Atomistry » Magnesium » PDB 5mh5-5ms0 » 5ml7
Atomistry »
  Magnesium »
    PDB 5mh5-5ms0 »
      5ml7 »

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

Go back to Magnesium Binding Sites List in 5ml7
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

Go back to Magnesium Binding Sites List in 5ml7
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

Go back to Magnesium Binding Sites List in 5ml7
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

Go back to Magnesium Binding Sites List in 5ml7
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

Go back to Magnesium Binding Sites List in 5ml7
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

Go back to Magnesium Binding Sites List in 5ml7
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

Go back to Magnesium Binding Sites List in 5ml7
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

Go back to Magnesium Binding Sites List in 5ml7
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy