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Magnesium in PDB 1mms: Crystal Structure of the Ribosomal Protein L11-Rna Complex

Protein crystallography data

The structure of Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms was solved by B.T.Wimberly, R.Guymon, J.P.Mccutcheon, S.W.White, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.890, 84.260, 155.510, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.4

Other elements in 1mms:

The structure of Crystal Structure of the Ribosomal Protein L11-Rna Complex also contains other interesting chemical elements:

Cadmium (Cd) 8 atoms
Mercury (Hg) 8 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Ribosomal Protein L11-Rna Complex (pdb code 1mms). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in 1mms

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Magnesium binding site 1 out of 19 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg210

b:32.0
occ:1.00
O C:HOH270 2.3 30.0 1.0
O4 C:U1094 2.3 36.2 1.0
OP2 C:A1073 2.3 35.8 1.0
O C:HOH268 2.4 32.8 1.0
O C:HOH269 2.5 22.9 1.0
O6 C:G1093 3.2 34.5 1.0
C4 C:U1094 3.5 36.2 1.0
P C:A1073 3.6 34.0 1.0
OP2 C:C1097 3.6 24.9 1.0
O C:HOH271 3.7 30.0 1.0
C6 C:G1093 4.0 27.5 1.0
C3' C:C1072 4.0 31.0 1.0
N3 C:U1094 4.0 13.4 1.0
OP1 C:A1073 4.1 23.0 1.0
N1 C:G1093 4.2 19.5 1.0
O3' C:C1072 4.3 33.2 1.0
OP1 C:C1097 4.3 42.4 1.0
C2' C:C1072 4.3 29.8 1.0
P C:C1097 4.4 34.6 1.0
C6 C:C1072 4.5 24.9 1.0
C5 C:U1094 4.6 27.4 1.0
C5 C:C1072 4.7 13.7 1.0
N1 C:C1072 4.8 21.9 1.0
O5' C:A1073 4.8 31.4 1.0
O C:HOH429 4.9 42.5 1.0
OP1 C:A1096 4.9 30.4 1.0

Magnesium binding site 2 out of 19 in 1mms

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Magnesium binding site 2 out of 19 in the Crystal Structure of the Ribosomal Protein L11-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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg215

b:23.1
occ:1.00
O C:HOH424 2.3 36.4 1.0
OP2 C:G1063 2.8 29.1 1.0
O C:HOH425 2.9 50.9 1.0
O3' C:U1061 3.1 23.5 1.0
O2' C:U1061 3.3 33.3 1.0
O5' C:G1062 3.3 14.1 1.0
OP1 C:G1062 3.3 15.0 1.0
OP1 C:A1070 3.3 18.5 1.0
P C:G1062 3.5 27.5 1.0
O5' C:A1070 3.7 30.5 1.0
P C:A1070 4.1 33.1 1.0
C2' C:U1061 4.2 32.3 1.0
C3' C:U1061 4.2 33.1 1.0
P C:G1063 4.2 32.9 1.0
C5' C:G1062 4.3 22.9 1.0
C1' C:U1061 4.5 40.6 1.0
C3' C:G1062 4.6 12.6 1.0
O C:HOH261 4.6 21.4 1.0
O2 C:U1061 4.7 62.3 1.0
O4' C:A1070 4.7 25.3 1.0
O3' C:G1062 4.8 33.2 1.0
C4' C:A1070 4.8 30.0 1.0
C5' C:A1070 4.8 21.1 1.0
OP2 C:G1062 5.0 24.5 1.0

Magnesium binding site 3 out of 19 in 1mms

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Magnesium binding site 3 out of 19 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg223

b:37.0
occ:1.00
N7 C:A1106 2.6 35.9 1.0
N6 C:A1106 2.9 42.6 1.0
O C:HOH232 3.3 46.9 1.0
C5 C:A1106 3.4 35.8 1.0
C6 C:A1106 3.5 33.0 1.0
C8 C:A1106 3.8 43.2 1.0
C5 C:C1105 4.1 31.4 1.0
C4 C:C1105 4.1 26.9 1.0
N4 C:C1105 4.3 32.0 1.0
OP2 C:A1106 4.5 36.4 1.0
O6 C:G1107 4.5 41.9 1.0
C6 C:C1105 4.6 27.2 1.0
C4 C:A1106 4.7 37.4 1.0
N3 C:C1105 4.7 26.5 1.0
N9 C:A1106 4.9 40.1 1.0
N1 C:A1106 4.9 29.0 1.0

Magnesium binding site 4 out of 19 in 1mms

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Magnesium binding site 4 out of 19 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg225

b:41.3
occ:1.00
N7 C:G1051 2.7 63.6 1.0
O C:HOH232 3.3 46.9 1.0
C8 C:G1051 3.7 57.5 1.0
C5 C:G1051 3.7 60.3 1.0
O6 C:G1051 3.8 71.4 1.0
C6 C:G1051 4.1 65.7 1.0
N4 C:C1052 4.4 45.4 1.0
N9 C:G1051 4.9 54.7 1.0
C4 C:G1051 4.9 56.6 1.0

Magnesium binding site 5 out of 19 in 1mms

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Magnesium binding site 5 out of 19 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg226

b:17.2
occ:1.00
OP1 C:A1073 2.6 23.0 1.0
OP2 C:A1070 2.9 18.1 1.0
OP1 C:C1072 3.0 25.8 1.0
O3' C:A1069 3.0 40.7 1.0
O C:HOH259 3.4 29.2 1.0
OP2 C:C1072 3.5 30.5 1.0
P C:C1072 3.5 27.2 1.0
P C:A1070 3.6 33.1 1.0
O5' C:C1072 3.9 16.0 1.0
P C:A1073 4.0 34.0 1.0
C1' C:A1069 4.1 37.6 1.0
C5' C:A1070 4.1 21.1 1.0
O2' C:A1069 4.2 43.6 1.0
MG C:MG257 4.2 18.6 1.0
C3' C:A1069 4.2 37.7 1.0
OP1 C:C1097 4.3 42.4 1.0
O5' C:A1070 4.4 30.5 1.0
N3 C:A1069 4.4 28.5 1.0
N7 C:A1073 4.4 30.5 1.0
C2' C:A1069 4.5 39.7 1.0
O C:HOH270 4.5 30.0 1.0
C5' C:C1072 4.5 23.1 1.0
OP2 C:A1073 4.6 35.8 1.0
O6 C:G1074 4.6 28.8 1.0
C4' C:A1069 4.7 21.9 1.0
O4' C:A1069 4.7 35.6 1.0
N9 C:A1069 4.9 33.8 1.0
O3' C:C1072 4.9 33.2 1.0
OP1 C:A1070 4.9 18.5 1.0
O C:HOH260 4.9 15.6 1.0
C8 C:A1073 5.0 31.1 1.0
O5' C:A1073 5.0 31.4 1.0
C4 C:A1069 5.0 31.8 1.0

Magnesium binding site 6 out of 19 in 1mms

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Magnesium binding site 6 out of 19 in the Crystal Structure of the Ribosomal Protein L11-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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg228

b:49.7
occ:1.00
N7 C:A1084 2.6 33.9 1.0
C8 C:A1084 3.5 38.2 1.0
C5 C:A1084 3.5 35.9 1.0
N6 C:A1084 3.6 38.0 1.0
C6 C:A1084 4.0 34.4 1.0
N6 C:A1085 4.4 26.2 1.0
O C:HOH241 4.4 34.2 1.0
O2' C:U1083 4.6 50.1 1.0
OP1 C:A1084 4.7 46.0 1.0
O3' C:U1083 4.7 53.8 1.0
N9 C:A1084 4.7 38.9 1.0
C4 C:A1084 4.7 36.9 1.0

Magnesium binding site 7 out of 19 in 1mms

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Magnesium binding site 7 out of 19 in the Crystal Structure of the Ribosomal Protein L11-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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg257

b:18.6
occ:1.00
O C:HOH260 2.2 15.6 1.0
OP1 C:C1072 2.2 25.8 1.0
O C:HOH261 2.3 21.4 1.0
O C:HOH259 2.3 29.2 1.0
OP2 C:A1070 2.3 18.1 1.0
O C:HOH258 2.4 22.9 1.0
P C:C1072 3.4 27.2 1.0
P C:A1070 3.7 33.1 1.0
O3' C:G1071 3.7 38.7 1.0
O C:HOH238 3.8 22.3 1.0
O6 C:G1062 4.0 28.3 1.0
O6 C:G1063 4.0 27.3 1.0
OP2 C:C1072 4.2 30.5 1.0
MG C:MG226 4.2 17.2 1.0
O C:HOH209 4.3 28.0 1.0
OP1 C:A1070 4.3 18.5 1.0
O C:HOH424 4.4 36.4 1.0
OP1 C:G1062 4.4 15.0 1.0
O5' C:A1070 4.4 30.5 1.0
N7 C:G1062 4.4 25.5 1.0
N4 C:C1075 4.5 22.6 1.0
O6 C:G1074 4.6 28.8 1.0
C5' C:A1070 4.6 21.1 1.0
O5' C:C1072 4.7 16.0 1.0
C6 C:G1062 4.7 31.7 1.0
O3' C:A1069 4.8 40.7 1.0
N4 C:C1064 4.9 29.0 1.0
C5 C:G1062 4.9 26.3 1.0
C5' C:C1072 4.9 23.1 1.0

Magnesium binding site 8 out of 19 in 1mms

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Magnesium binding site 8 out of 19 in the Crystal Structure of the Ribosomal Protein L11-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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg273

b:35.8
occ:1.00
O C:HOH275 2.3 34.9 1.0
O C:HOH276 2.3 31.1 1.0
O C:HOH277 2.5 31.0 1.0
O C:HOH274 2.5 21.8 1.0
O C:HOH278 2.6 50.0 1.0
O4 C:U1083 3.7 36.0 1.0
O C:HOH432 4.2 46.6 1.0
OP2 C:A1086 4.4 21.0 1.0
O4 C:U1082 4.4 29.5 1.0
C4 C:U1083 4.6 29.9 1.0
OP1 C:G1087 4.6 46.1 1.0
O4 C:U1081 4.7 12.7 1.0
OP1 C:A1086 4.7 32.0 1.0
P C:A1086 5.0 38.4 1.0

Magnesium binding site 9 out of 19 in 1mms

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Magnesium binding site 9 out of 19 in the Crystal Structure of the Ribosomal Protein L11-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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg437

b:47.8
occ:1.00
O C:HOH441 2.3 41.2 1.0
O C:HOH440 2.4 43.6 1.0
O C:HOH438 2.4 58.1 1.0
O C:HOH442 2.4 66.0 1.0
O C:HOH443 2.5 61.7 1.0
N7 C:G1054 3.6 39.3 1.0
O C:HOH243 4.1 61.2 1.0
O6 C:G1054 4.1 27.5 1.0
O6 C:G1056 4.4 52.7 1.0
C5 C:G1054 4.4 34.8 1.0
C8 C:G1054 4.5 35.7 1.0
O6 C:G1055 4.6 27.4 1.0
N7 C:G1055 4.6 32.9 1.0
C6 C:G1054 4.6 30.5 1.0
C5 C:U1053 4.9 39.6 1.0
C6 C:G1056 5.0 42.0 1.0

Magnesium binding site 10 out of 19 in 1mms

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Magnesium binding site 10 out of 19 in the Crystal Structure of the Ribosomal Protein L11-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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg318

b:17.5
occ:1.00
O4 D:U1101 2.4 25.0 1.0
O D:HOH391 2.7 26.1 1.0
O D:HOH305 2.8 14.2 1.0
C4 D:U1101 3.3 36.0 1.0
C5 D:U1101 3.6 24.9 1.0
O6 D:G1071 4.5 34.1 1.0
N3 D:U1101 4.5 17.9 1.0
N4 D:C1100 4.6 35.5 1.0
N4 D:C1102 4.6 15.5 1.0
CD D:CD390 4.6 66.3 1.0
N2 D:G1089 4.7 24.0 1.0
C5 D:C1100 4.8 32.0 1.0
O D:HOH396 4.8 38.7 1.0
C6 D:U1101 4.9 26.9 1.0
C4 D:C1100 5.0 36.2 1.0

Reference:

B.T.Wimberly, R.Guymon, J.P.Mccutcheon, S.W.White, V.Ramakrishnan. A Detailed View of A Ribosomal Active Site: the Structure of the L11-Rna Complex. Cell(Cambridge,Mass.) V. 97 491 1999.
ISSN: ISSN 0092-8674
PubMed: 10338213
DOI: 10.1016/S0092-8674(00)80759-X
Page generated: Mon Dec 14 06:29:18 2020

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