Magnesium in PDB 6zvh: EDF1-Ribosome Complex

Enzymatic activity of EDF1-Ribosome Complex

All present enzymatic activity of EDF1-Ribosome Complex:
4.2.99.18;

Other elements in 6zvh:

The structure of EDF1-Ribosome Complex also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Magnesium atom in the EDF1-Ribosome Complex (pdb code 6zvh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 30 binding sites of Magnesium where determined in the EDF1-Ribosome Complex, PDB code: 6zvh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 30 in 6zvh

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Magnesium binding site 1 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1901

b:18.3
occ:1.00
OP2 2:A669 2.2 13.9 1.0
OP2 2:A670 2.3 14.8 1.0
OP2 2:A668 2.8 14.8 1.0
O5' 2:A668 3.2 14.8 1.0
P 2:A669 3.6 13.9 1.0
P 2:A670 3.6 14.8 1.0
P 2:A668 3.6 14.8 1.0
OP1 2:U667 3.9 14.2 1.0
OP2 2:U667 4.2 14.2 1.0
OP1 2:A670 4.2 14.8 1.0
P 2:U667 4.3 14.2 1.0
O5' 2:A669 4.3 13.9 1.0
C5' 2:A668 4.4 14.8 1.0
C3' 2:A668 4.4 14.8 1.0
O5' 2:U667 4.4 14.2 1.0
OP1 2:A669 4.5 13.9 1.0
O3' 2:A668 4.5 14.8 1.0
C3' 2:A669 4.6 13.9 1.0
O5' 2:A670 4.6 14.8 1.0
O3' 2:A669 4.6 13.9 1.0
N7 2:A670 4.6 14.8 1.0
C8 2:A670 4.6 14.8 1.0
O3' 2:U667 4.7 14.2 1.0
OP1 2:A668 4.7 14.8 1.0
C5' 2:A669 4.8 13.9 1.0
C4' 2:A668 4.9 14.8 1.0

Magnesium binding site 2 out of 30 in 6zvh

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Magnesium binding site 2 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1902

b:20.7
occ:1.00
OP1 2:U1694 2.1 15.8 1.0
OP1 2:G1862 2.3 16.5 1.0
P 2:G1862 3.4 16.5 1.0
P 2:U1694 3.4 15.8 1.0
OP2 2:G1862 3.6 16.5 1.0
O3' 2:G1693 3.8 17.5 1.0
OP2 2:A1863 4.2 16.2 1.0
O5' 2:U1694 4.4 15.8 1.0
C5' 2:U1694 4.4 15.8 1.0
OP2 2:U1694 4.5 15.8 1.0
O3' 2:G1861 4.5 13.4 1.0
O5' 2:G1862 4.5 16.5 1.0
OP1 2:A1863 4.6 16.2 1.0
P 2:A1863 4.9 16.2 1.0

Magnesium binding site 3 out of 30 in 6zvh

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Magnesium binding site 3 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1903

b:18.6
occ:1.00
OP2 2:G999 3.3 17.7 1.0
OP1 2:A998 3.7 14.0 1.0
O a:GLY16 3.8 40.0 1.0
C5' 2:A998 4.3 14.0 1.0
P 2:G999 4.5 17.7 1.0
O5' 2:A998 4.6 14.0 1.0
C a:GLY16 4.6 40.0 1.0
P 2:A998 4.8 14.0 1.0
O3' 2:A998 4.8 14.0 1.0
N1 2:A1082 4.8 10.5 1.0
OP2 2:A1084 4.8 13.4 1.0
O3' 2:G1858 4.9 15.5 1.0
O2' 2:A1084 4.9 13.4 1.0

Magnesium binding site 4 out of 30 in 6zvh

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Magnesium binding site 4 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1904

b:18.2
occ:1.00
OP1 2:G16 2.3 17.0 1.0
P 2:G16 3.6 17.0 1.0
O2 2:C663 4.0 13.1 1.0
O6 2:G659 4.2 15.2 1.0
OP2 2:G16 4.2 17.0 1.0
OP2 2:U657 4.2 15.5 1.0
N2 2:G1164 4.3 14.8 1.0
O2' 2:C663 4.4 13.1 1.0
C5' 2:U657 4.5 15.5 1.0
O5' 2:G16 4.6 17.0 1.0
O3' 2:U15 4.6 13.2 1.0
O4' 2:U657 4.9 15.5 1.0
C5' 2:G16 4.9 17.0 1.0
C4' 2:U657 4.9 15.5 1.0

Magnesium binding site 5 out of 30 in 6zvh

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Magnesium binding site 5 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1905

b:20.6
occ:1.00
OP2 2:A91 2.8 21.8 1.0
O6 2:G446 2.9 21.1 1.0
N7 2:A91 3.2 21.8 1.0
OP2 2:G90 3.4 24.1 1.0
N1 2:A92 3.5 18.2 1.0
O5' 2:G90 3.6 24.1 1.0
C8 2:A91 3.7 21.8 1.0
C2 2:A92 3.7 18.2 1.0
C6 2:G446 3.9 21.1 1.0
P 2:G90 4.1 24.1 1.0
N1 2:G446 4.1 21.1 1.0
P 2:A91 4.2 21.8 1.0
C8 2:G90 4.3 24.1 1.0
C3' 2:G90 4.4 24.1 1.0
C5 2:A91 4.4 21.8 1.0
O5' 2:A91 4.5 21.8 1.0
N7 2:G90 4.5 24.1 1.0
C6 2:A92 4.6 18.2 1.0
OP1 2:G90 4.7 24.1 1.0
O3' 2:G90 4.8 24.1 1.0
C5' 2:G90 4.8 24.1 1.0
N6 2:A91 4.9 21.8 1.0
N3 2:A92 4.9 18.2 1.0
N6 2:A92 5.0 18.2 1.0

Magnesium binding site 6 out of 30 in 6zvh

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Magnesium binding site 6 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1906

b:17.7
occ:1.00
O6 2:G431 4.2 10.9 1.0
N4 2:C430 4.2 16.5 1.0
O6 2:G432 4.3 14.8 1.0
N7 2:G431 4.3 10.9 1.0
C5 2:C430 4.4 16.5 1.0
C4 2:C430 4.6 16.5 1.0
C6 2:G431 4.9 10.9 1.0
C5 2:G431 5.0 10.9 1.0

Magnesium binding site 7 out of 30 in 6zvh

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Magnesium binding site 7 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1907

b:20.8
occ:1.00
OP2 2:C450 3.4 18.5 1.0
OP1 2:C450 3.4 18.5 1.0
P 2:C450 3.9 18.5 1.0
OP2 2:G434 4.0 17.3 1.0
OP2 2:A435 4.1 16.2 1.0
OP1 2:A448 4.2 19.7 1.0
O5' 2:A449 4.2 20.7 1.0
O5' 2:G434 4.6 17.3 1.0
OP1 2:A449 4.6 20.7 1.0
C8 2:G434 4.7 17.3 1.0
N7 2:G434 4.8 17.3 1.0
N7 2:A435 4.8 16.2 1.0
C4' 2:A449 4.8 20.7 1.0
O3' 2:A449 4.9 20.7 1.0
P 2:G434 4.9 17.3 1.0
C5' 2:A449 5.0 20.7 1.0

Magnesium binding site 8 out of 30 in 6zvh

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Magnesium binding site 8 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1908

b:21.3
occ:1.00
OP2 2:A449 2.1 20.7 1.0
P 2:A449 3.4 20.7 1.0
NZ I:LYS23 3.9 22.4 1.0
OP1 2:A449 3.9 20.7 1.0
OP1 2:A435 4.3 16.2 1.0
O2 2:C450 4.3 18.5 1.0
O5' 2:A449 4.3 20.7 1.0
O6 2:G440 4.4 21.4 1.0
O3' 2:A448 4.5 19.7 1.0
O4' 2:C450 4.6 18.5 1.0
C2 2:C450 4.7 18.5 1.0
N4 2:C453 4.7 21.7 1.0
OP2 2:A435 4.8 16.2 1.0
O6 2:G452 4.8 19.8 1.0
P 2:A435 5.0 16.2 1.0
OP2 2:C450 5.0 18.5 1.0
N6 2:A439 5.0 22.1 1.0

Magnesium binding site 9 out of 30 in 6zvh

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Magnesium binding site 9 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1909

b:20.8
occ:1.00
OP2 2:A99 2.0 18.2 1.0
OP2 2:C409 2.0 16.5 1.0
OP2 2:U100 2.1 19.6 1.0
P 2:C409 3.3 16.5 1.0
P 2:A99 3.5 18.2 1.0
P 2:U100 3.5 19.6 1.0
O5' 2:C409 3.6 16.5 1.0
O4 2:U101 3.9 21.5 1.0
O3' 2:C98 4.1 16.5 1.0
OP1 2:A99 4.3 18.2 1.0
OP1 2:C409 4.3 16.5 1.0
O5' 2:U100 4.3 19.6 1.0
O3' 2:A99 4.3 18.2 1.0
C3' 2:A408 4.4 22.1 1.0
O3' 2:A408 4.4 22.1 1.0
C3' 2:A99 4.4 18.2 1.0
OP1 2:U100 4.4 19.6 1.0
O5' 2:A99 4.5 18.2 1.0
C5' 2:A99 4.7 18.2 1.0
OP2 2:G407 4.7 32.8 1.0
C4 2:U101 4.7 21.5 1.0
C5' 2:C409 5.0 16.5 1.0

Magnesium binding site 10 out of 30 in 6zvh

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Magnesium binding site 10 out of 30 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of EDF1-Ribosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1910

b:19.2
occ:1.00
OP2 2:A426 2.4 19.1 1.0
OP2 2:U427 2.4 20.2 1.0
P 2:A426 3.8 19.1 1.0
P 2:U427 3.8 20.2 1.0
N7 2:G410 4.0 16.1 1.0
O6 2:G411 4.0 14.7 1.0
N7 2:G411 4.1 14.7 1.0
O3' 2:G425 4.2 17.4 1.0
O6 2:G410 4.2 16.1 1.0
O2' 2:G425 4.2 17.4 1.0
C2' 2:G425 4.3 17.4 1.0
OP1 2:U427 4.4 20.2 1.0
OP2 2:G410 4.6 16.1 1.0
C5 2:G410 4.7 16.1 1.0
OP1 2:A426 4.7 19.1 1.0
O5' 2:U427 4.7 20.2 1.0
O5' 2:A426 4.7 19.1 1.0
O3' 2:A426 4.7 19.1 1.0
C6 2:G410 4.7 16.1 1.0
C6 2:G411 4.7 14.7 1.0
C3' 2:G425 4.8 17.4 1.0
C5 2:G411 4.8 14.7 1.0
C8 2:G410 4.9 16.1 1.0
C5' 2:A426 5.0 19.1 1.0

Reference:

N.K.Sinha, A.Ordureau, K.Best, J.A.Saba, B.Zinshteyn, E.Sundaramoorthy, A.Fulzele, D.M.Garshott, T.Denk, M.Thoms, J.A.Paulo, W.Harper, E.J.Bennett, R.Beckmann, R.Green. EDF1 Coordinates Cellular Responses to Ribosome Collisions. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32744497
DOI: 10.7554/ELIFE.58828
Page generated: Tue Dec 15 03:14:28 2020

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