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Magnesium in PDB 3cma: The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma was solved by M.Simonovic, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.79 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.316, 297.905, 573.138, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.5

Other elements in 3cma:

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium (Sr) 107 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 93;

Binding sites:

The binding sites of Magnesium atom in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 93 binding sites of Magnesium where determined in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 93 in 3cma

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Magnesium binding site 1 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8025

b:40.6
occ:1.00
 O 0:HOH4615 2.6 21.1 1.0
O 0:HOH5075 2.6 63.2 1.0
O A:HOH9104 2.7 0.9 1.0
OP1 0:U2115 2.8 26.4 1.0
O 0:HOH3896 2.8 53.0 1.0
O A:HOH9009 3.2 65.1 1.0
O A:ALA196 3.3 26.3 1.0
O A:HOH9002 3.4 61.5 1.0
OP2 0:G2272 3.8 37.5 1.0
O A:HOH8992 3.9 38.1 1.0
P 0:U2115 4.0 25.6 1.0
O 0:HOH4676 4.1 25.0 1.0
OP2 0:C2273 4.2 31.3 1.0
OP2 0:U2115 4.4 26.3 1.0
OP1 0:C2273 4.4 30.9 1.0
C A:ALA196 4.5 24.0 1.0
O A:VAL197 4.6 24.0 1.0
O A:HIS199 4.6 23.5 1.0
C A:VAL197 4.7 23.9 1.0
P 0:C2273 4.7 29.8 1.0
C A:HIS199 4.7 23.5 1.0
CA A:VAL197 4.7 23.1 1.0
O3' 0:C2114 4.7 24.5 1.0
CA A:GLY1 4.9 24.7 1.0
N A:PRO200 4.9 25.0 1.0
CA A:PRO200 5.0 24.8 1.0

Magnesium binding site 2 out of 93 in 3cma

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Magnesium binding site 2 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8051

b:58.3
occ:1.00
 C A:ASP26 2.6 58.8 1.0
NH2 A:ARG120 2.7 28.2 1.0
N A:LEU27 2.7 57.5 1.0
O 0:HOH5237 2.8 97.0 1.0
OP2 0:G1873 2.9 32.8 1.0
CA A:ASP26 3.0 58.4 1.0
OP1 0:G1873 3.0 33.0 1.0
O A:ASP26 3.1 60.3 1.0
P 0:G1873 3.2 32.8 1.0
CA A:LEU27 3.4 56.3 1.0
CZ A:ARG120 3.5 27.8 1.0
CB A:ASP26 3.5 59.9 1.0
NH1 A:ARG120 3.6 27.8 1.0
C A:LEU27 3.6 57.3 1.0
O3' 0:C1872 3.6 33.0 1.0
O A:LEU27 3.7 57.1 1.0
CB A:LEU27 3.8 55.1 1.0
CG A:LEU27 4.0 53.1 1.0
N A:GLU28 4.2 59.0 1.0
N A:ASP26 4.3 57.7 1.0
O 0:HOH6053 4.3 37.1 1.0
O A:ALA25 4.5 57.5 1.0
CG A:ASP26 4.5 60.8 1.0
NE A:ARG120 4.7 28.1 1.0
O A:HOH9037 4.7 40.6 1.0
CG A:GLU28 4.7 66.3 1.0
O 0:HOH9693 4.7 0.2 1.0
O5' 0:G1873 4.8 34.8 1.0
SR A:SR8930 4.8 72.4 1.0
C A:ALA25 4.8 57.1 1.0
CD1 A:LEU27 4.8 52.6 1.0
C3' 0:C1872 4.9 36.0 1.0
OD2 A:ASP26 5.0 62.5 1.0

Magnesium binding site 3 out of 93 in 3cma

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Magnesium binding site 3 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg8042

b:92.1
occ:1.00
 O B:HOH9151 2.6 57.8 1.0
O B:HOH9110 2.7 74.4 1.0
O U:HOH2221 3.2 54.1 1.0
O 0:HOH9675 3.4 62.2 1.0
OXT B:GLY337 3.4 57.0 1.0
O B:HOH9152 3.5 0.7 1.0
O B:HOH9026 3.5 40.8 1.0
C B:GLY337 4.2 55.5 1.0
O B:HOH9039 4.4 81.2 1.0
O 0:HOH4590 4.6 0.1 1.0
O B:GLY337 4.6 56.2 1.0
OE2 B:GLU333 4.7 60.4 1.0
O U:CYS32 4.7 44.4 1.0
CB U:SER33 4.8 42.0 1.0
O U:HOH3194 5.0 87.2 1.0
OE1 B:GLU333 5.0 58.7 1.0

Magnesium binding site 4 out of 93 in 3cma

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Magnesium binding site 4 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg8012

b:13.4
occ:1.00
 O C:HOH8663 2.4 32.9 1.0
OP2 0:G456 2.4 28.0 1.0
O C:HOH8561 2.5 71.1 1.0
O 0:HOH4510 2.5 46.9 1.0
O 0:HOH3336 2.5 29.9 1.0
O 0:HOH9556 2.6 28.4 1.0
O C:GLY86 3.0 32.4 1.0
P 0:G456 3.8 29.9 1.0
C C:LYS85 3.8 27.1 1.0
CA C:LYS85 4.0 27.4 1.0
C C:GLY86 4.1 30.6 1.0
OP1 0:A455 4.1 24.4 1.0
O C:LYS85 4.1 28.2 1.0
O 0:HOH6259 4.1 36.7 1.0
N C:GLY86 4.1 27.6 1.0
OP2 0:G458 4.2 29.8 1.0
OP1 0:G456 4.3 28.6 1.0
O 0:HOH4296 4.4 62.9 1.0
O5' 0:G456 4.5 30.2 1.0
O 0:HOH3379 4.6 42.5 1.0
N C:LYS85 4.6 27.9 1.0
CA C:GLY86 4.7 29.6 1.0
OP2 0:U457 4.8 24.4 1.0
O3' 0:A455 4.9 28.7 1.0
P 0:A455 4.9 24.9 1.0
OP2 0:A455 5.0 26.8 1.0

Magnesium binding site 5 out of 93 in 3cma

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Magnesium binding site 5 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg8054

b:18.9
occ:1.00
 O 0:HOH5126 2.6 62.8 1.0
OD1 K:ASN42 2.7 25.7 1.0
O 0:HOH6896 2.7 78.6 1.0
O 0:HOH9679 2.7 79.4 1.0
O K:HOH2121 2.7 33.6 1.0
O 0:HOH4319 2.8 18.8 1.0
O 0:HOH5562 3.3 67.5 1.0
O 0:HOH9557 3.3 0.8 1.0
O 0:HOH6399 3.8 80.9 1.0
CG K:ASN42 3.9 25.2 1.0
OP1 0:A2583 4.2 27.4 1.0
OP1 0:U1749 4.6 24.4 1.0
CA K:ASN42 4.6 26.9 1.0
OP2 0:G2584 4.7 27.3 1.0
ND2 K:ASN42 4.8 25.2 1.0
CB K:ASN42 4.8 25.3 1.0
N K:ASN42 4.8 28.2 1.0
OP1 0:U2546 4.9 24.8 1.0

Magnesium binding site 6 out of 93 in 3cma

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Magnesium binding site 6 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg8057

b:65.1
occ:1.00
 O T:HOH2868 2.4 31.4 1.0
O T:ASP117 2.5 0.1 1.0
O T:SER114 2.7 94.9 1.0
O T:LEU112 2.9 71.6 1.0
O T:ARG111 3.0 65.7 1.0
OE1 T:GLN37 3.0 60.0 1.0
C T:ASP117 3.3 0.3 1.0
CA T:SER118 3.4 0.3 1.0
C T:LEU112 3.6 72.5 1.0
OG T:SER114 3.6 93.0 1.0
C T:SER114 3.6 94.4 1.0
N T:SER118 3.7 0.0 1.0
N T:SER114 4.0 85.3 1.0
CA T:LEU112 4.0 70.4 1.0
CD T:GLN37 4.0 58.2 1.0
C T:ARG111 4.1 65.7 1.0
CA T:SER114 4.3 90.6 1.0
C T:SER118 4.3 0.9 1.0
CG T:GLN37 4.3 57.8 1.0
CB T:SER118 4.4 0.9 1.0
N T:GLU115 4.4 98.8 1.0
CB T:SER114 4.5 90.6 1.0
N T:LEU112 4.5 67.7 1.0
N T:GLU113 4.5 75.6 1.0
CA T:ASP117 4.5 0.9 1.0
N T:ALA119 4.5 0.1 1.0
CA T:GLU115 4.6 0.8 1.0
C T:GLU113 4.6 81.4 1.0
O T:TYR35 4.7 59.0 1.0
N T:ASP117 4.7 0.1 1.0
C T:GLU115 5.0 0.0 1.0
CA T:GLU113 5.0 79.3 1.0
CB T:ASP117 5.0 0.8 1.0

Magnesium binding site 7 out of 93 in 3cma

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Magnesium binding site 7 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg8086

b:46.8
occ:1.00
 O Y:HIS133 2.6 29.0 1.0
O Y:VAL139 2.7 27.1 1.0
O Y:HOH8890 2.8 36.4 1.0
O Y:LYS136 2.8 29.2 1.0
O Y:HOH8868 3.0 31.0 1.0
CA Y:LYS137 3.5 27.4 1.0
C Y:LYS136 3.7 27.6 1.0
C Y:VAL139 3.7 27.1 1.0
O Y:LYS137 3.7 26.9 1.0
C Y:HIS133 3.8 28.9 1.0
O Y:HOH8928 3.8 39.1 1.0
C Y:LYS137 3.8 26.6 1.0
N Y:LYS137 4.0 27.5 1.0
N Y:VAL139 4.2 25.8 1.0
CA Y:VAL139 4.5 26.1 1.0
CA Y:HIS133 4.6 29.4 1.0
N Y:SER140 4.6 28.4 1.0
CB Y:LYS137 4.7 28.4 1.0
CD2 Y:HIS133 4.7 27.8 1.0
O Y:HOH8841 4.7 24.3 1.0
N Y:HIS134 4.8 27.6 1.0
N Y:ARG138 4.8 25.7 1.0
CA Y:SER140 4.8 28.9 1.0
CB Y:HIS133 4.8 29.5 1.0
CA Y:HIS134 4.9 26.9 1.0
CB Y:VAL139 4.9 24.4 1.0
CA Y:LYS136 4.9 26.4 1.0
N Y:LYS136 4.9 26.0 1.0
CG Y:LYS137 4.9 31.6 1.0

Magnesium binding site 8 out of 93 in 3cma

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Magnesium binding site 8 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg8060

b:42.5
occ:1.00
 O 0:HOH9632 2.6 26.0 1.0
O 0:HOH7679 2.7 56.0 1.0
O 0:HOH9682 2.8 55.9 1.0
O 2:HOH7875 3.3 67.5 1.0
O 0:HOH9681 3.6 30.0 1.0
O 0:HOH9631 4.0 46.1 1.0
O 0:HOH5026 4.5 47.7 1.0
OD2 2:ASP15 4.7 55.6 1.0
OD1 2:ASP15 4.8 55.7 1.0
N7 0:G1443 4.8 38.5 1.0

Magnesium binding site 9 out of 93 in 3cma

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Magnesium binding site 9 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8001

b:22.6
occ:1.00
 O 0:HOH3095 2.4 1.0 1.0
OP2 0:C2534 2.5 34.1 1.0
OP2 0:C2533 2.5 33.5 1.0
OP2 0:A2483 2.7 37.2 1.0
O 0:HOH9570 2.7 48.1 1.0
O 0:HOH4504 2.7 83.1 1.0
O3' 0:G2482 3.2 36.2 1.0
P 0:A2483 3.5 37.3 1.0
O2' 0:A2532 3.6 37.5 1.0
O 0:HOH3558 3.7 53.5 1.0
O 0:HOH7210 3.7 0.5 1.0
P 0:C2533 3.8 37.0 1.0
O2' 0:G2482 3.9 34.0 1.0
P 0:C2534 3.9 32.8 1.0
O3' 0:A2532 4.0 34.8 1.0
C3' 0:G2482 4.5 34.9 1.0
OP1 0:A2483 4.5 34.9 1.0
OP2 0:U2484 4.5 44.4 1.0
OP2 0:A2485 4.6 38.5 1.0
C2' 0:G2482 4.6 33.5 1.0
OP1 0:C2534 4.7 33.9 1.0
O5' 0:A2483 4.7 37.0 1.0
O3' 0:C2533 4.7 31.9 1.0
O5' 0:C2533 4.7 33.2 1.0
C1' 0:G2482 4.7 33.4 1.0
C2' 0:A2532 4.7 35.2 1.0
O5' 0:C2534 4.8 32.9 1.0
C5' 0:A2483 4.8 34.8 1.0
C3' 0:C2533 4.9 30.7 1.0
O 0:HOH5208 4.9 14.7 1.0
N3 0:G2482 4.9 29.4 1.0
C3' 0:A2532 4.9 35.1 1.0
OP1 0:C2533 5.0 37.3 1.0

Magnesium binding site 10 out of 93 in 3cma

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Magnesium binding site 10 out of 93 in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8002

b:62.8
occ:1.00
 OP1 0:A2483 2.4 34.9 1.0
O6 0:G627 2.5 32.4 1.0
O 0:HOH9550 2.6 1.0 1.0
O 0:HOH9549 2.7 0.9 1.0
O 0:HOH3178 2.9 35.1 1.0
O 0:HOH5208 3.0 14.7 1.0
O2' 0:U625 3.3 24.0 1.0
O 0:HOH4422 3.7 35.6 1.0
P 0:A2483 3.7 37.3 1.0
C6 0:G627 3.7 30.4 1.0
O 0:HOH7921 3.7 67.5 1.0
OP1 0:C2534 3.7 33.9 1.0
O 0:HOH6726 3.9 63.1 1.0
O5' 0:A2483 4.1 37.0 1.0
OP2 0:A2483 4.4 37.2 1.0
C5 0:G627 4.5 29.6 1.0
N7 0:G627 4.5 28.7 1.0
O 0:HOH4026 4.5 54.1 1.0
C2' 0:U625 4.5 25.1 1.0
C5 0:U626 4.6 32.1 1.0
C4' 0:U625 4.6 26.6 1.0
N1 0:G627 4.8 29.1 1.0
O4 0:U626 4.8 33.6 1.0
O3' 0:U625 4.8 26.8 1.0
O3' 0:G2482 4.9 36.2 1.0
C1' 0:U625 4.9 24.6 1.0

Reference:

M.Simonovic, T.A.Steitz. Peptidyl-Cca Deacylation on the Ribosome Promoted By Induced Fit and the O3'-Hydroxyl Group of A76 of the Unacylated A-Site Trna. Rna V. 14 2372 2008.
ISSN: ISSN 1355-8382
PubMed: 18818369
DOI: 10.1261/RNA.1118908
Page generated: Wed Aug 14 11:26:23 2024

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