.0
CB A:SER216 4.6 20.8 1.0
N A:ASP215 4.6 18.0 1.0
C A:GLY12 4.6 13.5 1.0
C A:MET10 4.7 10.1 1.0
C A:GLY179 4.7 18.4 1.0
N A:THR13 4.7 13.9 1.0
OD1 A:ASN218 4.7 21.2 1.0
N A:MET10 4.8 11.3 1.0
CB A:THR13 4.9 14.3 1.0
CA A:ASP215 4.9 16.8 1.0
C A:BFD9 4.9 12.7 1.0
CG A:ASP219 5.0 12.7 1.0

Magnesium binding site 2 out of 4 in 1rlo

Go back to Magnesium Binding Sites List in 1rlo
Magnesium binding site 2 out of 4 in the Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:12.0
occ:1.00
 OD2 B:BFD9 2.0 13.9 1.0
OD1 B:ASP215 2.0 16.0 1.0
O B:HOH899 2.0 9.9 1.0
F2 B:BFD9 2.0 14.0 1.0
O B:ASP11 2.0 13.4 1.0
O B:HOH805 2.1 16.2 1.0
CG B:BFD9 2.9 16.4 1.0
CG B:ASP215 3.1 20.1 1.0
BE B:BFD9 3.2 14.7 1.0
C B:ASP11 3.2 14.5 1.0
OD1 B:BFD9 3.3 15.9 1.0
OD2 B:ASP215 3.4 19.1 1.0
OG B:SER216 3.8 30.0 1.0
CA B:ASP11 4.0 14.0 1.0
OD2 B:ASP219 4.0 17.4 1.0
CB B:ASP11 4.0 13.6 1.0
O B:GLY179 4.0 37.0 1.0
OG1 B:THR13 4.1 12.5 1.0
F1 B:BFD9 4.1 14.2 1.0
N B:ASP11 4.1 13.5 1.0
F3 B:BFD9 4.2 13.4 1.0
CB B:BFD9 4.2 15.7 1.0
N B:GLY12 4.3 13.4 1.0
CB B:ASP215 4.4 18.4 1.0
CA B:GLY179 4.4 36.9 1.0
CA B:GLY12 4.5 14.0 1.0
N B:SER216 4.6 19.1 1.0
C B:GLY12 4.6 15.2 1.0
OD1 B:ASN218 4.7 19.9 1.0
N B:ASP215 4.7 16.1 1.0
CB B:SER216 4.7 23.8 1.0
N B:THR13 4.7 15.4 1.0
C B:GLY179 4.7 38.0 1.0
C B:MET10 4.8 13.8 1.0
CB B:THR13 4.9 12.2 1.0
N B:MET10 4.9 14.4 1.0
CA B:ASP215 4.9 18.8 1.0
CG B:ASP219 5.0 17.5 1.0

Magnesium binding site 3 out of 4 in 1rlo

Go back to Magnesium Binding Sites List in 1rlo
Magnesium binding site 3 out of 4 in the Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:22.7
occ:1.00
 O C:HOH912 2.0 16.3 1.0
O C:HOH891 2.0 16.1 1.0
O C:ASP11 2.1 23.0 1.0
F2 C:BFD9 2.1 18.3 1.0
OD1 C:ASP215 2.1 21.8 1.0
OD2 C:BFD9 2.2 14.8 1.0
CG C:BFD9 3.1 17.9 1.0
CG C:ASP215 3.1 24.6 1.0
BE C:BFD9 3.2 17.3 1.0
C C:ASP11 3.3 23.5 1.0
OD1 C:BFD9 3.4 14.2 1.0
OD2 C:ASP215 3.4 25.3 1.0
O C:SER178 3.9 21.6 1.0
OD2 C:ASP219 4.0 16.3 1.0
OG1 C:THR13 4.0 23.2 1.0
CA C:ASP11 4.0 22.4 1.0
F1 C:BFD9 4.0 14.0 1.0
OG C:SER216 4.0 31.8 1.0
CB C:ASP11 4.1 26.4 1.0
N C:ASP11 4.2 19.8 1.0
N C:GLY12 4.3 24.8 1.0
F3 C:BFD9 4.3 19.6 1.0
CB C:BFD9 4.4 16.3 1.0
CB C:SER216 4.5 25.9 1.0
CA C:GLY12 4.5 24.1 1.0
CB C:ASP215 4.5 22.8 1.0
N C:SER216 4.6 22.3 1.0
OD1 C:ASN218 4.6 18.5 1.0
C C:GLY12 4.6 24.9 1.0
N C:ASP215 4.8 22.8 1.0
C C:MET10 4.8 20.6 1.0
O C:HOH875 4.8 28.5 1.0
N C:THR13 4.8 24.5 1.0
O C:HOH900 4.8 45.5 1.0
CB C:THR13 4.9 24.1 1.0
CG C:ASP219 4.9 16.6 1.0

Magnesium binding site 4 out of 4 in 1rlo

Go back to Magnesium Binding Sites List in 1rlo
Magnesium binding site 4 out of 4 in the Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Phospho-Aspartyl Intermediate Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:12.5
occ:1.00
 OD1 D:ASP215 2.0 11.7 1.0
O D:HOH895 2.0 13.9 1.0
O D:HOH896 2.1 12.5 1.0
F2 D:BFD9 2.1 12.9 1.0
O D:ASP11 2.1 10.3 1.0
OD2 D:BFD9 2.1 13.5 1.0
CG D:BFD9 3.0 16.2 1.0
CG D:ASP215 3.0 13.6 1.0
BE D:BFD9 3.2 14.8 1.0
C D:ASP11 3.2 13.5 1.0
OD1 D:BFD9 3.4 13.0 1.0
OD2 D:ASP215 3.4 13.2 1.0
OD2 D:ASP219 3.9 12.0 1.0
CA D:ASP11 4.0 13.0 1.0
O D:SER178 4.0 23.3 1.0
CB D:ASP11 4.0 14.9 1.0
OG1 D:THR13 4.1 11.3 1.0
F1 D:BFD9 4.1 13.1 1.0
N D:ASP11 4.1 13.0 1.0
F3 D:BFD9 4.2 15.3 1.0
N D:GLY12 4.3 14.3 1.0
OG D:SER216 4.3 23.5 1.0
CB D:BFD9 4.3 14.9 1.0
CB D:ASP215 4.4 10.3 1.0
CA D:GLY12 4.5 14.1 1.0
CB D:SER216 4.5 16.7 1.0
N D:SER216 4.5 14.6 1.0
OD1 D:ASN218 4.7 18.0 1.0
C D:GLY12 4.7 14.4 1.0
N D:ASP215 4.7 11.7 1.0
C D:MET10 4.8 13.6 1.0
N D:THR13 4.8 13.5 1.0
O D:HOH840 4.8 33.0 1.0
CG D:ASP219 4.9 14.6 1.0
CA D:ASP215 5.0 14.0 1.0
N D:MET10 5.0 14.0 1.0

Reference:

A.Roberts, S.Y.Lee, E.Mccullagh, R.E.Silversmith, D.E.Wemmer. Ybiv From Escherichia Coli K12 Is A Had Phosphatase. Proteins V. 58 790 2005.
ISSN: ISSN 0887-3585
PubMed: 15657928
DOI: 10.1002/PROT.20267
Page generated: Tue Aug 13 13:03:20 2024

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