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Magnesium in PDB 2zjp: Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans

Protein crystallography data

The structure of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans, PDB code: 2zjp was solved by J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.T.Spahn, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 169.900, 408.900, 694.500, 90.00, 90.00, 90.00
R / Rfree (%) 30 / 34

Other elements in 2zjp:

The structure of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Magnesium atom in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans (pdb code 2zjp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans, PDB code: 2zjp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 35 in 2zjp

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Magnesium binding site 1 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg167

b:68.6
occ:1.00
ND2 M:ASN58 3.1 0.4 1.0
CG M:ASN58 3.9 0.8 1.0
OP1 X:G2699 3.9 46.4 1.0
OP2 X:G2664 4.4 43.5 1.0
OP1 X:U2700 4.4 57.9 1.0
OD1 M:ASN58 4.5 0.9 1.0
CB M:ASN58 4.6 0.3 1.0

Magnesium binding site 2 out of 35 in 2zjp

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Magnesium binding site 2 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2881

b:77.2
occ:1.00
O4 X:U2057 3.2 93.0 1.0
O4 X:U2058 3.6 0.6 1.0
C4 X:U2057 3.9 94.0 1.0
C5 X:U2057 3.9 94.2 1.0
O4 X:U2222 3.9 53.5 1.0
N7 X:G2217 4.4 64.7 1.0
O6 X:G2221 4.5 81.0 1.0
C8 X:G2217 4.5 66.0 1.0
N6 X:A2060 4.6 1.0 1.0
C4 X:U2058 4.7 0.9 1.0
N7 X:A2220 4.8 0.3 1.0
C4 X:U2222 4.8 51.0 1.0
N7 X:G2221 4.8 85.6 1.0

Magnesium binding site 3 out of 35 in 2zjp

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Magnesium binding site 3 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2882

b:0.7
occ:1.00
OP1 X:G2415 2.6 86.3 1.0
P X:G2415 3.7 85.8 1.0
OP2 X:G2415 3.8 85.3 1.0
OP2 X:G2225 4.2 0.8 1.0
O2' X:U2224 4.3 76.7 1.0
O5' X:G2415 4.7 83.9 1.0
O3' X:A2414 4.8 0.6 1.0
C5' X:G2415 5.0 82.5 1.0

Magnesium binding site 4 out of 35 in 2zjp

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Magnesium binding site 4 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2883

b:0.6
occ:1.00
O4 X:U1370 3.2 0.9 1.0
O6 X:G1369 3.6 0.4 1.0
N7 X:G1369 4.1 0.3 1.0
C4 X:U1370 4.1 0.9 1.0
C6 X:G1369 4.4 0.3 1.0
OP2 X:C1385 4.5 0.9 1.0
C5 X:G1369 4.5 0.3 1.0
C5 X:U1370 4.8 0.1 1.0

Magnesium binding site 5 out of 35 in 2zjp

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Magnesium binding site 5 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2884

b:98.7
occ:1.00
OP2 X:A747 2.1 88.3 1.0
O5' X:G746 3.1 0.1 1.0
N1 X:A774 3.2 72.8 1.0
P X:A747 3.3 88.4 1.0
OP2 X:G746 3.5 0.5 1.0
C3' X:G746 3.6 0.8 1.0
P X:G746 3.6 0.7 1.0
O3' X:G746 3.7 1.0 1.0
N6 X:A774 3.8 60.9 1.0
OP1 X:G746 3.8 0.3 1.0
C6 X:A774 3.9 67.7 1.0
C5' X:G746 4.0 0.5 1.0
OP1 X:A747 4.1 86.8 1.0
C2 X:A774 4.1 76.8 1.0
C4' X:G746 4.3 0.8 1.0
O5' X:A747 4.6 86.9 1.0
C2' X:G746 4.8 0.9 1.0
OP2 X:G772 4.9 74.0 1.0
C8 X:G746 5.0 0.8 1.0

Magnesium binding site 6 out of 35 in 2zjp

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Magnesium binding site 6 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2885

b:98.4
occ:1.00
OP1 X:G772 3.1 75.0 1.0
OP1 X:C745 3.4 71.5 1.0
P X:G772 4.3 74.8 1.0
OP2 X:G772 4.5 74.0 1.0
OP2 X:G773 4.6 54.3 1.0
P X:C745 4.8 70.9 1.0
OP2 X:G746 4.9 0.5 1.0

Magnesium binding site 7 out of 35 in 2zjp

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Magnesium binding site 7 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2886

b:80.9
occ:1.00
OP2 X:G1767 2.0 0.9 1.0
P X:G1767 3.3 0.5 1.0
OP1 X:G1767 3.8 0.4 1.0
OP1 X:A1964 4.0 0.4 1.0
O5' X:G1767 4.1 0.7 1.0
OP1 X:U1766 4.3 0.5 1.0
O3' X:U1766 4.5 0.6 1.0
N7 X:G1767 4.6 0.5 1.0
OP2 X:A1964 4.8 0.2 1.0
C8 X:G1767 4.8 0.1 1.0
OP2 X:U1766 4.9 0.3 1.0
P X:A1964 4.9 0.8 1.0
P X:U1766 4.9 0.8 1.0

Magnesium binding site 8 out of 35 in 2zjp

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Magnesium binding site 8 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2887

b:98.7
occ:1.00
OP1 X:C1765 2.3 37.1 1.0
P X:C1765 3.2 36.7 1.0
OP2 X:C1765 3.3 38.0 1.0
OP2 X:A1777 3.9 23.5 1.0
O6 X:G1767 4.0 0.7 1.0
O2' X:G1763 4.2 78.0 1.0
O3' X:A1764 4.3 52.7 1.0
OP2 X:U1766 4.4 0.3 1.0
O5' X:C1765 4.4 34.4 1.0
N4 X:C1779 4.5 0.1 1.0
N3 X:G1763 4.6 75.4 1.0
OP1 X:A1777 4.6 22.1 1.0
N2 X:G1763 4.6 75.7 1.0
P X:A1777 4.7 24.9 1.0
N6 X:A1780 4.8 0.2 1.0
C6 X:G1767 5.0 0.2 1.0
N1 X:A1780 5.0 0.8 1.0

Magnesium binding site 9 out of 35 in 2zjp

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Magnesium binding site 9 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2888

b:73.4
occ:1.00
OP2 X:G2557 3.6 73.2 1.0
OP1 X:G2557 3.9 73.9 1.0
OP1 X:U2592 3.9 56.3 1.0
P X:G2557 4.3 73.2 1.0
N7 X:A2034 4.3 66.4 1.0
N7 X:A2593 4.3 18.5 1.0
NH1 B:ARG137 4.4 30.1 1.0
C8 X:A2034 4.5 65.5 1.0
OP2 X:A2034 4.5 58.8 1.0
OP1 X:C2033 4.9 1.0 1.0
OP2 X:A2593 4.9 15.7 1.0
C8 X:A2593 5.0 20.4 1.0
OP2 X:C2033 5.0 0.5 1.0

Magnesium binding site 10 out of 35 in 2zjp

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Magnesium binding site 10 out of 35 in the Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Thiopeptide Antibiotic Nosiheptide Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2889

b:0.2
occ:1.00
OP2 X:G2743 3.5 0.9 1.0
OP2 X:A2718 3.9 0.1 1.0
N7 X:G2743 4.1 0.7 1.0
N7 X:A2718 4.4 0.5 1.0
C8 X:G2743 4.5 0.3 1.0
OP2 X:G2742 4.5 0.5 1.0
OP1 X:G2742 4.8 0.6 1.0
P X:G2743 4.8 0.1 1.0
OP2 X:G2717 4.9 89.1 1.0
C5 X:U2719 4.9 0.3 1.0
P X:G2742 5.0 0.4 1.0
O5' X:G2742 5.0 0.4 1.0
C8 X:A2718 5.0 0.1 1.0

Reference:

J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, P.Fucini. Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off By Thiostrepton and Micrococcin. Mol.Cell V. 30 26 2008.
ISSN: ISSN 1097-2765
PubMed: 18406324
DOI: 10.1016/J.MOLCEL.2008.01.009
Page generated: Mon Dec 14 07:50:38 2020

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