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Magnesium in PDB 3ffu: Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium

Protein crystallography data

The structure of Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium, PDB code: 3ffu was solved by S.A.Messing, S.B.Gabelli, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.61 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.732, 68.749, 93.069, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 30.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium (pdb code 3ffu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium, PDB code: 3ffu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ffu

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Magnesium binding site 1 out of 6 in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium


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 Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg154

b:72.5
occ:1.00
 O A:HOH161 1.8 75.7 1.0
O A:HOH162 2.0 55.1 1.0
OE2 A:GLU70 2.2 69.0 1.0
O1B A:GTP4033 2.2 79.0 1.0
O A:HOH163 2.7 45.6 1.0
CD A:GLU70 2.9 68.4 1.0
MG A:MG155 2.9 71.5 1.0
OE1 A:GLU70 2.9 68.7 1.0
OE2 A:GLU73 3.2 64.4 1.0
PB A:GTP4033 3.3 83.2 1.0
O2B A:GTP4033 3.6 77.7 1.0
O A:HOH160 3.7 75.1 1.0
O3B A:GTP4033 3.8 88.7 1.0
NH1 A:ARG69 3.9 68.5 1.0
O1G A:GTP4033 4.3 95.3 1.0
CG A:GLU70 4.3 68.1 1.0
CD A:GLU73 4.4 64.7 1.0
N A:LYS56 4.4 68.6 1.0
OE2 A:GLU58 4.4 74.5 1.0
O A:HOH159 4.5 68.0 1.0
O A:LYS56 4.5 68.6 1.0
NH2 A:ARG69 4.6 68.3 1.0
O3A A:GTP4033 4.6 79.9 1.0
CZ A:ARG69 4.7 68.5 1.0
CA A:GLY55 4.8 69.0 1.0
PG A:GTP4033 4.8 96.4 1.0
OE2 A:GLU74 4.9 69.2 1.0
C A:GLY55 5.0 69.0 1.0

Magnesium binding site 2 out of 6 in 3ffu

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Magnesium binding site 2 out of 6 in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium


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 Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg155

b:71.5
occ:1.00
 O A:HOH161 1.7 75.7 1.0
O A:HOH160 1.8 75.1 1.0
O A:HOH159 2.0 68.0 1.0
O2B A:GTP4033 2.2 77.7 1.0
OE1 A:GLU70 2.2 68.7 1.0
OE2 A:GLU74 2.2 69.2 1.0
PB A:GTP4033 2.9 83.2 1.0
MG A:MG154 2.9 72.5 1.0
O3B A:GTP4033 3.0 88.7 1.0
MG A:MG156 3.1 71.3 1.0
O1B A:GTP4033 3.2 79.0 1.0
CD A:GLU70 3.3 68.4 1.0
CD A:GLU74 3.4 66.7 1.0
OE2 A:GLU70 3.7 69.0 1.0
OE2 A:GLU73 3.7 64.4 1.0
O A:GLY54 3.8 69.9 1.0
CG A:GLU74 4.0 65.8 1.0
O A:HOH158 4.2 74.8 1.0
OE1 A:GLU74 4.4 66.5 1.0
O3A A:GTP4033 4.4 79.9 1.0
O1A A:GTP4033 4.4 74.2 1.0
CG A:GLU70 4.6 68.1 1.0
PG A:GTP4033 4.6 96.4 1.0
CA A:GLY55 4.6 69.0 1.0
CD A:GLU73 4.7 64.7 1.0
C A:GLY54 4.7 69.2 1.0
O A:HOH162 4.7 55.1 1.0
CG A:GLU73 4.8 65.0 1.0
O A:HOH163 4.8 45.6 1.0
O A:HOH157 4.9 57.6 1.0
O1G A:GTP4033 5.0 95.3 1.0
CB A:GLU70 5.0 67.8 1.0

Magnesium binding site 3 out of 6 in 3ffu

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Magnesium binding site 3 out of 6 in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium


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 Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg156

b:71.3
occ:1.00
 O A:HOH157 2.0 57.6 1.0
O1A A:GTP4033 2.2 74.2 1.0
O2B A:GTP4033 2.2 77.7 1.0
OE2 A:GLU74 2.2 69.2 1.0
O A:GLY54 2.2 69.9 1.0
O A:HOH158 2.2 74.8 1.0
CD A:GLU74 2.8 66.7 1.0
OE1 A:GLU74 2.9 66.5 1.0
MG A:MG155 3.1 71.5 1.0
O A:HOH159 3.2 68.0 1.0
PB A:GTP4033 3.4 83.2 1.0
C A:GLY54 3.4 69.2 1.0
PA A:GTP4033 3.5 76.8 1.0
O3B A:GTP4033 3.7 88.7 1.0
O3A A:GTP4033 3.9 79.9 1.0
OE1 A:GLU70 4.0 68.7 1.0
CA A:GLY55 4.1 69.0 1.0
CG A:GLU74 4.2 65.8 1.0
N2 A:GTP4033 4.2 71.2 1.0
O2A A:GTP4033 4.2 77.1 1.0
N A:GLY54 4.2 69.4 1.0
N A:GLY55 4.2 68.9 1.0
O A:HOH161 4.4 75.7 1.0
OE2 A:GLU51 4.4 69.1 1.0
O A:HOH160 4.4 75.1 1.0
CA A:GLY54 4.4 69.2 1.0
O1B A:GTP4033 4.6 79.0 1.0
O5' A:GTP4033 4.6 75.8 1.0
NE2 A:HIS115 4.8 67.0 1.0
CD2 A:HIS115 4.8 66.2 1.0
CE1 A:HIS116 4.9 67.2 1.0
NE2 A:HIS116 4.9 66.4 1.0

Magnesium binding site 4 out of 6 in 3ffu

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Magnesium binding site 4 out of 6 in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium


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 Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg154

b:78.1
occ:1.00
 O B:HOH161 1.7 88.5 1.0
O B:HOH162 1.9 68.8 1.0
OE2 B:GLU70 2.2 72.7 1.0
O1B B:GTP4032 2.2 81.2 1.0
O B:HOH163 2.4 69.8 1.0
MG B:MG155 3.1 73.2 1.0
CD B:GLU70 3.3 70.2 1.0
PB B:GTP4032 3.4 85.3 1.0
OE2 B:GLU73 3.6 70.2 1.0
OE1 B:GLU70 3.8 70.4 1.0
OE2 B:GLU58 3.8 76.2 1.0
O2B B:GTP4032 3.9 79.6 1.0
NH1 B:ARG69 3.9 68.7 1.0
O3B B:GTP4032 4.0 91.1 1.0
O B:HOH160 4.4 78.2 1.0
O B:LYS56 4.4 70.9 1.0
O2G B:GTP4032 4.5 98.9 1.0
N B:LYS56 4.5 70.2 1.0
NH2 B:ARG69 4.5 68.7 1.0
CG B:GLU70 4.6 68.1 1.0
O3A B:GTP4032 4.7 81.5 1.0
CZ B:ARG69 4.7 68.8 1.0
PG B:GTP4032 4.7 99.5 1.0
O B:HOH159 4.7 76.9 1.0
O1G B:GTP4032 4.8 98.3 1.0
CD B:GLU73 4.8 68.7 1.0
CB B:LYS56 5.0 70.7 1.0
CD B:GLU58 5.0 74.8 1.0

Magnesium binding site 5 out of 6 in 3ffu

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Magnesium binding site 5 out of 6 in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium


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 Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg155

b:73.2
occ:1.00
 O B:HOH161 1.7 88.5 1.0
O B:HOH159 1.8 76.9 1.0
O B:HOH160 1.9 78.2 1.0
O2B B:GTP4032 2.2 79.6 1.0
OE1 B:GLU70 2.2 70.4 1.0
OE1 B:GLU74 2.7 68.7 1.0
PB B:GTP4032 2.7 85.3 1.0
CD B:GLU70 2.9 70.2 1.0
O3B B:GTP4032 2.9 91.1 1.0
OE2 B:GLU70 3.0 72.7 1.0
O1B B:GTP4032 3.0 81.2 1.0
MG B:MG154 3.1 78.1 1.0
MG B:MG156 3.4 70.6 1.0
OE2 B:GLU73 3.6 70.2 1.0
CD B:GLU74 3.8 68.4 1.0
O B:HOH158 4.0 82.2 1.0
CG B:GLU74 4.3 67.4 1.0
O B:GLY54 4.3 69.4 1.0
O3A B:GTP4032 4.3 81.5 1.0
PG B:GTP4032 4.4 99.5 1.0
CG B:GLU70 4.4 68.1 1.0
O B:HOH163 4.5 69.8 1.0
O1G B:GTP4032 4.6 98.3 1.0
O1A B:GTP4032 4.6 73.6 1.0
CD B:GLU73 4.6 68.7 1.0
O B:HOH162 4.7 68.8 1.0
CA B:GLY55 4.7 69.0 1.0
CG B:GLU73 4.8 68.8 1.0
OE2 B:GLU74 4.9 68.1 1.0

Magnesium binding site 6 out of 6 in 3ffu

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Magnesium binding site 6 out of 6 in the Structure of the Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium


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 Rna Pyrophosphohydrolase Bdrpph in Complex with Gtp and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg156

b:70.6
occ:1.00
 O B:HOH158 1.8 82.2 1.0
O B:HOH157 2.0 64.3 1.0
O1A B:GTP4032 2.2 73.6 1.0
OE1 B:GLU74 2.2 68.7 1.0
O2B B:GTP4032 2.2 79.6 1.0
O B:GLY54 2.2 69.4 1.0
CD B:GLU74 2.9 68.4 1.0
O B:HOH159 2.9 76.9 1.0
OE2 B:GLU74 3.0 68.1 1.0
PB B:GTP4032 3.4 85.3 1.0
C B:GLY54 3.4 68.4 1.0
MG B:MG155 3.4 73.2 1.0
PA B:GTP4032 3.5 77.5 1.0
O3B B:GTP4032 3.8 91.1 1.0
O3A B:GTP4032 3.9 81.5 1.0
OE1 B:GLU70 3.9 70.4 1.0
N2 B:GTP4032 4.0 70.0 1.0
CA B:GLY55 4.1 69.0 1.0
N B:GLY54 4.2 67.4 1.0
N B:GLY55 4.2 68.8 1.0
CG B:GLU74 4.2 67.4 1.0
OE2 B:GLU51 4.4 68.5 1.0
CA B:GLY54 4.4 67.9 1.0
O2A B:GTP4032 4.4 77.8 1.0
O B:HOH160 4.5 78.2 1.0
O5' B:GTP4032 4.5 75.9 1.0
O1B B:GTP4032 4.7 81.2 1.0
CD2 B:HIS115 4.7 64.9 1.0
CD B:GLU70 4.7 70.2 1.0
NE2 B:HIS115 4.8 65.0 1.0
NH2 B:ARG40 4.9 72.4 1.0
O B:HOH161 5.0 88.5 1.0

Reference:

S.A.Messing, S.B.Gabelli, Q.Liu, H.Celesnik, J.G.Belasco, S.A.Pineiro, L.M.Amzel. Structure and Biological Function of the Rna Pyrophosphohydrolase Bdrpph From Bdellovibrio Bacteriovorus. Structure V. 17 472 2009.
ISSN: ISSN 0969-2126
PubMed: 19278661
DOI: 10.1016/J.STR.2008.12.022
Page generated: Wed Aug 14 13:46:14 2024

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