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Magnesium in PDB 1hc8: Crystal Structure of A Conserved Ribosomal Protein-Rna Complex

Protein crystallography data

The structure of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex, PDB code: 1hc8 was solved by G.L.Conn, D.E.Draper, E.E.Lattman, A.G.Gittis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.8
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 150.675, 150.675, 63.841, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.3

Other elements in 1hc8:

The structure of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex also contains other interesting chemical elements:

Osmium (Os) 4 atoms
Potassium (K) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex (pdb code 1hc8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex, PDB code: 1hc8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in 1hc8

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Magnesium binding site 1 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1159

b:50.9
occ:1.00
O4 C:U108 3.6 36.8 1.0
C4 C:U108 3.8 37.7 1.0
C5 C:U108 3.8 38.4 1.0
N7 C:G109 4.1 42.7 1.0
O2' C:U110 4.2 50.2 1.0
O6 C:G109 4.4 41.5 1.0
O2 C:U110 4.4 44.7 1.0
N3 C:U108 4.6 36.3 1.0
C6 C:U108 4.7 38.9 1.0
C5 C:G109 5.0 42.1 1.0

Magnesium binding site 2 out of 21 in 1hc8

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Magnesium binding site 2 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1160

b:50.1
occ:1.00
O6 C:G121 3.7 42.8 1.0
N1 C:A139 3.7 40.1 1.0
N7 C:G121 4.1 38.7 1.0
OP1 C:A107 4.1 48.1 1.0
O4 C:U151 4.2 52.5 1.0
C6 C:G121 4.4 41.0 1.0
C2 C:A139 4.5 40.5 1.0
N6 C:A139 4.6 40.0 1.0
C5 C:G121 4.6 40.2 1.0
C6 C:A139 4.6 38.8 1.0
N4 C:C150 4.7 47.5 1.0

Magnesium binding site 3 out of 21 in 1hc8

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Magnesium binding site 3 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1161

b:45.9
occ:1.00
OP1 C:A148 2.2 47.0 1.0
P C:A148 3.4 46.7 1.0
OP1 C:G121 3.7 44.1 1.0
OP2 C:A148 3.9 47.4 1.0
O5' C:A148 4.1 47.6 1.0
OP2 C:G149 4.5 51.0 1.0
O3' C:U147 4.7 47.1 1.0
C5' C:A148 4.8 46.7 1.0
P C:G121 4.8 44.4 1.0
OP2 C:G121 4.9 46.4 1.0
O2' C:A120 5.0 49.1 1.0

Magnesium binding site 4 out of 21 in 1hc8

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Magnesium binding site 4 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1163

b:34.4
occ:1.00
OP1 C:C122 2.2 37.2 1.0
OP2 C:A120 2.4 46.8 1.0
P C:C122 3.3 37.6 1.0
O3' C:G121 3.6 39.7 1.0
P C:A120 3.7 44.8 1.0
OP2 C:C122 4.0 38.8 1.0
K C:K1162 4.0 16.2 1.0
OP1 C:G112 4.0 48.5 1.0
O6 C:G113 4.2 42.8 1.0
N7 C:G112 4.2 42.4 1.0
O5' C:A120 4.2 46.0 1.0
C5' C:A120 4.3 47.1 1.0
OP1 C:A120 4.3 45.4 1.0
O6 C:G112 4.5 41.2 1.0
O5' C:C122 4.6 37.1 1.0
O3' C:A119 4.8 44.4 1.0
O6 C:G124 4.9 43.9 1.0
C3' C:G121 4.9 40.4 1.0
N4 C:C125 4.9 41.4 1.0
C5 C:G112 5.0 42.0 1.0

Magnesium binding site 5 out of 21 in 1hc8

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Magnesium binding site 5 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1164

b:44.0
occ:1.00
O C:HOH2001 2.5 27.6 1.0
OP2 C:C152 3.5 51.2 1.0
OP1 C:C152 3.9 52.4 1.0
O6 C:G106 3.9 50.0 1.0
P C:C152 4.2 52.2 1.0
C6 C:G106 4.6 48.0 1.0
N1 C:G106 4.7 48.8 1.0
O6 C:G105 4.7 46.4 1.0
N6 C:A104 4.9 53.6 1.0
O3' C:U151 4.9 54.3 1.0
N7 C:A104 5.0 54.5 1.0

Magnesium binding site 6 out of 21 in 1hc8

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Magnesium binding site 6 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1165

b:38.4
occ:1.00
OP1 C:U116 2.2 41.1 1.0
OP1 D:A336 2.3 43.1 1.0
O3' C:U115 3.3 41.9 1.0
P C:U116 3.4 40.4 1.0
P D:A336 3.7 40.9 1.0
O3' D:A335 4.1 41.4 1.0
C5' C:U116 4.3 40.9 1.0
O5' C:U116 4.4 40.8 1.0
OP2 C:U116 4.4 40.1 1.0
O5' D:A336 4.5 41.3 1.0
O2' C:U115 4.5 42.8 1.0
C5' D:A336 4.5 39.2 1.0
O2' D:C354 4.6 49.5 1.0
C3' C:U115 4.7 41.3 1.0
OP2 D:A336 4.8 40.2 1.0

Magnesium binding site 7 out of 21 in 1hc8

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Magnesium binding site 7 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1166

b:55.9
occ:1.00
O1B C:GTP101 2.8 78.9 1.0
O3B C:GTP101 2.9 79.5 1.0
O2A C:GTP101 3.2 73.1 1.0
PB C:GTP101 3.3 77.7 1.0
O3A C:GTP101 3.7 75.6 1.0
O3G C:GTP101 3.9 82.0 1.0
PG C:GTP101 3.9 82.2 1.0
PA C:GTP101 4.0 72.3 1.0
O5' C:GTP101 4.4 71.5 1.0
O2G C:GTP101 4.4 82.0 1.0
O2B C:GTP101 4.7 78.0 1.0

Magnesium binding site 8 out of 21 in 1hc8

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Magnesium binding site 8 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1167

b:39.9
occ:1.00
O4 C:U144 2.0 58.1 1.0
OP2 C:A123 2.1 45.8 1.0
C4 C:U144 3.2 56.1 1.0
O6 C:G143 3.3 46.6 1.0
P C:A123 3.5 45.5 1.0
C5 C:U144 4.1 56.1 1.0
C6 C:G143 4.1 45.2 1.0
N3 C:U144 4.2 55.3 1.0
O3' C:C122 4.2 43.3 1.0
C3' C:C122 4.2 42.1 1.0
OP1 C:A146 4.3 43.5 1.0
OP1 C:A123 4.3 41.9 1.0
C2' C:C122 4.4 43.1 1.0
OP2 C:U147 4.5 39.9 1.0
O5' C:A123 4.6 43.0 1.0
N1 C:G143 4.7 44.9 1.0
C5' C:A123 4.7 42.6 1.0
C2 C:A119 5.0 45.0 1.0

Magnesium binding site 9 out of 21 in 1hc8

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Magnesium binding site 9 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


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 A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1168

b:42.2
occ:1.00
N1 C:A111 3.6 52.7 1.0
C6 C:A111 3.6 52.3 1.0
C2 C:A111 3.9 53.1 1.0
C5 C:A111 4.0 53.3 1.0
N6 C:A111 4.0 52.3 1.0
C4 C:A111 4.2 53.4 1.0
N3 C:A111 4.3 53.5 1.0
N7 C:A111 4.8 54.2 1.0
OP1 C:A119 4.8 44.1 1.0
MG C:MG1172 4.9 38.1 1.0

Magnesium binding site 10 out of 21 in 1hc8

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Magnesium binding site 10 out of 21 in the Crystal Structure of A Conserved Ribosomal Protein-Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of A Conserved Ribosomal Protein-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1172

b:38.1
occ:1.00
OP2 C:G113 3.5 42.7 1.0
O2' C:A111 3.9 53.2 1.0
OP1 C:G113 4.4 41.4 1.0
P C:G113 4.5 40.0 1.0
OP1 C:A120 4.6 45.4 1.0
N3 C:A111 4.7 53.5 1.0
MG C:MG1168 4.9 42.2 1.0

Reference:

G.L.Conn, A.G.Gittis, E.E.Lattman, V.K.Misra, D.E.Draper. A Compact Rna Tertiary Structure Contains A Buried Backbone-K+ Complex J.Mol.Biol. V. 318 963 2002.
ISSN: ISSN 0022-2836
PubMed: 12054794
DOI: 10.1016/S0022-2836(02)00147-X
Page generated: Mon Dec 14 05:59:09 2020

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