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Magnesium in PDB 8cam: Evernimicin Bound to the 50S Subunit

Other elements in 8cam:

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

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Potassium (K) 72 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 246 in 8cam

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Magnesium binding site 1 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3002

b:31.4
occ:1.00
OP2 a:C1604 1.8 30.2 1.0
O a:HOH7982 2.1 34.9 1.0
OP1 a:A1603 2.1 32.4 1.0
OP1 a:A1395 2.1 38.2 1.0
O a:HOH3424 2.1 31.4 1.0
O a:HOH8083 2.4 28.6 1.0
P a:C1604 3.2 33.1 1.0
P a:A1603 3.3 32.2 1.0
P a:A1395 3.4 34.5 1.0
OP1 a:C1604 3.8 33.9 1.0
O5' a:A1603 3.8 34.0 1.0
O3' a:U1394 3.9 37.0 1.0
O a:HOH5768 4.0 34.2 1.0
OP1 a:C1306 4.0 45.3 1.0
C5' a:A1603 4.0 32.0 1.0
OP2 a:A1603 4.1 34.9 1.0
O5' a:C1604 4.1 28.5 1.0
OP2 a:A1395 4.1 36.3 1.0
K a:K3305 4.1 33.9 1.0
O3' a:A1603 4.3 32.7 1.0
O a:HOH3992 4.3 56.0 1.0
O a:HOH3668 4.4 29.9 1.0
O3' a:U1602 4.5 32.1 1.0
O5' a:A1395 4.5 35.4 1.0
C3' a:A1603 4.6 32.2 1.0
O a:HOH3791 4.7 35.0 1.0
C4' a:A1603 4.9 32.2 1.0

Magnesium binding site 2 out of 246 in 8cam

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Magnesium binding site 2 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3003

b:29.0
occ:1.00
O a:HOH3432 1.9 31.8 1.0
OP1 a:A572 1.9 25.1 1.0
O a:HOH6879 2.1 26.8 1.0
O a:HOH3894 2.1 31.4 1.0
O a:HOH8199 2.1 29.2 1.0
O a:HOH5254 2.1 31.1 1.0
P a:A572 3.2 22.0 1.0
OP2 a:A572 3.7 23.2 1.0
O5' a:A572 4.0 24.5 1.0
O a:HOH7986 4.1 35.7 1.0
O a:HOH4826 4.1 34.1 1.0
OP1 a:A983 4.2 40.4 1.0
N7 a:A572 4.2 22.4 1.0
C8 a:A572 4.3 22.8 1.0
O a:HOH3979 4.3 42.2 1.0
O3' a:U571 4.4 24.4 1.0
O a:HOH6536 4.6 34.2 1.0
NH1 q:ARG79 4.7 25.7 1.0
C4' a:U571 4.8 23.5 1.0
C5 a:U573 4.8 23.2 1.0
C3' a:U571 4.9 22.9 1.0

Magnesium binding site 3 out of 246 in 8cam

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Magnesium binding site 3 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3004

b:41.3
occ:1.00
O a:HOH5726 2.1 38.6 1.0
O a:HOH8293 2.1 37.6 1.0
O a:HOH7163 2.4 41.9 1.0
O a:HOH8374 2.4 48.4 1.0
O4' a:G1288 4.3 33.9 1.0
OP1 a:C1646 4.3 37.7 1.0
OP2 a:A1276 4.3 39.0 1.0
OP2 a:C1646 4.4 40.9 1.0
O a:HOH7648 4.4 37.2 1.0
O a:HOH4088 4.5 43.2 1.0
OP1 a:G1649 4.5 37.3 1.0
C4' a:G1288 4.7 36.5 1.0
C1' a:G1288 4.8 32.9 1.0
N3 a:A1287 4.8 32.0 1.0
P a:C1646 4.9 37.4 1.0

Magnesium binding site 4 out of 246 in 8cam

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Magnesium binding site 4 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3005

b:19.5
occ:1.00
OP1 a:U810 2.0 20.1 1.0
O a:HOH3468 2.1 20.0 1.0
O a:HOH7575 2.1 20.8 1.0
O a:HOH7850 2.1 21.4 1.0
O a:HOH7787 2.1 22.9 1.0
N7 a:A1253 2.2 19.9 1.0
C8 a:A1253 3.0 19.2 1.0
P a:U810 3.3 19.4 1.0
C5 a:A1253 3.4 19.8 1.0
O a:HOH4613 3.9 29.7 1.0
N6 a:A1253 3.9 20.0 1.0
OP2 a:U810 4.0 20.0 1.0
O5' a:U810 4.0 19.1 1.0
C6 a:A1253 4.1 19.6 1.0
O a:HOH4682 4.1 25.9 1.0
O a:HOH8540 4.2 40.6 1.0
N9 a:A1253 4.3 20.2 1.0
OP1 a:U811 4.4 22.0 1.0
O a:HOH8500 4.4 36.7 1.0
O a:HOH6722 4.4 34.7 1.0
C4 a:A1253 4.5 19.9 1.0
C5' a:U810 4.5 19.9 1.0
O3' a:G809 4.5 19.6 1.0
C5' a:U811 4.6 20.9 1.0
O2' a:G1252 4.6 24.4 1.0
O2' a:C565 4.7 20.3 1.0

Magnesium binding site 5 out of 246 in 8cam

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Magnesium binding site 5 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3006

b:44.4
occ:1.00
O a:HOH4002 2.0 47.3 1.0
OP1 a:A2766 2.0 40.1 1.0
O a:HOH7866 2.0 48.3 1.0
O a:HOH5889 2.1 43.0 1.0
O a:HOH6406 2.1 45.2 1.0
O a:HOH5128 2.3 47.0 1.0
OP2 a:C2767 3.2 35.5 1.0
P a:A2766 3.4 35.1 1.0
O a:HOH6542 3.5 47.1 1.0
O a:HOH4232 4.1 55.5 1.0
O3' a:A2765 4.1 35.2 1.0
O4 a:U2769 4.2 38.5 1.0
OP2 a:A2766 4.3 41.9 1.0
O5' a:A2766 4.4 36.0 1.0
N7 a:G2645 4.5 32.3 1.0
O a:HOH5916 4.5 47.5 1.0
O4 a:U2768 4.6 34.7 1.0
P a:C2767 4.6 34.7 1.0
C8 a:G2645 4.7 31.5 1.0
C5' a:A2766 4.7 32.7 1.0
C5 a:C2767 4.8 35.0 1.0
O a:HOH5908 4.9 48.8 1.0

Magnesium binding site 6 out of 246 in 8cam

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Magnesium binding site 6 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3007

b:22.1
occ:1.00
OP1 a:C1670 2.0 22.4 1.0
OP2 a:U1671 2.0 24.0 1.0
O a:HOH4649 2.1 24.4 1.0
O a:HOH7670 2.1 22.3 1.0
O a:HOH7856 2.1 23.1 1.0
O a:HOH5590 2.1 21.4 1.0
P a:C1670 3.4 20.8 1.0
P a:U1671 3.4 23.5 1.0
O5' a:C1670 4.1 22.1 1.0
O a:HOH8576 4.1 41.1 1.0
OP1 a:U1671 4.1 26.4 1.0
O a:HOH6090 4.1 20.4 1.0
OP2 a:C1670 4.2 20.4 1.0
O5' a:U1671 4.3 24.0 1.0
OP2 a:G2550 4.3 25.6 1.0
C5' a:C1670 4.3 23.4 1.0
O a:HOH8508 4.3 38.7 1.0
OP2 a:G2549 4.4 28.1 1.0
O3' a:A1669 4.4 21.7 1.0
O a:HOH4858 4.4 27.4 1.0
O3' a:C1670 4.4 23.3 1.0
O a:HOH6491 4.5 26.4 1.0
C5 a:U1671 4.5 21.2 1.0
C5' a:G2549 4.7 26.4 1.0
O a:HOH6404 4.7 40.4 1.0
C3' a:C1670 4.8 22.6 1.0
C6 a:U1671 4.9 21.9 1.0

Magnesium binding site 7 out of 246 in 8cam

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Magnesium binding site 7 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3008

b:23.0
occ:1.00
OP2 a:C740 1.9 25.0 1.0
OP1 a:A1783 2.0 25.1 1.0
OP2 a:A1784 2.0 23.9 1.0
O a:HOH5934 2.1 24.3 1.0
O a:HOH6495 2.1 23.5 1.0
O a:HOH4941 2.1 24.5 1.0
P a:A1784 3.3 22.0 1.0
P a:C740 3.4 24.9 1.0
P a:A1783 3.4 22.3 1.0
OP1 a:A1784 3.7 23.0 1.0
O a:HOH6583 4.0 24.4 1.0
O a:HOH6150 4.0 43.2 1.0
O a:HOH7413 4.0 21.8 1.0
OP2 a:A1783 4.1 23.7 1.0
O a:HOH8141 4.1 49.5 1.0
OP1 a:C740 4.2 25.8 1.0
O5' a:C740 4.2 26.4 1.0
O3' a:A1783 4.2 22.0 1.0
O5' a:A1783 4.3 23.0 1.0
O a:HOH4003 4.3 48.9 1.0
O a:HOH8486 4.3 34.5 1.0
O3' a:A739 4.3 25.9 1.0
O3' a:U1782 4.4 25.4 1.0
OP2 a:U741 4.4 27.9 1.0
O5' a:A1784 4.5 22.3 1.0
C3' a:A1783 4.6 21.8 1.0
C5' a:A1783 4.6 21.8 1.0
O a:HOH5839 4.6 44.5 1.0
O a:HOH7491 4.6 44.5 1.0
C5' a:C740 4.7 26.5 1.0
O a:HOH6679 4.9 21.8 1.0
C3' a:A739 5.0 27.6 1.0

Magnesium binding site 8 out of 246 in 8cam

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Magnesium binding site 8 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3009

b:20.6
occ:1.00
O a:HOH6220 2.1 19.4 1.0
O a:HOH7746 2.1 21.0 1.0
O6 a:G450 2.1 22.5 1.0
OP1 a:A453 2.1 23.2 1.0
O a:HOH5312 2.1 19.7 1.0
O a:HOH7114 2.1 22.1 1.0
C6 a:G450 3.2 22.1 1.0
P a:A453 3.4 20.9 1.0
N7 a:G450 3.8 20.1 1.0
C5 a:G450 3.8 21.5 1.0
O a:HOH3656 3.9 35.2 1.0
O a:HOH8402 3.9 32.8 1.0
OP2 a:A453 4.1 23.0 1.0
O5' a:A453 4.1 25.1 1.0
K a:K3277 4.1 27.9 1.0
N7 a:A449 4.1 21.0 1.0
O a:HOH3465 4.2 33.2 1.0
C5' a:A453 4.3 24.8 1.0
N1 a:G450 4.3 22.5 1.0
O a:HOH8235 4.4 33.8 1.0
OP2 a:A449 4.4 26.4 1.0
OP1 a:A454 4.4 32.3 1.0
O a:HOH6926 4.4 24.1 1.0
O3' a:G452 4.6 24.7 1.0
N6 a:A449 4.6 24.7 1.0
O a:HOH4270 4.6 49.7 1.0
C5' a:U448 4.6 27.1 1.0
O a:HOH4818 4.9 32.2 1.0
C5 a:A449 4.9 21.4 1.0
C8 a:A449 4.9 21.1 1.0

Magnesium binding site 9 out of 246 in 8cam

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Magnesium binding site 9 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3010

b:36.0
occ:1.00
O a:HOH5860 2.0 37.4 1.0
O a:HOH7683 2.0 36.9 1.0
OP1 a:U120 2.0 34.6 1.0
O a:HOH4627 2.1 33.0 1.0
O a:HOH4745 2.1 38.7 1.0
O a:HOH5874 2.4 30.0 1.0
P a:U120 3.4 32.6 1.0
OP2 a:G123 3.7 38.2 1.0
O5' a:U120 3.9 33.1 1.0
O a:HOH4969 3.9 44.9 1.0
C5' a:U120 4.1 34.0 1.0
O a:HOH6463 4.1 32.6 1.0
O a:HOH4583 4.1 39.8 1.0
OP2 a:U120 4.2 34.1 1.0
O6 a:G124 4.3 31.1 1.0
OP2 a:G122 4.3 37.4 1.0
N7 a:G123 4.4 29.0 1.0
O3' a:A119 4.6 33.3 1.0
O a:HOH3603 4.8 31.9 1.0
C3' a:A119 4.8 31.4 1.0
O a:HOH5432 4.9 32.5 1.0
N7 a:G124 5.0 30.2 1.0
C8 a:G123 5.0 29.2 1.0

Magnesium binding site 10 out of 246 in 8cam

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Magnesium binding site 10 out of 246 in the Evernimicin 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 Evernimicin Bound to the 50S Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg3011

b:29.1
occ:1.00
OP1 a:A2268 1.9 31.1 1.0
O a:HOH6528 2.0 31.2 1.0
O a:HOH5499 2.1 27.9 1.0
O a:HOH6577 2.1 31.6 1.0
OP1 a:G2269 2.1 33.1 1.0
O a:HOH4971 2.1 27.6 1.0
P a:A2268 3.3 28.3 1.0
P a:G2269 3.4 30.1 1.0
O a:HOH4221 3.8 36.1 1.0
O3' a:A2268 4.1 30.4 1.0
OP2 a:G2269 4.1 30.7 1.0
C3' a:A2267 4.1 29.4 1.0
OP2 a:A2268 4.1 32.1 1.0
O6 a:G2271 4.2 35.4 1.0
O3' a:A2267 4.2 31.8 1.0
N3 a:A2267 4.2 29.4 1.0
O a:HOH6597 4.2 27.0 1.0
O a:HOH8600 4.3 44.5 1.0
O5' a:A2268 4.3 26.9 1.0
C5' a:A2268 4.4 30.0 1.0
OP2 a:A2267 4.4 36.4 1.0
C2 a:A2267 4.4 29.9 1.0
O a:HOH3814 4.5 34.6 1.0
O a:HOH5011 4.5 31.1 1.0
O5' a:G2269 4.5 35.9 1.0
O a:HOH7506 4.5 30.5 1.0
O a:HOH3428 4.7 27.1 1.0
C3' a:A2268 4.7 30.4 1.0
O a:HOH3788 4.7 40.1 1.0
C2' a:A2267 4.8 31.8 1.0
O5' a:A2267 4.8 30.0 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 20:31:29 2024

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