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Magnesium in PDB 5gaf: Rnc in Complex with Srp

Other elements in 5gaf:

The structure of Rnc in Complex with Srp also contains other interesting chemical elements:

Zinc (Zn) 1 atom

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 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 310; Page 32, Binding sites: 311 - 320; Page 33, Binding sites: 321 - 330; Page 34, Binding sites: 331 - 340; Page 35, Binding sites: 341 - 350; Page 36, Binding sites: 351 - 360; Page 37, Binding sites: 361 - 370; Page 38, Binding sites: 371 - 380; Page 39, Binding sites: 381 - 390; Page 40, Binding sites: 391 - 400; Page 41, Binding sites: 401 - 410; Page 42, Binding sites: 411 - 420; Page 43, Binding sites: 421 - 430; Page 44, Binding sites: 431 - 431;

Binding sites:

The binding sites of Magnesium atom in the Rnc in Complex with Srp (pdb code 5gaf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 431 binding sites of Magnesium where determined in the Rnc in Complex with Srp, PDB code: 5gaf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 431 in 5gaf

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Magnesium binding site 1 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg101

b:60.0
occ:1.00
OP1 A:A2602 2.7 60.0 1.0
OP1 2:C75 3.0 60.0 1.0
OP1 2:A76 3.0 60.0 1.0
P 2:A76 3.9 60.0 1.0
OP2 2:A76 4.0 60.0 1.0
OP1 A:C2601 4.0 60.0 1.0
N1 A:A2439 4.1 60.0 1.0
P A:A2602 4.1 60.0 1.0
OP2 A:U2585 4.2 60.0 1.0
O5' A:A2602 4.4 60.0 1.0
P 2:C75 4.4 60.0 1.0
OP1 A:U2585 4.5 60.0 1.0
O5' 2:A76 4.6 60.0 1.0
P A:C2601 4.8 60.0 1.0
C2 A:A2439 4.8 60.0 1.0
N6 A:A2439 4.8 60.0 1.0
O5' A:C2601 4.8 60.0 1.0
C5' 2:C75 4.8 60.0 1.0
O3' A:C2601 4.9 60.0 1.0
P A:U2585 4.9 60.0 1.0
C6 A:A2439 4.9 60.0 1.0

Magnesium binding site 2 out of 431 in 5gaf

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Magnesium binding site 2 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:60.0
occ:1.00
OP2 A:A447 3.8 60.0 1.0
O6 A:G473 4.4 60.0 1.0
O6 A:G474 4.5 60.0 1.0
O4 A:U29 4.5 60.0 1.0
C5 A:U29 4.5 60.0 1.0
OP2 A:A28 4.6 60.0 1.0
N4 A:C31 4.6 60.0 1.0
OP2 A:U29 4.6 60.0 1.0
O5' A:A447 4.6 60.0 1.0
O6 A:G30 4.8 60.0 1.0
C4 A:U29 4.8 60.0 1.0
P A:A447 4.8 60.0 1.0
C2' A:A447 5.0 60.0 1.0

Magnesium binding site 3 out of 431 in 5gaf

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Magnesium binding site 3 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:60.0
occ:1.00
OP2 A:U120 1.9 60.0 1.0
P A:U120 3.3 60.0 1.0
OP1 A:U120 3.9 60.0 1.0
O3' A:A119 4.2 60.0 1.0
N7 A:G122 4.2 60.0 1.0
O5' A:U120 4.2 60.0 1.0
C5' A:U120 4.3 60.0 1.0
O6 A:G123 4.3 60.0 1.0
O6 A:G122 4.4 60.0 1.0
N7 A:G121 4.8 60.0 1.0
C5 A:G122 5.0 60.0 1.0

Magnesium binding site 4 out of 431 in 5gaf

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Magnesium binding site 4 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:60.0
occ:1.00
OP1 A:U120 2.2 60.0 1.0
P A:U120 3.6 60.0 1.0
OP2 A:G123 3.7 60.0 1.0
N7 A:G123 3.9 60.0 1.0
O6 A:G124 4.0 60.0 1.0
O5' A:U120 4.2 60.0 1.0
C8 A:G123 4.4 60.0 1.0
OP2 A:U120 4.4 60.0 1.0
N7 A:G124 4.5 60.0 1.0
OP2 A:G122 4.5 60.0 1.0
C5' A:U120 4.6 60.0 1.0
NH1 d:ARG19 4.7 60.0 1.0
O3' A:A119 4.7 60.0 1.0
C6 A:G124 4.9 60.0 1.0
C3' A:A119 4.9 60.0 1.0
P A:G123 5.0 60.0 1.0

Magnesium binding site 5 out of 431 in 5gaf

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Magnesium binding site 5 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:60.0
occ:1.00
OP2 A:A218 2.4 60.0 1.0
N6 A:A219 3.5 60.0 1.0
OP1 A:A428 3.7 60.0 1.0
O5' A:A217 3.8 60.0 1.0
P A:A218 3.9 60.0 1.0
N7 A:A218 3.9 60.0 1.0
O6 A:G220 4.1 60.0 1.0
OP2 A:A217 4.1 60.0 1.0
C8 A:A218 4.3 60.0 1.0
P A:A217 4.3 60.0 1.0
O5' A:A218 4.4 60.0 1.0
N7 A:A219 4.4 60.0 1.0
OP1 A:A217 4.4 60.0 1.0
C3' A:A217 4.6 60.0 1.0
C6 A:A219 4.6 60.0 1.0
C5' A:A217 4.6 60.0 1.0
OP1 A:U427 4.7 60.0 1.0
O3' A:A217 4.7 60.0 1.0
P A:A428 4.9 60.0 1.0
C5 A:A219 4.9 60.0 1.0
OP1 A:A218 4.9 60.0 1.0

Magnesium binding site 6 out of 431 in 5gaf

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Magnesium binding site 6 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:60.0
occ:1.00
OP1 A:U419 2.1 60.0 1.0
P A:U419 3.6 60.0 1.0
C5' A:U419 4.1 60.0 1.0
O3' A:C418 4.3 60.0 1.0
O5' A:U419 4.3 60.0 1.0
N7 A:G230 4.4 60.0 1.0
OP2 A:U419 4.5 60.0 1.0
C8 A:G230 5.0 60.0 1.0

Magnesium binding site 7 out of 431 in 5gaf

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Magnesium binding site 7 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3006

b:60.0
occ:1.00
OP2 A:G450 2.1 60.0 1.0
O E:SER80 3.5 60.0 1.0
OP2 A:G452 3.6 60.0 1.0
P A:G450 3.6 60.0 1.0
O E:GLY81 3.8 60.0 1.0
C E:SER80 4.2 60.0 1.0
O5' A:G450 4.4 60.0 1.0
OP1 A:A449 4.4 60.0 1.0
OP1 A:G450 4.4 60.0 1.0
CA E:SER80 4.4 60.0 1.0
O3' A:A449 4.6 60.0 1.0
OP2 A:U451 4.6 60.0 1.0
O5' A:A449 4.7 60.0 1.0
OP2 A:A449 4.8 60.0 1.0
P A:A449 4.8 60.0 1.0
C E:GLY81 4.8 60.0 1.0
P A:G452 5.0 60.0 1.0

Magnesium binding site 8 out of 431 in 5gaf

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Magnesium binding site 8 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3007

b:60.0
occ:1.00
OP1 A:A453 2.1 60.0 1.0
O6 A:G450 2.3 60.0 1.0
C6 A:G450 3.4 60.0 1.0
P A:A453 3.5 60.0 1.0
MG A:MG3225 3.6 60.0 1.0
N7 A:G450 4.1 60.0 1.0
C5 A:G450 4.1 60.0 1.0
OP2 A:A449 4.3 60.0 1.0
C5' A:A453 4.3 60.0 1.0
OP2 A:A453 4.3 60.0 1.0
O5' A:A453 4.3 60.0 1.0
OP1 A:A454 4.3 60.0 1.0
O3' A:G452 4.5 60.0 1.0
N1 A:G450 4.6 60.0 1.0
N7 A:A449 4.7 60.0 1.0
OP1 A:A471 4.9 60.0 1.0
C5' A:U448 5.0 60.0 1.0

Magnesium binding site 9 out of 431 in 5gaf

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Magnesium binding site 9 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3008

b:60.0
occ:1.00
OP1 A:C527 2.5 60.0 1.0
OP1 A:A526 2.7 60.0 1.0
OP1 A:A528 3.2 60.0 1.0
P A:C527 3.7 60.0 1.0
O5' A:C527 4.0 60.0 1.0
P A:A526 4.2 60.0 1.0
C3' A:C527 4.2 60.0 1.0
C5' A:C527 4.3 60.0 1.0
OP2 A:C527 4.3 60.0 1.0
P A:A528 4.6 60.0 1.0
C4' A:C527 4.7 60.0 1.0
O5' A:A526 4.8 60.0 1.0
O3' A:C527 4.9 60.0 1.0
O3' A:A526 5.0 60.0 1.0

Magnesium binding site 10 out of 431 in 5gaf

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Magnesium binding site 10 out of 431 in the Rnc in Complex with Srp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Rnc in Complex with Srp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3009

b:60.0
occ:1.00
OP1 A:C560 3.3 60.0 1.0
OP1 A:A1008 3.9 60.0 1.0
N7 A:A1008 3.9 60.0 1.0
OP1 A:G2038 4.0 60.0 1.0
C8 A:A1008 4.3 60.0 1.0
P A:C560 4.5 60.0 1.0
OP2 A:C560 4.8 60.0 1.0

Reference:

A.Jomaa, D.Boehringer, M.Leibundgut, N.Ban. Structures of the E. Coli Translating Ribosome with Srp and Its Receptor and with the Translocon Nat Commun V. 7 10471 2016.
ISSN: ESSN 2041-1723
PubMed: 26804923
DOI: 10.1038/NCOMMS10471
Page generated: Mon Dec 14 20:20:48 2020

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