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Barium in PDB 7v9e: Crystal Structure of A Methyl Transferase Ribozyme

Protein crystallography data

The structure of Crystal Structure of A Methyl Transferase Ribozyme, PDB code: 7v9e was solved by J.Deng, D.M.J.Lilley, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.43 / 2.30
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 50.381, 52.507, 99.939, 90, 90, 90
R / Rfree (%) 24.4 / 27.1

Other elements in 7v9e:

The structure of Crystal Structure of A Methyl Transferase Ribozyme also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of A Methyl Transferase Ribozyme (pdb code 7v9e). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the Crystal Structure of A Methyl Transferase Ribozyme, PDB code: 7v9e:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Barium binding site 1 out of 9 in 7v9e

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Barium binding site 1 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:24.2
occ:0.60
 O2' A:A36 2.8 41.0 1.0
OP2 A:A37 2.8 44.6 1.0
O3' A:A36 3.0 38.1 1.0
P A:A37 3.6 47.0 1.0
C2' A:A36 3.8 45.5 1.0
C3' A:A36 3.9 42.5 1.0
H3' A:A36 4.1 51.1 1.0
H1' A:A36 4.2 48.5 1.0
H5' A:A37 4.4 57.8 1.0
OP2 A:C35 4.5 49.0 1.0
H2' A:A36 4.6 54.7 1.0
O5' A:A37 4.6 45.7 1.0
C1' A:A36 4.6 40.3 1.0
OP1 A:A37 4.7 42.6 1.0
H5'' A:A37 4.7 57.8 1.0
C5' A:A37 4.8 48.1 1.0
O4 A:U7 4.8 38.8 1.0

Barium binding site 2 out of 9 in 7v9e

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Barium binding site 2 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:30.4
occ:0.58
 O A:HOH214 2.4 33.2 1.0
O6 A:G31 2.7 45.3 1.0
N7 A:G31 3.0 41.6 1.0
O A:HOH208 3.1 32.5 1.0
C6 A:G31 3.4 42.6 1.0
N7 A:G30 3.5 53.5 1.0
C5 A:G31 3.5 46.2 1.0
C5 A:G30 4.1 50.6 1.0
C8 A:G31 4.2 42.4 1.0
O6 A:G30 4.2 43.6 1.0
O A:HOH230 4.2 43.3 1.0
C8 A:G30 4.3 55.7 1.0
C6 A:G30 4.4 48.5 1.0
H8 A:G30 4.4 66.9 1.0
H42 A:C18 4.5 51.7 1.0
H8 A:G31 4.5 51.0 1.0
O6 A:G32 4.6 45.8 1.0
N7 A:G32 4.6 40.8 1.0
N1 A:G31 4.8 47.2 1.0
C4 A:G31 4.9 50.2 1.0
OP2 A:G30 4.9 55.2 1.0

Barium binding site 3 out of 9 in 7v9e

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Barium binding site 3 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba104

b:61.2
occ:0.40
 O A:HOH220 2.9 59.8 1.0
OP2 A:U7 4.9 48.8 1.0

Barium binding site 4 out of 9 in 7v9e

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Barium binding site 4 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba105

b:54.1
occ:0.45
 H41 A:C65 4.0 51.9 1.0
OP1 A:C38 4.4 54.2 1.0
H42 A:C65 4.5 51.9 1.0
N4 A:C65 4.6 43.2 1.0
H3' A:A37 4.7 59.5 1.0
O6 A:G5 4.7 52.0 1.0
O6 A:G4 5.0 51.1 1.0
O2' A:A37 5.0 46.8 1.0

Barium binding site 5 out of 9 in 7v9e

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Barium binding site 5 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba106

b:46.3
occ:0.40
 O A:HOH220 3.3 59.8 1.0
OP1 A:U7 4.5 52.5 1.0

Barium binding site 6 out of 9 in 7v9e

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Barium binding site 6 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba107

b:69.0
occ:0.48
 O A:HOH232 3.8 56.6 1.0

Barium binding site 7 out of 9 in 7v9e

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Barium binding site 7 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba108

b:84.3
occ:0.75
 O A:HOH219 2.6 52.2 1.0
O6 A:G53 2.8 77.5 1.0
O A:HOH203 2.8 62.8 1.0
O4 A:U52 2.9 72.0 1.0
C4 A:U52 3.8 73.0 1.0
C6 A:G53 3.9 78.2 1.0
H5 A:U52 4.1 87.5 1.0
O A:HOH228 4.1 60.9 1.0
N7 A:G53 4.4 72.0 1.0
C5 A:U52 4.4 72.9 1.0
H61 A:A57 4.4 87.6 1.0
C5 A:G53 4.5 73.5 1.0
N3 A:U52 4.9 71.2 1.0
H62 A:A57 4.9 87.6 1.0
N6 A:A57 4.9 72.9 1.0
H3 A:U52 4.9 85.5 1.0
OP1 A:A55 5.0 78.9 1.0

Barium binding site 8 out of 9 in 7v9e

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Barium binding site 8 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba109

b:62.3
occ:0.56
 OP2 A:G41 2.7 55.6 1.0
O4 A:U45 3.3 49.1 1.0
H5 A:U45 3.4 55.7 1.0
P A:G41 3.8 51.8 1.0
C4 A:U45 4.0 50.0 1.0
C5 A:U45 4.0 46.3 1.0
O3' A:A40 4.1 59.1 1.0
OP1 A:G41 4.4 68.0 1.0
HN9 A:GUN101 4.4 49.0 1.0
H62 A:A46 4.6 61.5 1.0
OP2 A:A44 4.6 57.1 1.0
O A:HOH216 4.7 45.8 1.0

Barium binding site 9 out of 9 in 7v9e

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Barium binding site 9 out of 9 in the Crystal Structure of A Methyl Transferase Ribozyme


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of A Methyl Transferase Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba110

b:120.1
occ:0.76
 N7 A:G49 3.3 68.6 1.0
O6 A:G49 4.0 64.1 1.0
N7 A:A48 4.0 60.7 1.0
C5 A:G49 4.2 64.7 1.0
C8 A:G49 4.3 68.2 1.0
O4 A:U50 4.3 67.7 1.0
H8 A:G49 4.3 81.9 1.0
C6 A:G49 4.5 64.8 1.0
C8 A:A48 4.5 62.7 1.0
C5 A:A48 4.5 62.6 1.0
H62 A:A48 4.5 66.4 1.0
OP2 A:G49 4.6 72.5 1.0
H8 A:A48 4.6 75.4 1.0
H3' A:A48 4.9 79.8 1.0
H61 A:A59 4.9 78.3 1.0
N6 A:A48 4.9 55.2 1.0
H5 A:U50 4.9 79.6 1.0
OP2 A:A48 4.9 68.1 1.0
C6 A:A48 4.9 57.0 1.0

Reference:

J.Deng, T.J.Wilson, J.Wang, X.Peng, M.Li, X.Lin, W.Liao, D.M.J.Lilley, L.Huang. Structure and Mechanism of A Methyltransferase Ribozyme. Nat.Chem.Biol. V. 18 556 2022.
ISSN: ESSN 1552-4469
PubMed: 35301479
DOI: 10.1038/S41589-022-00982-Z
Page generated: Tue Apr 4 17:22:57 2023

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