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Magnesium in PDB 5ml7: Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui

Protein crystallography data

The structure of Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui, PDB code: 5ml7 was solved by A.G.Gabdulkhakov, T.V.Tishchenko, N.A.Nevskaya, S.V.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.836, 136.836, 70.110, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 29.1

Other elements in 5ml7:

The structure of Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui (pdb code 5ml7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui, PDB code: 5ml7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5ml7

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Magnesium binding site 1 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2302

b:18.8
occ:1.00
 O6 A:G2156 1.9 63.2 1.0
OP2 A:C2154 2.0 94.7 1.0
C6 A:G2156 3.2 61.5 1.0
P A:C2154 3.3 94.9 1.0
O2' A:A2158 3.8 55.5 1.0
O3' A:G2153 3.8 90.0 1.0
OP1 A:A2160 4.0 57.4 1.0
N1 A:G2156 4.1 54.9 1.0
OP1 A:C2154 4.1 96.9 1.0
C5 A:G2156 4.2 60.9 1.0
O5' A:C2154 4.5 82.5 1.0
N7 A:G2156 4.5 60.4 1.0
C3' A:G2153 4.5 93.9 1.0
OP2 A:A2155 4.6 100.0 1.0
C2' A:A2158 4.6 61.4 1.0
C5' A:U2159 4.8 62.2 1.0
O5' A:G2153 4.8 84.5 1.0
O3' A:A2158 4.9 76.2 1.0
N7 A:A2155 5.0 52.7 1.0
C3' A:A2158 5.0 67.5 1.0
O2' A:U2152 5.0 81.0 1.0

Magnesium binding site 2 out of 8 in 5ml7

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Magnesium binding site 2 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2303

b:64.1
occ:1.00
 O A:HOH2402 1.9 31.7 1.0
O A:HOH2401 2.0 51.0 1.0
O A:HOH2406 2.0 25.8 1.0
OP1 A:U2217 2.4 52.6 1.0
O A:HOH2408 2.5 13.3 1.0
P A:U2217 3.7 58.0 1.0
O6 A:G2166 4.0 91.2 1.0
C5' A:U2217 4.1 51.5 1.0
OP2 A:U2217 4.2 63.8 1.0
N6 A:A2164 4.3 61.2 1.0
O5' A:U2217 4.4 55.5 1.0
N1 A:G2166 4.4 94.8 1.0
C6 A:G2166 4.5 90.5 1.0
C4' A:A2216 4.8 59.5 1.0
O6 A:G2165 4.8 52.0 1.0
N7 A:A2164 4.8 70.3 1.0
O3' A:A2216 4.9 57.0 1.0
N7 A:G2165 5.0 86.6 1.0
C5' A:A2216 5.0 61.9 1.0

Magnesium binding site 3 out of 8 in 5ml7

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Magnesium binding site 3 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2304

b:47.0
occ:1.00
 OP2 A:C2187 2.3 0.4 1.0
O A:HOH2409 2.4 59.1 1.0
P A:C2187 3.4 0.7 1.0
N7 A:G2188 3.7 0.6 1.0
O5' A:C2187 3.8 0.6 1.0
C5 A:C2187 3.9 0.2 1.0
OP2 A:G2188 4.0 0.2 1.0
OP1 A:C2187 4.1 0.3 1.0
C6 A:C2187 4.3 0.5 1.0
O6 A:G2188 4.5 0.4 1.0
C8 A:G2188 4.5 0.2 1.0
C5 A:G2188 4.7 0.0 1.0
O3' A:G2186 4.8 0.7 1.0
C5' A:C2187 4.9 0.9 1.0
C4 A:C2187 4.9 0.8 1.0
C6 A:G2188 5.0 0.8 1.0

Magnesium binding site 4 out of 8 in 5ml7

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Magnesium binding site 4 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2301

b:37.8
occ:1.00
 O B:HOH2407 1.8 24.6 1.0
O B:HOH2408 2.1 43.4 1.0
OP1 B:U2217 2.2 46.8 1.0
O B:HOH2410 2.3 43.4 1.0
O B:HOH2406 2.7 38.8 1.0
O B:HOH2404 2.9 13.4 1.0
P B:U2217 3.4 49.6 1.0
O5' B:U2217 3.7 46.9 1.0
OP2 B:U2217 4.0 54.0 1.0
O6 B:G2165 4.3 38.3 1.0
N1 B:G2166 4.4 47.0 1.0
O6 B:G2166 4.4 54.6 1.0
N7 B:A2164 4.4 51.9 1.0
N6 B:A2164 4.4 49.6 1.0
C6 B:G2166 4.7 49.1 1.0
O3' B:A2216 4.7 47.0 1.0
N7 B:G2165 4.8 45.3 1.0
C4' B:A2216 4.8 47.8 1.0
C5' B:U2217 5.0 48.1 1.0
C5' B:A2216 5.0 45.8 1.0

Magnesium binding site 5 out of 8 in 5ml7

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Magnesium binding site 5 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2302

b:26.7
occ:1.00
 O B:HOH2409 1.9 48.4 1.0
OP2 B:C2154 1.9 95.9 1.0
O6 B:G2156 2.1 40.5 1.0
O B:HOH2403 2.7 24.5 1.0
O B:HOH2402 2.8 25.6 1.0
O B:HOH2405 3.1 45.3 1.0
C6 B:G2156 3.2 41.6 1.0
P B:C2154 3.3 96.7 1.0
OP1 B:C2154 3.8 96.2 1.0
N1 B:G2156 4.0 39.2 1.0
O5' B:C2154 4.2 75.5 1.0
C5 B:G2156 4.3 44.6 1.0
O3' B:G2153 4.4 86.2 1.0
O2' B:A2158 4.4 52.0 1.0
N7 B:G2156 4.7 49.4 1.0
OP2 B:A2155 4.7 67.9 1.0
OP2 B:A2160 4.8 51.9 1.0
C3' B:G2153 4.8 80.5 1.0
N7 B:A2155 4.8 33.4 1.0
C5' B:U2159 4.9 47.5 1.0
OP1 B:A2160 4.9 59.6 1.0
C2' B:A2158 5.0 47.6 1.0

Magnesium binding site 6 out of 8 in 5ml7

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Magnesium binding site 6 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2303

b:48.1
occ:1.00
 O2 B:C2209 2.2 59.7 1.0
C2 B:C2209 3.4 54.0 1.0
N3 B:C2209 4.2 55.8 1.0
C1' B:C2209 4.2 52.2 1.0
N1 B:C2209 4.3 50.7 1.0
O2' B:C2209 4.3 58.4 1.0
N6 B:A2208 4.5 34.9 1.0
C2' B:C2209 4.6 55.2 1.0
O4' B:A2210 4.9 57.2 1.0

Magnesium binding site 7 out of 8 in 5ml7

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Magnesium binding site 7 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2304

b:2.1
occ:0.50
 OP2 B:A2167 2.1 50.2 1.0
P B:A2167 3.6 55.6 1.0
O5' B:A2167 4.3 58.5 1.0
OP1 B:A2167 4.4 56.0 1.0
C3' B:G2166 4.5 53.4 1.0
C8 B:A2167 4.5 66.6 1.0
O3' B:G2166 4.6 54.0 1.0
C8 B:G2166 4.7 57.4 1.0
N7 B:A2167 4.8 68.8 1.0
O5' B:G2166 4.8 50.5 1.0
N7 B:G2166 4.9 57.3 1.0

Magnesium binding site 8 out of 8 in 5ml7

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Magnesium binding site 8 out of 8 in the Crystal Structure of L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui


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 L1-Stalk Fragment of 23S Rrna From Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2305

b:36.6
occ:1.00
 OP2 B:G2156 2.4 61.4 1.0
OP2 B:A2158 2.7 85.0 1.0
P B:G2156 3.8 67.0 1.0
N7 B:G2156 3.8 49.4 1.0
OP1 B:A2155 3.9 88.6 1.0
P B:A2158 4.0 79.5 1.0
O5' B:A2155 4.0 62.0 1.0
C8 B:G2156 4.0 54.1 1.0
O5' B:G2156 4.0 71.3 1.0
OP2 B:C2157 4.2 68.3 1.0
O3' B:C2157 4.2 64.5 1.0
P B:A2155 4.3 76.4 1.0
OP2 B:A2155 4.4 67.9 1.0
O B:HOH2403 4.4 24.5 1.0
O3' B:A2155 4.6 60.9 1.0
C3' B:A2155 4.6 61.3 1.0
C5' B:A2155 4.8 59.0 1.0
OP1 B:G2156 4.9 68.4 1.0
OP1 B:A2158 5.0 91.7 1.0
O B:HOH2405 5.0 45.3 1.0

Reference:

A.G.Gabdulkhakov, T.V.Tishchenko, A.Mikhaylina, M.Garber, N.A.Nevskaya, S.V.Nikonov. Crystal Structure of the 23S Rrna Fragment Specific to R-Protein L1 and Designed Model of the Ribosomal L1 Stalk From Haloarcula Marismortui Crystals 2017.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST7020037
Page generated: Sun Sep 29 21:57:10 2024

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