Magnesium in PDB 8cgv: Tiamulin Bound to the 50S Subunit

Other elements in 8cgv:

The structure of Tiamulin Bound to the 50S Subunit also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Potassium (K) 83 atoms
Fluorine (F) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 219 in 8cgv

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Magnesium binding site 1 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3004

b:17.0
occ:1.00
OP2 a:C946 2.0 20.2 1.0
OP2 a:A945 2.0 17.9 1.0
O a:HOH8108 2.1 21.1 1.0
O a:HOH7616 2.1 19.3 1.0
O a:HOH6554 2.1 20.6 1.0
O a:HOH8141 2.1 19.2 1.0
P a:A945 3.3 16.1 1.0
P a:C946 3.3 18.0 1.0
O3' a:C944 3.5 17.4 1.0
O a:HOH7942 4.0 34.9 1.0
OP1 a:C946 4.0 20.7 1.0
O a:HOH7991 4.0 34.2 1.0
O5' a:C946 4.1 18.2 1.0
O5' a:A945 4.2 18.9 1.0
C5' a:A945 4.2 19.6 1.0
O a:HOH6872 4.3 26.9 1.0
O2' a:C944 4.3 19.5 1.0
OP2 a:G822 4.3 19.8 1.0
O a:HOH7283 4.3 36.0 1.0
C4' a:A945 4.3 19.2 1.0
O3' a:A945 4.4 18.9 1.0
OP1 a:A945 4.5 18.1 1.0
O2' a:A821 4.5 17.8 1.0
O a:HOH6917 4.5 26.9 1.0
O a:HOH8387 4.5 17.0 1.0
O3' a:A821 4.5 18.9 1.0
C3' a:A945 4.7 19.4 1.0
C3' a:C944 4.8 17.5 1.0

Magnesium binding site 2 out of 219 in 8cgv

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Magnesium binding site 2 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3005

b:37.8
occ:1.00
O a:HOH8851 2.0 41.8 1.0
O a:HOH8874 2.1 44.5 1.0
O a:HOH8895 2.1 40.0 1.0
O a:HOH4269 2.1 33.3 1.0
O a:HOH7427 2.1 34.9 1.0
O a:HOH5784 2.1 33.5 1.0
N7 a:G493 4.1 27.4 1.0
O a:HOH7538 4.2 42.7 1.0
O6 a:G493 4.3 26.5 1.0
OP2 a:A492 4.3 34.8 1.0
N7 a:G494 4.4 26.2 1.0
O6 a:G494 4.5 27.6 1.0
O a:HOH4571 4.7 38.9 1.0
C5 a:G493 4.8 25.4 1.0
C6 a:G493 4.9 24.6 1.0

Magnesium binding site 3 out of 219 in 8cgv

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Magnesium binding site 3 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3006

b:26.0
occ:1.00
O a:HOH8711 2.0 29.0 1.0
O a:HOH7619 2.1 29.3 1.0
O a:HOH4689 2.1 36.4 1.0
O a:HOH4551 2.1 31.0 1.0
O a:HOH3409 2.1 29.5 1.0
O a:HOH5111 2.1 33.2 1.0
O a:HOH8620 3.9 46.0 1.0
OP2 a:A28 4.1 23.6 1.0
O6 a:G474 4.1 22.4 1.0
O4 a:U29 4.3 21.3 1.0
OP2 a:A447 4.3 26.0 1.0
O6 a:G30 4.3 20.7 1.0
C5 a:U29 4.3 20.3 1.0
O a:HOH6259 4.4 38.0 1.0
O a:HOH6093 4.4 43.9 1.0
O6 a:G473 4.4 24.4 1.0
OP2 a:U29 4.5 22.6 1.0
C4 a:U29 4.6 19.5 1.0
N4 a:C31 4.6 19.2 1.0
O p:HOH317 4.7 46.9 1.0
O a:HOH3455 4.8 29.3 1.0
O2' a:A447 4.9 22.0 1.0

Magnesium binding site 4 out of 219 in 8cgv

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Magnesium binding site 4 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3007

b:40.0
occ:1.00
O a:HOH4305 2.0 36.2 1.0
OP2 a:A218 2.1 37.1 1.0
O a:HOH7522 2.1 39.9 1.0
O a:HOH5278 2.1 39.8 1.0
O a:HOH8274 2.1 42.4 1.0
O a:HOH6492 2.1 41.0 1.0
P a:A218 3.5 36.1 1.0
N6 a:A219 4.0 35.4 1.0
O5' a:A218 4.1 39.1 1.0
N7 a:A218 4.2 36.0 1.0
OP1 a:A428 4.2 44.9 1.0
N7 a:A219 4.3 33.8 1.0
OP1 a:A218 4.3 43.6 1.0
O6 a:G220 4.4 34.5 1.0
C8 a:A218 4.4 35.9 1.0
O5' a:A217 4.5 36.3 1.0
O3' a:A217 4.6 36.5 1.0
OP1 a:A217 4.7 40.1 1.0
OP2 a:U427 4.7 48.0 1.0
OP2 a:A217 4.8 38.8 1.0
C3' a:A217 4.8 35.5 1.0
P a:A217 4.9 37.0 1.0
C6 a:A219 4.9 34.1 1.0
C5 a:A219 5.0 33.5 1.0

Magnesium binding site 5 out of 219 in 8cgv

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Magnesium binding site 5 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3008

b:39.5
occ:1.00
OP1 a:U419 2.0 33.7 1.0
O a:HOH7998 2.0 40.3 1.0
O a:HOH6694 2.0 44.2 1.0
O a:HOH8845 2.1 47.2 1.0
O a:HOH5330 2.1 43.2 1.0
O a:HOH6045 2.1 38.8 1.0
P a:U419 3.4 30.6 1.0
O3' a:C418 3.9 30.0 1.0
C5' a:U419 4.0 29.2 1.0
O a:HOH5754 4.0 53.1 1.0
O5' a:U419 4.1 31.8 1.0
N7 a:G230 4.1 33.5 1.0
O a:HOH4577 4.2 49.9 1.0
O a:HOH7817 4.3 35.5 1.0
O a:HOH5467 4.4 33.1 1.0
OP2 a:U419 4.5 34.6 1.0
C8 a:G230 4.7 34.8 1.0

Magnesium binding site 6 out of 219 in 8cgv

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Magnesium binding site 6 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3009

b:16.7
occ:1.00
OP2 a:G450 1.9 19.5 1.0
O a:HOH4417 2.1 20.1 1.0
O a:HOH7594 2.1 18.5 1.0
O a:HOH7947 2.1 19.1 1.0
O e:HOH436 2.1 18.4 1.0
O a:HOH4431 2.1 18.4 1.0
P a:G450 3.4 17.8 1.0
O e:GLY81 3.8 19.4 1.0
O a:HOH3443 3.8 30.8 1.0
O a:HOH3964 4.0 22.3 1.0
OP2 a:G452 4.0 23.3 1.0
O a:HOH8496 4.0 39.0 1.0
O5' a:G450 4.1 17.8 1.0
OP1 a:G450 4.2 20.2 1.0
OP1 a:A449 4.2 20.8 1.0
OP2 a:U451 4.3 22.4 1.0
O e:SER80 4.3 20.8 1.0
O3' a:A449 4.4 18.6 1.0
C e:SER80 4.5 18.8 1.0
O a:HOH8661 4.6 32.3 1.0
OP2 a:A449 4.6 20.7 1.0
CA e:SER80 4.7 18.9 1.0
O5' a:A449 4.7 19.1 1.0
P a:A449 4.7 18.5 1.0
C3' a:A449 4.8 17.9 1.0
C e:GLY81 4.9 19.1 1.0

Magnesium binding site 7 out of 219 in 8cgv

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Magnesium binding site 7 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3010

b:15.5
occ:1.00
O6 a:G450 2.0 16.2 1.0
OP1 a:A453 2.0 17.9 1.0
O a:HOH8099 2.1 16.6 1.0
O a:HOH7665 2.1 16.1 1.0
O a:HOH7017 2.1 16.2 1.0
O a:HOH6056 2.1 15.6 1.0
C6 a:G450 3.1 16.3 1.0
P a:A453 3.3 17.1 1.0
C5 a:G450 3.9 16.9 1.0
N7 a:G450 3.9 18.4 1.0
K a:K3259 3.9 24.5 1.0
O a:HOH8768 4.0 28.5 1.0
OP2 a:A453 4.0 18.4 1.0
O a:HOH3302 4.0 28.9 1.0
O5' a:A453 4.1 19.0 1.0
O a:HOH3421 4.1 25.6 1.0
N7 a:A449 4.2 17.9 1.0
C5' a:A453 4.2 19.1 1.0
N1 a:G450 4.3 16.5 1.0
O a:HOH8661 4.3 32.3 1.0
O a:HOH4789 4.4 22.0 1.0
OP1 a:A454 4.4 23.1 1.0
O3' a:G452 4.4 18.4 1.0
OP2 a:A449 4.5 20.7 1.0
O a:HOH3443 4.6 30.8 1.0
N6 a:A449 4.7 19.0 1.0
O a:HOH3659 4.7 35.1 1.0
C5' a:U448 4.8 21.3 1.0

Magnesium binding site 8 out of 219 in 8cgv

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Magnesium binding site 8 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3011

b:23.4
occ:1.00
OP1 a:A526 1.9 26.1 1.0
OP1 a:C527 2.0 24.7 1.0
O a:HOH7258 2.0 27.7 1.0
O a:HOH5235 2.1 25.2 1.0
O a:HOH7781 2.1 27.6 1.0
O a:HOH7661 2.1 28.4 1.0
P a:A526 3.3 22.5 1.0
P a:C527 3.4 21.6 1.0
OP2 a:A526 4.0 23.4 1.0
O5' a:A526 4.0 23.7 1.0
OP2 a:C527 4.2 24.6 1.0
O5' a:C527 4.2 22.6 1.0
OP1 a:A528 4.3 25.2 1.0
C5' a:A526 4.4 23.4 1.0
O3' a:A526 4.4 22.9 1.0
O3' a:U525 4.4 24.0 1.0
O a:HOH5107 4.4 44.4 1.0
C5' a:C527 4.5 22.4 1.0
C3' a:A526 4.6 22.1 1.0
O a:HOH6770 4.7 43.1 1.0
C3' a:C527 4.8 22.7 1.0

Magnesium binding site 9 out of 219 in 8cgv

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Magnesium binding site 9 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3012

b:27.0
occ:1.00
O a:HOH5141 2.1 29.6 1.0
O a:HOH8883 2.1 30.0 1.0
O a:HOH5253 2.1 26.2 1.0
O a:HOH7868 2.1 28.9 1.0
O a:HOH3911 2.1 26.4 1.0
O a:HOH7496 2.1 31.4 1.0
O a:HOH4554 3.8 35.1 1.0
O a:HOH7125 3.8 32.9 1.0
O a:HOH5962 4.0 38.8 1.0
O a:HOH8897 4.2 46.2 1.0
OP2 a:C560 4.2 25.9 1.0
OP1 a:A1008 4.2 24.8 1.0
O a:HOH7345 4.2 33.4 1.0
OP1 a:C560 4.2 26.2 1.0
O a:HOH8585 4.4 39.6 1.0
O a:HOH7586 4.4 32.4 1.0
O i:HOH206 4.5 52.3 1.0
OP1 a:G2038 4.5 22.9 1.0
OP1 a:G559 4.5 26.0 1.0
P a:C560 4.6 22.8 1.0
O a:HOH4508 4.8 41.4 1.0

Magnesium binding site 10 out of 219 in 8cgv

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Magnesium binding site 10 out of 219 in the Tiamulin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tiamulin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3013

b:13.7
occ:1.00
OP1 a:U567 2.0 15.5 1.0
O a:HOH7622 2.1 16.2 1.0
O a:HOH5993 2.1 15.8 1.0
O a:HOH3833 2.1 16.6 1.0
O a:HOH6736 2.1 16.2 1.0
O a:HOH7645 2.1 15.4 1.0
P a:U567 3.3 15.3 1.0
O3' a:U566 3.7 16.3 1.0
O a:HOH8184 4.0 19.1 1.0
O4 a:U810 4.1 17.8 1.0
OP2 a:G808 4.2 18.6 1.0
C5' a:U567 4.2 16.6 1.0
O5' a:U567 4.2 16.2 1.0
N7 a:G809 4.3 15.6 1.0
O a:HOH6718 4.3 17.4 1.0
OP2 a:G809 4.4 18.4 1.0
O k:HOH214 4.4 19.3 1.0
OP2 a:U567 4.4 17.8 1.0
ND1 k:HIS35 4.5 26.9 1.0
O a:HOH7558 4.6 30.4 1.0
C8 a:G809 4.9 15.8 1.0
CE1 k:HIS35 4.9 28.4 1.0
O a:HOH6177 5.0 23.7 1.0

Reference:

H.Paternoga, C.Crowe-Mcauliffe, L.V.Bock, T.O.Koller, M.Morici, B.Beckert, A.G.Myasnikov, H.Grubmueller, J.Novacek, D.N.Wilson. Structural Conservation of Antibiotic Interaction with Ribosomes To Be Published.
Page generated: Thu Oct 3 21:31:51 2024

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