Atomistry » Magnesium » PDB 4r17-4rcy » 4r4v
Atomistry »
  Magnesium »
    PDB 4r17-4rcy »
      4r4v »

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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Go back to Magnesium Binding Sites List in 4r4v
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

Last articles

Mg in 3T7D
Mg in 3T9D
Mg in 3T9C
Mg in 3T9A
Mg in 3T9B
Mg in 3T99
Mg in 3T8V
Mg in 3T80
Mg in 3T5P
Mg in 3T8Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy