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Magnesium in PDB 5m73: Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain

Protein crystallography data

The structure of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain, PDB code: 5m73 was solved by M.M.M.Becker, K.Wild, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.39 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.567, 139.306, 152.246, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28

Other elements in 5m73:

The structure of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain also contains other interesting chemical elements:

Potassium (K) 10 atoms

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 - 45;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain (pdb code 5m73). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 45 binding sites of Magnesium where determined in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain, PDB code: 5m73:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 45 in 5m73

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Magnesium binding site 1 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:69.6
occ:1.00
K A:K328 3.0 0.1 1.0
O6 A:G204 3.4 0.4 1.0
O6 A:G194 3.5 0.7 1.0
O4 A:U195 3.5 0.5 1.0
O6 A:G203 3.7 0.6 1.0
C6 A:G203 4.4 0.5 1.0
C6 A:G204 4.4 0.4 1.0
N7 A:G204 4.4 0.5 1.0
C4 A:U195 4.6 0.9 1.0
C6 A:G194 4.7 0.7 1.0
N7 A:G203 4.7 1.0 1.0
C5 A:G203 4.8 0.8 1.0
C5 A:G204 4.8 0.0 1.0

Magnesium binding site 2 out of 45 in 5m73

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Magnesium binding site 2 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:73.8
occ:1.00
O4 A:U132 2.3 0.4 1.0
C4 A:U132 3.4 0.4 1.0
N2 A:G164 3.4 0.8 1.0
N1 A:G164 3.6 0.6 1.0
C5 A:U132 3.8 0.6 1.0
C2 A:G164 4.1 1.0 1.0
N6 A:A131 4.5 0.1 1.0
N3 A:U132 4.6 0.2 1.0
N1 A:A176 4.6 0.7 1.0
C6 A:G164 4.7 0.6 1.0
N7 A:A131 4.8 0.4 1.0
O6 A:G164 4.8 0.3 1.0
C2 A:A176 4.9 0.2 1.0

Magnesium binding site 3 out of 45 in 5m73

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Magnesium binding site 3 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:98.3
occ:1.00
O6 A:G239 3.0 0.9 1.0
O6 A:G238 3.4 0.3 1.0
N7 A:G238 3.7 1.0 1.0
N4 A:C111 3.9 0.2 1.0
OP2 A:G109 3.9 0.0 1.0
C6 A:G239 4.0 0.6 1.0
MG A:MG317 4.1 80.2 1.0
C6 A:G238 4.1 0.6 1.0
N6 A:A240 4.2 0.5 1.0
C5 A:G238 4.2 0.9 1.0
N1 A:A240 4.3 0.3 1.0
C6 A:A240 4.3 0.4 1.0
N7 A:G239 4.6 0.6 1.0
C5 A:G239 4.6 0.5 1.0
C8 A:G238 4.8 0.3 1.0
P A:G109 4.9 0.1 1.0

Magnesium binding site 4 out of 45 in 5m73

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Magnesium binding site 4 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:87.6
occ:1.00
O4 A:U241 2.5 0.5 1.0
C4 A:U241 3.7 0.4 1.0
NZ D:LYS558 4.1 0.8 1.0
C5 A:U241 4.4 0.3 1.0
N6 A:A240 4.5 0.5 1.0
CE D:LYS558 4.7 0.1 1.0
N3 A:U241 4.7 0.5 1.0
N7 A:A240 4.8 1.0 1.0

Magnesium binding site 5 out of 45 in 5m73

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Magnesium binding site 5 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:42.9
occ:1.00
OP2 A:G178 1.7 0.9 1.0
C5' A:G178 2.7 0.9 1.0
P A:G178 2.9 0.6 1.0
C3' A:G177 3.0 0.5 1.0
O5' A:G178 3.2 0.4 1.0
O3' A:G177 3.4 0.2 1.0
C5' A:G177 3.4 0.2 1.0
C4' A:G177 3.7 0.5 1.0
C8 A:G178 3.8 0.2 1.0
C4' A:G178 4.0 0.3 1.0
O4' A:G178 4.1 1.0 1.0
C2' A:G177 4.2 0.9 1.0
OP1 A:G178 4.2 0.5 1.0
N7 A:G178 4.4 0.1 1.0
O5' A:G177 4.5 1.0 1.0
O4' A:G177 4.6 0.2 1.0
C3' A:G178 4.7 0.1 1.0
N9 A:G178 4.8 0.3 1.0
C1' A:G177 4.8 0.9 1.0
N9 A:G177 4.9 0.1 1.0

Magnesium binding site 6 out of 45 in 5m73

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Magnesium binding site 6 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:73.2
occ:1.00
O2' A:A131 4.0 0.3 1.0
C1' A:A131 4.7 0.8 1.0
O4' A:A131 4.9 0.3 1.0

Magnesium binding site 7 out of 45 in 5m73

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Magnesium binding site 7 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:68.2
occ:1.00
O2 A:U134 4.1 0.2 1.0
C2 A:A163 4.3 0.7 1.0
N3 A:A163 4.8 1.0 1.0
OP1 A:G165 4.8 0.0 1.0
O3' A:G164 4.9 0.0 1.0

Magnesium binding site 8 out of 45 in 5m73

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Magnesium binding site 8 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:81.0
occ:1.00
MG A:MG312 4.1 85.2 1.0
N7 A:G153 4.2 0.3 1.0
O6 A:G153 4.4 0.1 1.0
N7 A:G154 4.8 0.0 1.0
C5 A:G153 4.9 0.8 1.0

Magnesium binding site 9 out of 45 in 5m73

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Magnesium binding site 9 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:72.4
occ:1.00
O6 A:G198 3.0 0.4 1.0
N4 A:C196 3.5 0.8 1.0
C6 A:G198 3.9 0.3 1.0
O6 A:G197 4.0 0.6 1.0
MG A:MG310 4.3 58.1 1.0
C4 A:C196 4.4 0.4 1.0
N1 A:G198 4.4 0.4 1.0
C5 A:C196 4.5 0.8 1.0
MG A:MG323 4.6 81.6 1.0

Magnesium binding site 10 out of 45 in 5m73

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Magnesium binding site 10 out of 45 in the Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Human Srp S Domain with SRP72 Rna-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:58.1
occ:1.00
N7 A:G198 3.2 1.0 1.0
O6 A:G198 3.2 0.4 1.0
C6 A:G198 3.9 0.3 1.0
C5 A:G198 3.9 0.2 1.0
N7 A:G197 3.9 0.6 1.0
C8 A:G198 4.3 0.4 1.0
MG A:MG309 4.3 72.4 1.0
OP2 A:G197 4.3 0.7 1.0
C8 A:G197 4.6 0.1 1.0
C5 A:G197 4.8 0.8 1.0

Reference:

M.M.Becker, K.Lapouge, B.Segnitz, K.Wild, I.Sinning. Structures of Human SRP72 Complexes Provide Insights Into Srp Rna Remodeling and Ribosome Interaction. Nucleic Acids Res. V. 45 470 2017.
ISSN: ESSN 1362-4962
PubMed: 27899666
DOI: 10.1093/NAR/GKW1124
Page generated: Mon Dec 14 20:50:36 2020

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