Magnesium in PDB 7a0s: 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I

Protein crystallography data

The structure of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I, PDB code: 7a0s was solved by E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.67 / 3.22
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 169.995, 410.736, 697.778, 90, 90, 90
R / Rfree (%) 22.4 / 25.3

Other elements in 7a0s:

The structure of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I also contains other interesting chemical elements:

Sodium (Na) 1 atom
Calcium (Ca) 5 atoms
Potassium (K) 1 atom

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 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 310; Page 32, Binding sites: 311 - 320; Page 33, Binding sites: 321 - 330; Page 34, Binding sites: 331 - 340; Page 35, Binding sites: 341 - 350; Page 36, Binding sites: 351 - 360; Page 37, Binding sites: 361 - 367;

Binding sites:

The binding sites of Magnesium atom in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I (pdb code 7a0s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 367 binding sites of Magnesium where determined in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I, PDB code: 7a0s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 367 in 7a0s

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Magnesium binding site 1 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2902

b:105.5
occ:1.00
OP1 X:U2057 2.4 104.9 1.0
OP2 X:G2218 3.0 115.0 1.0
P X:U2057 3.7 104.4 1.0
OP2 X:U2219 3.8 116.0 1.0
P X:G2218 4.2 117.2 1.0
OP2 X:U2057 4.2 104.7 1.0
O A:PRO228 4.2 105.0 1.0
O5' X:G2218 4.3 117.8 1.0
OP1 X:U2219 4.4 114.5 1.0
CA A:PRO232 4.5 109.1 1.0
O5' X:U2057 4.5 104.8 1.0
O3' X:G2217 4.5 116.4 1.0
P X:U2219 4.6 116.0 1.0
C5' X:G2218 4.7 119.6 1.0
OP2 X:U2058 4.8 109.7 1.0
O2' X:G2217 4.8 115.2 1.0
CB A:PRO232 4.8 110.1 1.0
O3' X:C2056 4.8 103.4 1.0
CG A:PRO232 4.9 110.3 1.0
N A:PRO232 4.9 108.9 1.0

Magnesium binding site 2 out of 367 in 7a0s

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Magnesium binding site 2 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2903

b:89.2
occ:1.00
OP1 X:U800 1.9 91.2 1.0
OP2 X:C803 2.3 101.1 1.0
P X:U800 3.2 92.0 1.0
P X:C803 3.5 100.3 1.0
OP2 X:U800 3.8 92.2 1.0
OP1 X:C803 3.9 100.1 1.0
O3' X:C799 4.1 90.8 1.0
C5' X:A802 4.2 94.1 1.0
OP2 X:C804 4.2 95.5 1.0
O3' X:A802 4.4 92.8 1.0
O5' X:U800 4.4 92.8 1.0
N6 X:A1771 4.4 92.9 1.0
C4' X:A802 4.4 93.3 1.0
C3' X:A802 4.6 93.1 1.0
O5' X:C803 4.7 100.1 1.0
N7 X:A1771 4.9 92.2 1.0
C5' X:C803 4.9 100.7 1.0
C6 X:A1771 5.0 92.2 1.0

Magnesium binding site 3 out of 367 in 7a0s

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Magnesium binding site 3 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2904

b:62.1
occ:1.00
OP1 X:U2000 2.5 82.0 1.0
P X:U2000 3.9 81.7 1.0
OP2 X:A587 4.0 84.4 1.0
OP2 X:U2000 4.4 81.7 1.0
OP1 X:A2041 4.5 81.3 1.0
OP2 X:G2001 4.7 83.4 1.0
O5' X:U2000 4.7 81.9 1.0
OP2 X:G586 4.8 85.0 1.0

Magnesium binding site 4 out of 367 in 7a0s

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Magnesium binding site 4 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2905

b:84.6
occ:1.00
OP1 X:U823 2.0 93.3 1.0
N7 X:G1266 2.6 92.0 1.0
P X:U823 3.3 93.3 1.0
C8 X:G1266 3.5 91.4 1.0
OP2 X:U823 3.6 93.4 1.0
C5 X:G1266 3.7 91.5 1.0
O6 X:G1266 3.9 92.6 1.0
OP1 X:U824 4.1 96.2 1.0
C6 X:G1266 4.2 91.8 1.0
O5' X:U823 4.2 94.1 1.0
O3' X:G822 4.5 92.4 1.0
O2' X:C574 4.5 91.6 1.0
C5' X:U824 4.6 96.1 1.0
N9 X:G1266 4.7 90.5 1.0
O3' X:C574 4.8 93.4 1.0
O2' X:G1265 4.8 91.6 1.0
C4 X:G1266 4.8 90.6 1.0
C5' X:U823 4.9 94.1 1.0

Magnesium binding site 5 out of 367 in 7a0s

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Magnesium binding site 5 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2906

b:94.6
occ:1.00
OP2 X:A743 2.3 101.4 1.0
OP1 X:A774 2.4 94.7 0.4
OP2 X:C744 2.6 100.2 1.0
OP1 X:G776 3.4 104.0 1.0
P X:A774 3.5 93.8 0.4
C5' X:A774 3.5 94.4 0.4
O5' X:A774 3.6 94.1 0.4
P X:A743 3.8 102.1 1.0
P X:C744 4.0 100.2 1.0
O3' X:G742 4.2 102.7 1.0
OP1 X:U775 4.2 101.1 1.0
C5' X:U775 4.2 102.5 1.0
OP2 X:A774 4.3 93.1 0.4
C5' X:A743 4.3 103.4 1.0
C3' X:A743 4.5 102.2 1.0
O5' X:A743 4.6 103.1 1.0
O3' X:A743 4.6 101.5 1.0
OP1 X:A743 4.7 101.6 1.0
OP1 X:C744 4.7 99.7 1.0
O3' X:G773 4.8 96.6 1.0
P X:G776 4.8 105.0 1.0
O5' X:G776 4.8 104.6 1.0

Magnesium binding site 6 out of 367 in 7a0s

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Magnesium binding site 6 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2907

b:75.7
occ:1.00
OP2 X:G2039 2.6 82.5 1.0
OP2 X:A2040 2.7 82.9 1.0
N6 X:A2041 3.4 80.7 1.0
P X:G2039 3.6 83.0 1.0
OP1 X:G2039 3.7 83.5 1.0
P X:A2040 4.1 82.9 1.0
OP1 X:G2484 4.3 86.8 1.0
O5' X:G2039 4.4 82.7 1.0
N7 X:A2041 4.4 80.4 1.0
O2' X:A2482 4.4 82.7 1.0
C6 X:A2041 4.5 80.5 1.0
N7 X:A2040 4.5 81.3 1.0
O5' X:A2040 4.6 82.4 1.0
N6 X:A2042 4.6 81.7 1.0
C8 X:A2040 4.7 81.3 1.0
C3' X:A2482 4.8 83.5 1.0
OP1 X:A2040 4.8 83.4 1.0
C5 X:A2041 4.8 80.3 1.0
C2' X:A2482 4.9 83.2 1.0
O3' X:A2482 4.9 83.7 1.0
OP2 X:A2482 5.0 83.3 1.0

Magnesium binding site 7 out of 367 in 7a0s

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Magnesium binding site 7 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2908

b:49.8
occ:1.00
O6 X:G2699 3.6 77.9 1.0
O4 X:U2693 4.4 76.6 1.0
O6 X:G2698 4.5 78.3 1.0
N7 X:G2697 4.5 79.1 1.0
O6 X:G2697 4.6 78.6 1.0
C6 X:G2699 4.6 78.1 1.0
N7 X:G2698 4.7 79.1 1.0
C4 X:U2693 4.9 76.4 1.0
N3 X:U2693 4.9 76.5 1.0

Magnesium binding site 8 out of 367 in 7a0s

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Magnesium binding site 8 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2909

b:68.6
occ:1.00
OP2 X:C1340 2.0 79.5 1.0
P X:C1340 3.2 79.4 1.0
OP1 X:C1340 3.4 79.8 1.0
N7 X:G1337 3.6 83.1 1.0
C8 X:G1337 3.9 82.7 1.0
O6 X:G1341 4.0 81.4 1.0
OP1 X:U1339 4.0 78.8 1.0
OP2 X:U1339 4.0 78.7 1.0
O5' X:C1340 4.0 79.5 1.0
N7 X:G1341 4.2 82.1 1.0
P X:U1339 4.4 78.5 1.0
O3' X:U1339 4.5 78.9 1.0
C5 X:G1337 4.6 83.2 1.0
C6 X:G1341 4.8 81.6 1.0
C5 X:G1341 4.9 81.9 1.0
N9 X:G1337 5.0 82.6 1.0

Magnesium binding site 9 out of 367 in 7a0s

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Magnesium binding site 9 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2910

b:70.1
occ:1.00
OP1 X:G2665 4.0 80.5 1.0
OP2 X:U2666 4.1 78.9 1.0
OP1 X:U2666 4.6 78.5 1.0
OP2 X:G2698 4.8 80.1 1.0
P X:U2666 4.8 78.6 1.0

Magnesium binding site 10 out of 367 in 7a0s

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Magnesium binding site 10 out of 367 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2911

b:59.7
occ:1.00
OP1 X:G2557 4.0 77.5 1.0
OP2 X:A2034 4.1 77.0 1.0
OP1 X:U2592 4.2 76.6 1.0
OP2 X:G2557 4.3 77.1 1.0
N7 X:A2034 4.4 77.6 1.0
N7 X:A2593 4.4 77.5 1.0
OP1 X:C2033 4.6 76.2 1.0
P X:G2557 4.6 77.4 1.0
NH1 B:ARG137 4.7 84.6 1.0
OP2 X:A2593 4.8 76.4 1.0
C8 X:A2034 4.8 77.8 1.0
C8 X:A2593 5.0 77.4 1.0

Reference:

E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I To Be Published.
Page generated: Sat Aug 21 15:13:55 2021

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