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Magnesium in PDB 4r4v: Crystal Structure of the Vs Ribozyme - G638A Mutant

Protein crystallography data

The structure of Crystal Structure of the Vs Ribozyme - G638A Mutant, PDB code: 4r4v was solved by J.A.Piccirilli, N.B.Suslov, S.Dasgupta, H.Huang, D.M.J.Lilley, P.A.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.07 / 3.07
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 102.229, 102.229, 215.020, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.4

Other elements in 4r4v:

The structure of Crystal Structure of the Vs Ribozyme - G638A Mutant also contains other interesting chemical elements:

Potassium (K) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Vs Ribozyme - G638A Mutant (pdb code 4r4v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Vs Ribozyme - G638A Mutant, PDB code: 4r4v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4r4v

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Magnesium binding site 1 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:68.5
occ:1.00
 O A:HOH907 2.2 58.6 1.0
O A:HOH906 2.8 29.8 1.0
H41 A:C764 3.2 50.4 1.0
N4 A:C764 4.0 42.0 1.0
H42 A:C764 4.2 50.4 1.0
H41 A:C765 4.5 46.4 1.0
H42 A:C765 4.6 46.4 1.0
O6 A:G654 4.7 39.4 1.0
H5 A:C764 4.7 51.4 1.0
N4 A:C765 4.9 38.7 1.0

Magnesium binding site 2 out of 9 in 4r4v

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Magnesium binding site 2 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:60.1
occ:1.00
 O A:HOH912 2.2 39.5 1.0
O A:HOH916 2.2 47.7 1.0
O A:HOH915 2.2 28.6 1.0
O A:HOH913 2.2 61.1 1.0
O A:HOH911 2.2 74.0 1.0
O A:HOH914 2.2 36.4 1.0
H41 A:C741 3.0 45.4 1.0
H41 A:C742 3.5 39.2 1.0
N4 A:C741 3.8 37.8 1.0
H5 A:C741 4.0 37.2 1.0
H42 A:C741 4.1 45.4 1.0
N4 A:C742 4.2 32.7 1.0
H42 A:C742 4.3 39.2 1.0
C5 A:C741 4.6 31.0 1.0
C4 A:C741 4.6 35.2 1.0

Magnesium binding site 3 out of 9 in 4r4v

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Magnesium binding site 3 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:27.2
occ:1.00
 O A:HOH920 2.2 47.9 1.0
O A:HOH917 2.2 41.0 1.0
O A:HOH922 2.2 58.3 1.0
O A:HOH921 2.2 52.0 1.0
O A:HOH918 2.2 57.4 1.0
O A:HOH919 2.2 52.0 1.0
H41 A:C758 2.9 37.9 1.0
H62 A:A759 3.5 55.2 1.0
N4 A:C758 3.7 31.6 1.0
H5 A:C758 3.8 35.9 1.0
H42 A:C758 4.1 37.9 1.0
N6 A:A759 4.2 46.0 1.0
H61 A:A759 4.3 55.2 1.0
C5 A:C758 4.4 29.9 1.0
C4 A:C758 4.5 29.3 1.0
H41 A:C760 4.8 74.3 1.0
H42 A:C760 4.9 74.3 1.0
O A:HOH926 4.9 33.2 1.0

Magnesium binding site 4 out of 9 in 4r4v

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Magnesium binding site 4 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


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 the Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:42.2
occ:1.00
 O A:HOH928 2.2 42.4 1.0
O A:HOH926 2.2 33.2 1.0
O A:HOH924 2.2 40.5 1.0
O A:HOH923 2.2 40.7 1.0
O A:HOH927 2.2 42.9 1.0
O A:HOH925 2.2 40.7 1.0
H8 A:A756 3.2 27.8 1.0
H2' A:A756 3.9 32.2 1.0
C8 A:A756 4.1 23.2 1.0
O2' A:A756 4.1 32.3 1.0
HO2' A:A756 4.5 38.8 1.0
C2' A:A756 4.5 26.9 1.0
N7 A:A756 4.7 18.9 1.0

Magnesium binding site 5 out of 9 in 4r4v

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Magnesium binding site 5 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


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 the Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg807

b:59.0
occ:1.00
 O A:HOH929 2.2 53.7 1.0
O A:HOH931 2.2 40.6 1.0
O A:HOH932 2.2 80.9 1.0
O A:HOH933 2.2 47.3 1.0
O A:HOH930 2.2 62.8 1.0
O A:HOH934 2.2 51.9 1.0
H1 A:HOH929 2.8 64.4 1.0
H1 A:HOH931 2.8 48.7 1.0
H1 A:HOH932 2.8 97.1 1.0
H1 A:HOH933 2.8 56.8 1.0
H1 A:HOH930 2.8 75.4 1.0
H1 A:HOH934 2.8 62.2 1.0
H41 A:C748 3.4 33.1 1.0
H41 A:C747 3.7 41.3 1.0
N4 A:C748 4.1 27.6 1.0
H41 A:C726 4.2 32.9 1.0
H42 A:C748 4.2 33.1 1.0
N4 A:C747 4.3 34.4 1.0
H42 A:C747 4.6 41.3 1.0
H42 A:C726 4.6 32.9 1.0
N4 A:C726 4.8 27.4 1.0
H5 A:C747 4.8 45.5 1.0

Magnesium binding site 6 out of 9 in 4r4v

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Magnesium binding site 6 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


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 the Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg808

b:35.9
occ:1.00
 O A:HOH910 2.3 31.0 1.0
O A:HOH909 2.7 33.4 1.0
N7 A:A656 3.9 32.9 1.0
OP2 A:A656 4.0 48.0 1.0
OP2 A:G655 4.0 30.0 1.0
H8 A:A656 4.2 41.5 1.0
H3' A:G655 4.3 42.8 1.0
C8 A:A656 4.5 34.6 1.0
H62 A:A656 4.6 38.5 1.0
O5' A:G655 4.6 32.5 1.0
H8 A:G655 4.6 40.8 1.0
OP2 A:G716 4.8 36.3 1.0
P A:G655 4.8 36.9 1.0
H5' A:G717 4.8 30.6 1.0
N7 A:G716 4.9 29.3 1.0
C8 A:G655 4.9 34.0 1.0
O5' A:G717 5.0 20.9 1.0
H8 A:G716 5.0 35.5 1.0
N7 A:G655 5.0 34.7 1.0

Magnesium binding site 7 out of 9 in 4r4v

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Magnesium binding site 7 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg812

b:47.6
occ:1.00
 H41 A:C768 3.5 32.2 1.0
N4 A:C768 4.3 26.8 1.0
H42 A:C768 4.4 32.2 1.0
H5 A:C768 5.0 28.5 1.0

Magnesium binding site 8 out of 9 in 4r4v

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Magnesium binding site 8 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg813

b:62.1
occ:1.00
 H41 A:C785 3.9 69.0 1.0
N4 A:C785 4.6 57.5 1.0
H42 A:C785 4.9 69.0 1.0
H5 A:C785 4.9 72.7 1.0

Magnesium binding site 9 out of 9 in 4r4v

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Magnesium binding site 9 out of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range:

Reference:

N.B.Suslov, S.Dasgupta, H.Huang, J.R.Fuller, D.M.Lilley, P.A.Rice, J.A.Piccirilli. Crystal Structure of the Varkud Satellite Ribozyme. Nat.Chem.Biol. V. 11 840 2015.
ISSN: ISSN 1552-4450
PubMed: 26414446
DOI: 10.1038/NCHEMBIO.1929
Page generated: Tue Aug 20 02:51:16 2024

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