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Magnesium in PDB 1w2b: Trigger Factor Ribosome Binding Domain in Complex with 50S

Protein crystallography data

The structure of Trigger Factor Ribosome Binding Domain in Complex with 50S, PDB code: 1w2b was solved by L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 210.746, 298.871, 574.173, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 26.8

Other elements in 1w2b:

The structure of Trigger Factor Ribosome Binding Domain in Complex with 50S also contains other interesting chemical elements:

Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 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 - 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 - 117;

Binding sites:

The binding sites of Magnesium atom in the Trigger Factor Ribosome Binding Domain in Complex with 50S (pdb code 1w2b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the Trigger Factor Ribosome Binding Domain in Complex with 50S, PDB code: 1w2b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in 1w2b

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Magnesium binding site 1 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3001

b:20.6
occ:1.00
 OP2 0:C2533 2.3 21.4 1.0
OP2 0:A2483 2.4 16.0 1.0
O 0:HOH3338 2.5 25.6 1.0
O 0:HOH3201 2.5 10.6 1.0
OP2 0:C2534 2.7 19.2 1.0
O 0:HOH4104 2.9 16.4 1.0
O2' 0:G2482 3.0 24.5 1.0
O3' 0:G2482 3.1 27.8 1.0
P 0:A2483 3.3 15.0 1.0
OP2 0:U2484 3.4 28.4 1.0
O 0:HOH3357 3.4 28.5 1.0
C5' 0:A2483 3.7 15.0 1.0
P 0:C2533 3.7 17.6 1.0
O 0:HOH5975 3.7 27.5 1.0
O5' 0:A2483 3.8 16.9 1.0
C2' 0:G2482 4.0 23.1 1.0
O2' 0:A2532 4.0 31.1 1.0
P 0:C2534 4.1 17.4 1.0
O5' 0:C2533 4.1 18.6 1.0
C3' 0:G2482 4.2 25.3 1.0
OP1 0:C2533 4.5 19.6 1.0
O 0:HOH5813 4.6 29.7 1.0
O3' 0:C2533 4.6 15.1 1.0
OP1 0:A2483 4.7 16.5 1.0
C2' 0:A2532 4.7 30.8 1.0
OP1 0:C2534 4.7 20.3 1.0
P 0:U2484 4.8 16.6 1.0
MG 0:MG3002 4.8 20.8 1.0
OP2 0:A2485 4.8 18.8 1.0
O3' 0:A2532 4.8 30.7 1.0
C4' 0:A2483 4.9 15.0 1.0
C3' 0:C2533 4.9 15.1 1.0

Magnesium binding site 2 out of 117 in 1w2b

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Magnesium binding site 2 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3002

b:20.8
occ:1.00
 O6 0:G627 2.3 20.3 1.0
OP2 0:A2483 2.5 16.0 1.0
O 0:HOH3667 2.5 19.5 1.0
O 0:HOH4160 2.5 15.6 1.0
O 0:HOH3357 2.6 28.5 1.0
OP1 0:C2534 2.7 20.3 1.0
OP1 0:A2483 2.8 16.5 1.0
P 0:A2483 2.9 15.0 1.0
C6 0:G627 3.5 19.9 1.0
O5' 0:A2483 3.5 16.9 1.0
O4 0:U626 3.7 15.0 1.0
P 0:C2534 3.7 17.4 1.0
O 0:HOH5982 3.8 34.4 1.0
OP2 0:C2534 4.1 19.2 1.0
N1 0:G627 4.1 19.2 1.0
O3' 0:C2533 4.2 15.1 1.0
C5 0:U626 4.2 15.0 1.0
C4 0:U626 4.3 15.0 1.0
O 0:HOH5975 4.4 27.5 1.0
O3' 0:G2482 4.4 27.8 1.0
O 0:HOH5409 4.5 22.7 1.0
O2' 0:U625 4.5 15.0 1.0
O 0:HOH6084 4.6 38.3 1.0
C5 0:G627 4.6 19.2 1.0
O 0:HOH3915 4.7 19.1 1.0
C5' 0:A2483 4.8 15.0 1.0
MG 0:MG3001 4.8 20.6 1.0
OP2 0:U2535 5.0 15.2 1.0

Magnesium binding site 3 out of 117 in 1w2b

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Magnesium binding site 3 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3003

b:16.3
occ:1.00
 OP2 0:A876 2.3 15.0 1.0
OP2 0:G877 2.3 15.0 1.0
O 0:HOH3940 2.6 16.6 1.0
O A:HOH425 2.6 8.9 1.0
OP1 0:A2624 2.7 15.8 1.0
O 0:HOH6607 2.8 16.2 1.0
P 0:A876 3.1 20.1 1.0
O3' 0:A875 3.2 15.5 1.0
O5' 0:A876 3.5 16.1 1.0
P 0:G877 3.7 15.0 1.0
O A:HOH485 3.7 24.4 1.0
O A:ALA193 3.8 15.0 1.0
O2' 0:A875 3.9 18.2 1.0
P 0:A2624 4.1 15.1 1.0
C5' 0:A876 4.1 16.1 1.0
O3' 0:A876 4.2 16.2 1.0
OP1 0:G877 4.3 15.0 1.0
O A:HOH493 4.4 24.1 1.0
O3' 0:G2623 4.4 15.5 1.0
C3' 0:A876 4.4 17.8 1.0
O A:HOH454 4.5 23.6 1.0
C3' 0:A875 4.5 15.5 1.0
OP1 0:A876 4.5 15.0 1.0
OD1 A:ASN195 4.7 15.5 1.0
O5' 0:G877 4.8 15.0 1.0
C2' 0:A875 4.8 16.4 1.0
C4' 0:A876 4.8 17.2 1.0
C5' 0:A2624 4.9 15.1 1.0
C A:ALA193 4.9 15.0 1.0
O5' 0:A2624 4.9 15.1 1.0

Magnesium binding site 4 out of 117 in 1w2b

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Magnesium binding site 4 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3004

b:16.6
occ:1.00
 O 0:HOH6043 2.2 6.2 1.0
O 0:HOH5690 2.2 15.7 1.0
O 0:HOH3800 2.3 7.5 1.0
O 0:HOH4693 2.3 13.0 1.0
O6 0:G456 2.3 15.0 1.0
OP1 0:A459 2.5 20.9 1.0
C6 0:G456 3.4 17.1 1.0
O 0:HOH4016 3.8 40.5 1.0
O 0:HOH3652 3.8 14.8 1.0
P 0:A459 3.9 15.0 1.0
C5 0:G456 4.2 18.3 1.0
N7 0:G456 4.2 15.6 1.0
O 0:HOH3762 4.2 26.5 1.0
C5' 0:A459 4.4 15.0 1.0
O5' 0:A459 4.5 15.0 1.0
OP1 0:A460 4.5 15.0 1.0
O 0:HOH7274 4.5 21.4 1.0
N7 0:A455 4.5 15.0 1.0
OP2 0:A455 4.5 15.0 1.0
N1 0:G456 4.5 17.7 1.0
OP2 0:A459 4.6 23.0 1.0
CE C:LYS85 4.6 15.0 1.0
N6 0:A455 4.9 15.0 1.0
C5' 0:U454 4.9 15.0 1.0
O3' 0:G458 4.9 15.0 1.0
OP2 0:A477 4.9 16.8 1.0
OP2 0:C478 4.9 16.8 1.0
OP1 0:A477 5.0 19.4 1.0
CD C:LYS85 5.0 15.0 1.0

Magnesium binding site 5 out of 117 in 1w2b

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Magnesium binding site 5 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3005

b:19.2
occ:1.00
 OP2 0:A1839 2.1 15.0 1.0
OP1 0:A1836 2.2 15.0 1.0
O 0:HOH3812 2.2 18.4 1.0
O 0:HOH5187 2.3 6.7 1.0
O 0:HOH4022 2.4 10.3 1.0
OP1 0:U1838 2.5 16.1 1.0
O 0:HOH7313 2.9 10.0 1.0
O 0:HOH3373 3.3 17.5 1.0
P 0:A1839 3.5 15.0 1.0
O 0:HOH3257 3.6 24.0 1.0
P 0:A1836 3.6 15.0 1.0
P 0:U1838 3.9 15.0 1.0
O 0:HOH4700 4.1 22.7 1.0
O5' 0:A1836 4.2 17.2 1.0
C2' 0:U1835 4.3 15.0 1.0
O5' 0:A1839 4.3 15.0 1.0
OP1 0:A1839 4.4 19.1 1.0
MG 0:MG3007 4.4 16.2 1.0
O5' 0:U1838 4.4 15.5 1.0
C8 0:A1839 4.4 15.5 1.0
C3' 0:U1835 4.4 15.0 1.0
N7 0:A1839 4.4 15.0 1.0
O3' 0:U1838 4.5 15.2 1.0
O3' 0:U1835 4.5 15.0 1.0
OP2 0:A1836 4.5 15.3 1.0
OP2 0:G1837 4.6 35.7 1.0
C5' 0:U1838 4.7 15.0 1.0
C3' 0:U1838 4.8 15.0 1.0
OP2 0:U1838 4.8 15.2 1.0
O2' 0:U1835 4.9 15.0 1.0
O3' 0:G1837 4.9 26.7 1.0

Magnesium binding site 6 out of 117 in 1w2b

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Magnesium binding site 6 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3006

b:21.8
occ:1.00
 O 0:HOH3786 2.2 26.0 1.0
O 0:HOH5079 2.3 19.8 1.0
O 0:HOH4349 2.3 17.8 1.0
OP2 0:C822 2.4 15.0 1.0
OP2 0:U821 2.4 15.0 1.0
OP1 0:G854 2.5 17.2 1.0
OP1 0:G856 3.1 32.2 1.0
OP1 0:U855 3.5 18.4 1.0
O 0:HOH4546 3.5 22.7 1.0
P 0:U821 3.6 32.5 1.0
O5' 0:U821 3.7 39.0 1.0
P 0:G854 3.7 15.0 1.0
P 0:C822 3.8 17.5 1.0
O 0:HOH3525 3.9 25.7 1.0
O5' 0:G854 4.0 15.0 1.0
O3' 0:G820 4.2 20.0 1.0
C5' 0:U855 4.2 15.0 1.0
C3' 0:U821 4.3 36.4 1.0
OP2 0:G854 4.3 18.6 1.0
O3' 0:U821 4.4 36.6 1.0
C5' 0:G854 4.5 15.0 1.0
P 0:G856 4.5 15.0 1.0
C5 0:C822 4.7 15.0 1.0
OP1 0:C822 4.7 15.0 1.0
P 0:U855 4.7 19.7 1.0
O5' 0:C822 4.8 18.1 1.0
O5' 0:G856 4.9 15.0 1.0
OP1 0:U821 4.9 15.0 1.0
C6 0:U821 4.9 15.0 1.0
O5' 0:U855 4.9 16.7 1.0
C5' 0:U821 4.9 37.0 1.0
O 0:HOH3275 5.0 30.7 1.0

Magnesium binding site 7 out of 117 in 1w2b

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Magnesium binding site 7 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3007

b:16.2
occ:1.00
 OP1 0:A1839 2.3 19.1 1.0
O 0:HOH3433 2.3 18.4 1.0
OP2 0:A1840 2.3 15.0 1.0
O 0:HOH3235 2.4 7.0 1.0
OP2 0:U832 2.4 15.0 1.0
O 0:HOH7313 2.5 10.0 1.0
O 0:HOH3373 2.7 17.5 1.0
O 0:HOH6774 3.3 12.4 1.0
P 0:A1839 3.3 15.0 1.0
P 0:U832 3.5 15.0 1.0
OP2 0:A1839 3.5 15.0 1.0
P 0:A1840 3.7 15.0 1.0
OP1 0:U832 3.7 15.0 1.0
OP1 0:A1840 4.2 15.0 1.0
O5' 0:U832 4.2 15.0 1.0
O5' 0:A1839 4.3 15.0 1.0
MG 0:MG3005 4.4 19.2 1.0
O3' 0:U1838 4.5 15.2 1.0
O3' 0:A1839 4.6 15.0 1.0
C3' 0:A1839 4.6 15.0 1.0
O5' 0:A1840 4.7 15.0 1.0
O 0:HOH3812 4.8 18.4 1.0
O3' 0:U831 4.8 15.0 1.0
C5' 0:A1839 4.8 15.0 1.0
O 0:HOH8029 4.9 40.2 1.0

Magnesium binding site 8 out of 117 in 1w2b

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Magnesium binding site 8 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3008

b:17.5
occ:1.00
 OP1 0:U919 2.3 15.1 1.0
OP1 0:A2465 2.4 34.8 1.0
O 0:HOH4166 2.5 13.7 1.0
O 0:HOH3405 2.5 21.7 1.0
O 0:HOH3429 2.5 12.1 1.0
OP1 0:C2464 2.5 15.7 1.0
OP2 0:U919 2.9 15.1 1.0
P 0:U919 3.0 15.0 1.0
P 0:A2465 3.5 25.6 1.0
O 0:HOH4799 3.7 24.6 1.0
O 0:HOH6876 3.7 29.8 1.0
O5' 0:U919 3.8 15.0 1.0
P 0:C2464 3.9 15.0 1.0
O 0:HOH3446 3.9 31.2 1.0
OP2 0:A2465 4.0 37.5 1.0
O5' 0:A2465 4.0 26.4 1.0
O5' 0:C2464 4.1 18.2 1.0
O 0:HOH6743 4.3 24.8 1.0
C5' 0:C2464 4.4 19.1 1.0
O3' 0:G918 4.4 15.0 1.0
OP1 0:G2466 4.5 53.3 1.0
C5' 0:U919 4.5 15.0 1.0
O 0:HOH6588 4.6 16.5 1.0
C5' 0:A2465 4.7 24.3 1.0
O3' 0:A2463 4.8 15.9 1.0
O3' 0:C2464 4.8 17.6 1.0
OP2 0:C2464 4.9 20.0 1.0

Magnesium binding site 9 out of 117 in 1w2b

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Magnesium binding site 9 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3009

b:19.6
occ:1.00
 OP1 0:G2611 2.2 15.7 1.0
O 0:HOH5605 2.2 15.2 1.0
O 0:HOH3618 2.3 12.3 1.0
O 0:HOH4998 2.4 16.7 1.0
OP1 0:A2612 2.5 21.1 1.0
O 0:HOH3577 2.5 17.2 1.0
NA 0:NA3109 2.9 69.5 1.0
O3' 0:U2610 3.2 15.0 1.0
P 0:G2611 3.2 15.1 1.0
O 0:HOH3487 3.5 26.5 1.0
O 0:HOH3486 3.8 16.3 1.0
P 0:A2612 3.9 15.1 1.0
OP2 0:G2094 3.9 15.0 1.0
OP1 0:G2094 4.0 15.0 1.0
C5' 0:G2611 4.2 15.1 1.0
OP2 0:G2093 4.2 15.0 1.0
O5' 0:G2611 4.2 15.2 1.0
P 0:G2094 4.3 15.0 1.0
OP2 0:G2611 4.4 15.2 1.0
C3' 0:U2610 4.4 15.0 1.0
C4' 0:U2610 4.5 15.0 1.0
O3' 0:G2093 4.6 15.0 1.0
OP2 0:A2612 4.6 22.5 1.0
O3' 0:G2611 4.7 15.1 1.0
O 0:HOH8411 4.7 13.3 1.0
C3' 0:G2611 4.8 15.1 1.0
O2' 0:U2610 4.8 15.0 1.0
O 0:HOH8260 4.9 18.7 1.0
O5' 0:A2612 4.9 15.1 1.0
C5' 0:U2610 4.9 15.0 1.0

Magnesium binding site 10 out of 117 in 1w2b

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Magnesium binding site 10 out of 117 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg3010

b:17.9
occ:1.00
 O 0:HOH3645 2.1 19.4 1.0
O 0:HOH3386 2.1 17.5 1.0
O 0:HOH4069 2.2 23.3 1.0
N7 0:G854 2.3 15.3 1.0
O 0:HOH4764 2.3 22.2 1.0
N7 0:G824 2.4 27.4 1.0
C8 0:G824 3.0 29.1 1.0
C8 0:G854 3.1 16.8 1.0
C5 0:G854 3.5 16.5 1.0
C5 0:G824 3.6 26.8 1.0
O6 0:G854 3.9 18.0 1.0
OP2 0:G854 3.9 18.6 1.0
C6 0:G854 4.1 16.9 1.0
OP2 0:U823 4.1 29.1 1.0
OP2 0:G824 4.2 26.9 1.0
N9 0:G824 4.3 29.9 1.0
O6 0:G824 4.3 29.8 1.0
C6 0:G824 4.4 27.7 1.0
N9 0:G854 4.4 15.8 1.0
C4 0:G854 4.6 16.3 1.0
C4 0:G824 4.6 27.4 1.0
OP2 0:C853 4.6 15.0 1.0
O5' 0:G824 4.8 15.0 1.0
C5 0:C853 4.8 15.0 1.0
C5 0:U823 4.9 24.4 1.0
O5' 0:C853 4.9 15.4 1.0
O 0:HOH3275 4.9 30.7 1.0
C6 0:C853 5.0 15.0 1.0

Reference:

L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, N.Ban. Trigger Factor in Complex with the Ribosome Forms A Molecular Cradle For Nascent Proteins Nature V. 431 590 2004.
ISSN: ISSN 0028-0836
PubMed: 15334087
DOI: 10.1038/NATURE02899
Page generated: Tue Aug 13 16:43:06 2024

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