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Magnesium in PDB 5yjj: Crystal Structure of Pnpase From Staphylococcus Epidermidis

Enzymatic activity of Crystal Structure of Pnpase From Staphylococcus Epidermidis

All present enzymatic activity of Crystal Structure of Pnpase From Staphylococcus Epidermidis:
2.7.7.8;

Protein crystallography data

The structure of Crystal Structure of Pnpase From Staphylococcus Epidermidis, PDB code: 5yjj was solved by R.Raj, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.04 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 93.190, 93.160, 143.150, 73.54, 87.61, 60.07
R / Rfree (%) 23.7 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pnpase From Staphylococcus Epidermidis (pdb code 5yjj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Pnpase From Staphylococcus Epidermidis, PDB code: 5yjj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5yjj

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Magnesium binding site 1 out of 6 in the Crystal Structure of Pnpase From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pnpase From Staphylococcus Epidermidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.5
occ:1.00
 O1 A:PO4801 2.7 13.7 1.0
OD1 A:ASP496 3.0 27.8 1.0
N A:SER441 3.1 30.0 1.0
O A:HOH912 3.1 14.8 1.0
CB A:ALA469 3.2 16.2 1.0
CB A:SER441 3.3 20.0 1.0
CA A:SER441 3.4 30.0 1.0
OD2 A:ASP496 3.4 34.2 1.0
O A:HOH1040 3.6 30.0 1.0
CG A:ASP496 3.6 28.1 1.0
OG A:SER441 3.6 20.0 1.0
C A:GLY440 4.0 18.7 1.0
CG1 A:ILE485 4.0 16.8 1.0
CE A:LYS498 4.0 14.4 1.0
CD1 A:ILE485 4.1 21.8 1.0
CA A:GLY440 4.1 16.7 1.0
P A:PO4801 4.1 14.3 1.0
O A:ILE485 4.3 17.1 1.0
O4 A:PO4801 4.6 7.1 1.0
CA A:ALA469 4.7 17.1 1.0
NZ A:LYS498 4.8 21.4 1.0
O3 A:PO4801 4.8 24.0 1.0
O A:GLY440 4.9 27.3 1.0
C A:SER441 4.9 30.0 1.0
CB A:ASP496 5.0 24.2 1.0

Magnesium binding site 2 out of 6 in 5yjj

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Magnesium binding site 2 out of 6 in the Crystal Structure of Pnpase From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pnpase From Staphylococcus Epidermidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.4
occ:1.00
 OD1 B:ASP496 3.0 27.7 1.0
O1 B:PO4801 3.0 17.9 1.0
OD2 B:ASP496 3.1 29.4 1.0
CG B:ASP496 3.2 28.2 1.0
O B:HOH914 3.2 18.8 1.0
O B:HOH969 3.2 22.5 1.0
CB B:ALA469 3.4 18.9 1.0
N B:SER441 3.5 10.9 1.0
CG1 B:ILE485 3.7 20.7 1.0
CD1 B:ILE485 3.7 21.8 1.0
CB B:SER441 3.7 18.9 1.0
CA B:SER441 4.0 14.3 1.0
O B:ILE485 4.2 16.1 1.0
CE B:LYS498 4.2 21.6 1.0
C B:GLY440 4.3 17.0 1.0
OG B:SER441 4.3 22.0 1.0
CA B:GLY440 4.3 15.9 1.0
P B:PO4801 4.5 14.4 1.0
CB B:ASP496 4.5 24.6 1.0
CB B:ASP490 4.9 31.1 1.0
CA B:ALA469 4.9 18.6 1.0
CB B:ILE485 5.0 22.6 1.0
C B:ILE485 5.0 18.2 1.0
O4 B:PO4801 5.0 8.7 1.0

Magnesium binding site 3 out of 6 in 5yjj

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Magnesium binding site 3 out of 6 in the Crystal Structure of Pnpase From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pnpase From Staphylococcus Epidermidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.2
occ:1.00
 O C:HOH1098 2.3 21.7 1.0
OD1 C:ASP496 2.8 21.4 1.0
O1 C:PO4801 3.0 17.9 1.0
OD2 C:ASP496 3.1 32.7 1.0
O C:HOH934 3.2 29.1 1.0
CG C:ASP496 3.2 25.7 1.0
O C:HOH910 3.3 16.4 1.0
CB C:ALA469 3.5 15.4 1.0
N C:SER441 3.6 14.6 1.0
CD1 C:ILE485 3.6 17.4 1.0
CG1 C:ILE485 3.7 17.1 1.0
CB C:SER441 3.8 18.1 1.0
CA C:SER441 4.0 16.8 1.0
O C:ILE485 4.2 16.2 1.0
CE C:LYS498 4.3 22.0 1.0
C C:GLY440 4.3 14.3 1.0
OG C:SER441 4.4 21.1 1.0
CA C:GLY440 4.4 17.4 1.0
P C:PO4801 4.4 15.5 1.0
CB C:ASP496 4.6 25.8 1.0
O4 C:PO4801 4.9 9.0 1.0
CB C:ASP490 4.9 27.9 1.0
CA C:ALA469 4.9 16.3 1.0
CB C:ILE485 5.0 20.1 1.0

Magnesium binding site 4 out of 6 in 5yjj

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Magnesium binding site 4 out of 6 in the Crystal Structure of Pnpase From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pnpase From Staphylococcus Epidermidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:28.7
occ:1.00
 O4 D:PO4801 2.1 13.7 1.0
P D:PO4801 3.4 17.5 1.0
O D:HOH1130 3.5 24.7 1.0
OD2 D:ASP490 3.5 39.3 1.0
OD2 D:ASP496 3.8 25.7 1.0
O3 D:PO4801 3.8 23.9 1.0
O D:HOH932 3.9 16.2 1.0
O2 D:PO4801 3.9 22.4 1.0
N D:SER441 4.0 13.4 1.0
CG D:ASP490 4.1 31.2 1.0
CB D:ASP490 4.2 24.0 1.0
CA D:GLY440 4.3 16.0 1.0
CG D:ASP496 4.4 16.5 1.0
O D:HOH1072 4.5 31.5 1.0
O1 D:PO4801 4.6 14.6 1.0
C D:GLY440 4.7 15.7 1.0
OD1 D:ASP496 4.8 17.5 1.0
CA D:SER441 4.9 18.4 1.0
N D:GLY440 5.0 24.1 1.0

Magnesium binding site 5 out of 6 in 5yjj

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Magnesium binding site 5 out of 6 in the Crystal Structure of Pnpase From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pnpase From Staphylococcus Epidermidis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg802

b:27.8
occ:1.00
 OD1 E:ASP496 2.6 26.6 1.0
CB E:ALA469 3.0 16.8 1.0
OD2 E:ASP496 3.0 29.5 1.0
CG E:ASP496 3.2 26.7 1.0
O4 E:PO4801 3.2 13.7 1.0
CB E:SER441 3.4 16.8 1.0
N E:SER441 3.5 13.2 1.0
CA E:SER441 3.7 14.7 1.0
NZ E:LYS498 3.7 22.4 1.0
CD1 E:ILE485 3.8 20.0 1.0
OG E:SER441 3.8 22.3 1.0
CG1 E:ILE485 3.8 18.9 1.0
CE E:LYS498 4.0 17.1 1.0
C E:GLY440 4.3 17.4 1.0
P E:PO4801 4.4 12.1 1.0
CA E:ALA469 4.5 16.6 1.0
O E:ILE485 4.5 17.4 1.0
O1 E:PO4801 4.5 10.0 1.0
CA E:GLY440 4.6 16.5 1.0
CB E:ASP496 4.6 24.9 1.0
CG E:LYS498 4.9 15.7 1.0
CD E:LYS498 4.9 19.2 1.0

Magnesium binding site 6 out of 6 in 5yjj

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Magnesium binding site 6 out of 6 in the Crystal Structure of Pnpase From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Pnpase From Staphylococcus Epidermidis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg802

b:26.5
occ:1.00
 O4 F:PO4801 2.8 12.9 1.0
O F:HOH1088 2.8 27.4 1.0
O F:HOH926 3.0 21.2 1.0
OD1 F:ASP496 3.0 22.4 1.0
N F:SER441 3.2 15.7 1.0
OD2 F:ASP496 3.3 23.8 1.0
CB F:ALA469 3.4 16.2 1.0
CG F:ASP496 3.4 24.3 1.0
CB F:SER441 3.6 19.3 1.0
CA F:SER441 3.7 17.8 1.0
CG1 F:ILE485 3.8 19.6 1.0
C F:GLY440 3.9 20.6 1.0
CA F:GLY440 4.1 19.5 1.0
CD1 F:ILE485 4.1 20.5 1.0
OG F:SER441 4.2 18.0 1.0
O F:ILE485 4.2 16.8 1.0
P F:PO4801 4.3 12.5 1.0
CE F:LYS498 4.4 21.6 1.0
O F:HOH943 4.6 28.5 1.0
CB F:ASP496 4.8 24.7 1.0
O1 F:PO4801 4.8 9.0 1.0
CA F:ALA469 4.9 15.7 1.0
O F:GLY440 4.9 22.8 1.0

Reference:

R.Raj, S.Mitra, B.Gopal. Characterization of Staphylococcus Epidermidis Polynucleotide Phosphorylase and Its Interactions with Ribonucleases Rnase J1 and Rnase J2. Biochem. Biophys. Res. V. 495 2078 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 29242153
DOI: 10.1016/J.BBRC.2017.12.056
Page generated: Mon Sep 30 11:16:22 2024

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