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Magnesium in PDB 4jzv: Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket

Enzymatic activity of Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket

All present enzymatic activity of Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket:
3.6.1.55;

Protein crystallography data

The structure of Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket, PDB code: 4jzv was solved by J.Piton, V.Larue, Y.Thillier, A.Dorleans, O.Pellegrini, I.Li De La Sierra-Gallay, J.J.Vasseur, F.Debart, C.Tisne, C.Condon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.34 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.158, 138.025, 35.684, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket (pdb code 4jzv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket, PDB code: 4jzv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4jzv

Go back to Magnesium Binding Sites List in 4jzv
Magnesium binding site 1 out of 3 in the Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket


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 the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:43.7
occ:1.00
 O3G C:GCP1 2.0 0.0 1.0
O A:HOH330 2.1 35.9 1.0
O A:GLY52 2.3 32.8 1.0
OE2 A:GLU72 2.3 39.7 1.0
O A:HOH329 2.8 49.5 1.0
O2B C:GCP1 2.9 0.5 1.0
MG A:MG202 2.9 42.8 1.0
OE2 A:GLU68 3.3 46.6 1.0
C A:GLY52 3.4 33.3 1.0
OE1 A:GLU115 3.4 64.5 1.0
PG C:GCP1 3.4 0.2 1.0
CD A:GLU72 3.4 47.4 1.0
CA A:GLY53 3.5 32.6 1.0
N A:GLY53 3.9 31.0 1.0
OE1 A:GLU72 3.9 34.5 1.0
OE2 A:GLU115 3.9 69.6 1.0
PB C:GCP1 3.9 0.5 1.0
CD A:GLU115 4.0 73.1 1.0
O1G C:GCP1 4.1 0.2 1.0
C3B C:GCP1 4.1 0.3 1.0
CD A:GLU68 4.2 55.7 1.0
O5' C:GCP1 4.3 0.3 1.0
O3A C:GCP1 4.4 0.5 1.0
O2G C:GCP1 4.5 0.1 1.0
NH2 A:ARG46 4.6 55.1 1.0
CA A:GLY52 4.6 28.6 1.0
CG A:GLU72 4.7 35.2 1.0
OE1 A:GLU68 4.8 50.0 1.0
N A:GLY52 4.8 27.9 1.0
C A:GLY53 4.9 38.4 1.0

Magnesium binding site 2 out of 3 in 4jzv

Go back to Magnesium Binding Sites List in 4jzv
Magnesium binding site 2 out of 3 in the Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket


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 the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:42.8
occ:1.00
 OE1 A:GLU115 2.0 64.5 1.0
OE2 A:GLU68 2.1 46.6 1.0
O A:HOH332 2.2 47.2 1.0
OE2 A:GLU72 2.4 39.7 1.0
O3G C:GCP1 2.4 0.0 1.0
MG A:MG201 2.9 43.7 1.0
CD A:GLU68 3.2 55.7 1.0
CD A:GLU115 3.2 73.1 1.0
PG C:GCP1 3.3 0.2 1.0
CD A:GLU72 3.3 47.4 1.0
OE1 A:GLU68 3.5 50.0 1.0
CG A:GLU72 3.6 35.2 1.0
O2G C:GCP1 3.6 0.1 1.0
O1G C:GCP1 3.6 0.2 1.0
OE2 A:GLU115 3.9 69.6 1.0
O A:HOH330 4.1 35.9 1.0
O A:GLY52 4.1 32.8 1.0
OE1 A:GLU71 4.1 51.2 1.0
CG A:GLU115 4.3 54.1 1.0
OE1 A:GLU72 4.4 34.5 1.0
CG A:GLU68 4.5 38.9 1.0
CB A:GLU71 4.9 31.6 1.0
C3B C:GCP1 4.9 0.3 1.0
CB A:GLU68 5.0 28.0 1.0

Magnesium binding site 3 out of 3 in 4jzv

Go back to Magnesium Binding Sites List in 4jzv
Magnesium binding site 3 out of 3 in the Crystal Structure of the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket


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 the Bacillus Subtilis Pyrophosphohydrolase Bsrpph Bound to A Non-Hydrolysable Triphosphorylated Dinucleotide Rna (Pcp- Pgpg) - Second Guanosine Residue in Guanosine Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:84.3
occ:1.00
 OE2 B:GLU68 2.0 65.4 1.0
OE2 B:GLU115 2.3 90.0 1.0
OE2 B:GLU72 2.5 65.7 1.0
O B:HOH307 2.8 52.1 1.0
CD B:GLU68 2.8 75.4 1.0
O B:HOH337 3.0 60.0 1.0
OE1 B:GLU68 3.1 75.1 1.0
CD B:GLU115 3.2 94.8 1.0
O B:HOH325 3.2 50.3 1.0
O B:GLY52 3.2 41.5 1.0
OE1 B:GLU115 3.5 89.0 1.0
CD B:GLU72 3.6 67.2 1.0
CG B:GLU68 4.1 55.1 1.0
C B:GLY52 4.3 40.6 1.0
CA B:GLY53 4.3 43.7 1.0
CG B:GLU72 4.3 49.8 1.0
CG B:GLU115 4.4 73.5 1.0
OE1 B:GLU72 4.5 56.5 1.0
N B:GLY53 4.7 39.4 1.0
O B:HOH335 4.8 67.7 1.0
CB B:GLU68 4.8 41.3 1.0

Reference:

J.Piton, V.Larue, Y.Thillier, A.Dorleans, O.Pellegrini, I.Li De La Sierra-Gallay, J.J.Vasseur, F.Debart, C.Tisne, C.Condon. Bacillus Subtilis Rna Deprotection Enzyme Rpph Recognizes Guanosine in the Second Position of Its Substrates. Proc.Natl.Acad.Sci.Usa V. 110 8858 2013.
ISSN: ISSN 0027-8424
PubMed: 23610407
DOI: 10.1073/PNAS.1221510110
Page generated: Sat Aug 17 03:22:09 2024

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