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Magnesium in PDB 1q7y: Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit

Protein crystallography data

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y was solved by J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 28

Other elements in 1q7y:

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit 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 Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit (pdb code 1q7y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in 1q7y

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Magnesium binding site 1 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8001

b:31.7
occ:1.00
OP2 A:C2534 1.9 30.8 1.0
O A:HOH7252 2.1 24.2 1.0
O A:HOH8693 2.1 34.9 1.0
OP2 A:C2533 2.2 34.0 1.0
OP2 A:A2483 2.4 36.0 1.0
O A:HOH3126 2.4 12.6 1.0
O3' A:G2482 3.2 34.3 1.0
P A:A2483 3.3 35.6 1.0
P A:C2534 3.3 31.3 1.0
P A:C2533 3.6 34.1 1.0
O2' A:G2482 3.8 36.3 1.0
O3' A:A2532 4.0 34.8 1.0
O A:HOH9157 4.0 37.8 1.0
O A:HOH3827 4.1 34.1 1.0
O3' A:C2533 4.1 32.7 1.0
OP1 A:A2483 4.1 36.0 1.0
O A:HOH5860 4.2 64.7 1.0
OP1 A:C2534 4.2 31.9 1.0
O5' A:C2534 4.2 31.6 1.0
O5' A:C2533 4.3 33.0 1.0
C3' A:C2533 4.3 33.1 1.0
O2' A:A2532 4.3 35.1 1.0
OP2 A:U2484 4.4 39.3 1.0
C3' A:G2482 4.4 34.7 1.0
C5 A:C2534 4.6 43.3 1.0
C2' A:G2482 4.6 35.8 1.0
O5' A:A2483 4.6 37.1 1.0
OP1 A:C2533 4.8 37.6 1.0
O A:HOH6962 4.8 23.0 1.0
C1' A:G2482 4.9 37.1 1.0
C5' A:A2483 4.9 36.2 1.0
OP2 A:U2535 4.9 43.0 1.0
C6 A:C2534 4.9 42.4 1.0

Magnesium binding site 2 out of 117 in 1q7y

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Magnesium binding site 2 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8002

b:15.4
occ:1.00
O A:HOH7231 1.7 30.2 1.0
O6 A:G627 1.8 30.1 1.0
OP1 A:A2483 2.1 36.0 1.0
O A:HOH3827 2.3 34.1 1.0
OP1 A:C2534 2.3 31.9 1.0
O A:HOH7230 2.3 34.4 1.0
C6 A:G627 3.0 30.0 1.0
P A:A2483 3.3 35.6 1.0
O4 A:U626 3.4 28.7 1.0
O A:HOH8780 3.4 0.0 1.0
P A:C2534 3.5 31.3 1.0
N1 A:G627 3.7 29.1 1.0
OP2 A:A2483 3.7 36.0 1.0
O A:HOH5374 3.9 16.9 1.0
OP2 A:C2534 4.0 30.8 1.0
C5 A:G627 4.1 29.9 1.0
O5' A:A2483 4.2 37.1 1.0
O2' A:U625 4.2 29.2 1.0
C4 A:U626 4.2 25.7 1.0
O3' A:C2533 4.3 32.7 1.0
O3' A:G2482 4.4 34.3 1.0
C5 A:U626 4.5 24.6 1.0
OP2 A:U2535 4.5 43.0 1.0
O A:HOH9635 4.6 15.2 1.0
N7 A:G627 4.6 29.1 1.0
O5' A:C2534 4.7 31.6 1.0
C3' A:G2482 4.8 34.7 1.0
O A:HOH6592 4.9 24.9 1.0
O2 A:C2071 5.0 31.6 1.0

Magnesium binding site 3 out of 117 in 1q7y

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Magnesium binding site 3 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8003

b:30.4
occ:1.00
OP1 A:A2624 1.7 27.1 1.0
O A:HOH9341 1.9 46.1 1.0
OP2 A:G877 1.9 32.1 1.0
O A:HOH3174 2.4 15.7 1.0
O A:HOH8542 2.5 25.5 1.0
OP2 A:A876 2.6 36.8 1.0
P A:G877 3.0 31.7 1.0
P A:A2624 3.1 27.4 1.0
OP1 A:G877 3.4 32.1 1.0
O3' A:G2623 3.6 31.0 1.0
OP2 A:A2624 3.9 28.1 1.0
P A:A876 3.9 37.0 1.0
O3' A:A876 3.9 31.6 1.0
OD1 C:ASN195 4.0 40.3 1.0
O A:HOH5763 4.0 0.3 1.0
O C:HOH8628 4.1 8.9 1.0
O5' A:A876 4.2 37.8 1.0
O A:HOH8541 4.2 31.2 1.0
O5' A:G877 4.2 32.5 1.0
O5' A:A2624 4.2 27.8 1.0
O A:HOH6652 4.4 99.7 1.0
C5' A:A876 4.4 34.9 1.0
O3' A:A875 4.4 35.5 1.0
O A:HOH3975 4.5 41.3 1.0
C3' A:A876 4.5 32.3 1.0
O C:HOH8621 4.5 31.2 1.0
C5' A:A2624 4.6 28.5 1.0
O C:ALA193 4.7 34.4 1.0
O C:HOH8550 4.8 32.9 1.0
MG A:MG8013 4.8 21.3 1.0
CG C:ASN195 4.9 37.8 1.0

Magnesium binding site 4 out of 117 in 1q7y

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Magnesium binding site 4 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8004

b:43.7
occ:1.00
O A:HOH8569 1.5 13.3 1.0
OP1 A:A459 1.8 29.5 1.0
O6 A:G456 2.0 40.0 1.0
O A:HOH9294 2.0 7.7 1.0
O A:HOH3290 2.0 8.2 1.0
O A:HOH7237 2.4 7.8 1.0
P A:A459 3.1 31.2 1.0
C6 A:G456 3.2 39.7 1.0
O A:HOH8851 3.7 23.0 1.0
O5' A:A459 3.7 33.4 1.0
OP2 A:A459 3.8 32.7 1.0
C5' A:A459 4.0 35.2 1.0
C5 A:G456 4.0 39.0 1.0
N7 A:G456 4.1 38.6 1.0
O3' A:G458 4.2 32.6 1.0
N1 A:G456 4.3 40.2 1.0
OP1 A:A460 4.3 37.7 1.0
CE E:LYS85 4.3 27.5 1.0
O A:HOH3025 4.5 15.1 1.0
OP1 A:A477 4.5 32.9 1.0
N7 A:A455 4.6 37.0 1.0
O A:HOH5455 4.7 20.1 1.0
OP2 A:A455 4.7 26.6 1.0
CD E:LYS85 4.7 28.3 1.0
NZ E:LYS85 4.8 25.9 1.0
OP2 A:A477 4.9 31.7 1.0
OP2 A:A460 4.9 35.0 1.0
O A:HOH7238 4.9 25.8 1.0
O A:HOH4900 4.9 57.0 1.0
O A:HOH3212 5.0 34.4 1.0

Magnesium binding site 5 out of 117 in 1q7y

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Magnesium binding site 5 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8005

b:68.9
occ:1.00
O A:HOH7254 1.6 30.7 1.0
O A:HOH7253 1.8 1.9 1.0
OP1 A:U1838 1.8 28.2 1.0
OP2 A:A1839 2.0 27.8 1.0
OP1 A:A1836 2.2 37.6 1.0
O A:HOH3122 2.7 4.6 1.0
P A:U1838 3.3 29.0 1.0
P A:A1839 3.4 27.6 1.0
O A:HOH5055 3.5 33.6 1.0
P A:A1836 3.5 38.7 1.0
O A:HOH8529 3.8 7.9 1.0
C3' A:G1837 4.0 33.2 1.0
O5' A:A1836 4.0 39.1 1.0
OP2 A:U1838 4.1 30.1 1.0
O A:HOH4996 4.1 19.4 1.0
OP2 A:G1837 4.1 39.6 1.0
O3' A:U1838 4.1 28.4 1.0
O3' A:G1837 4.2 31.4 1.0
O5' A:U1838 4.2 25.5 1.0
O A:HOH7328 4.3 39.5 1.0
OP2 A:A1836 4.3 37.5 1.0
O5' A:A1839 4.3 28.9 1.0
OP1 A:A1839 4.3 29.4 1.0
C5' A:U1838 4.3 27.3 1.0
C3' A:U1838 4.5 29.0 1.0
O3' A:U1835 4.6 37.0 1.0
C2' A:U1835 4.6 37.2 1.0
C3' A:U1835 4.7 37.3 1.0
O A:HOH9153 4.9 10.8 1.0
O A:HOH9411 4.9 28.5 1.0

Magnesium binding site 6 out of 117 in 1q7y

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Magnesium binding site 6 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8006

b:33.1
occ:1.00
O A:HOH9326 1.9 13.0 1.0
OP2 A:C822 1.9 41.7 1.0
OP1 A:G854 2.0 32.2 1.0
O A:HOH3263 2.1 51.8 1.0
OP2 A:U821 2.2 41.5 1.0
O A:HOH3128 2.5 13.5 1.0
P A:G854 3.2 32.5 1.0
P A:C822 3.3 41.5 1.0
P A:U821 3.6 41.8 1.0
O5' A:G854 3.8 31.0 1.0
OP2 A:G854 3.9 28.7 1.0
O5' A:U821 3.9 42.6 1.0
O A:HOH9718 3.9 21.8 1.0
O3' A:U821 3.9 42.3 1.0
OP1 A:G856 4.0 48.8 1.0
OP1 A:C822 4.0 42.8 1.0
C3' A:U821 4.0 41.9 1.0
OP1 A:U855 4.1 37.6 1.0
C5' A:G854 4.2 30.8 1.0
O3' A:G820 4.3 40.2 1.0
NA A:NA8327 4.4 24.6 1.0
O5' A:C822 4.4 42.5 1.0
O3' A:C853 4.4 31.2 1.0
OP1 A:U821 4.7 40.6 1.0
C5 A:C822 4.8 45.3 1.0
O A:HOH4497 4.8 44.0 1.0
O A:HOH8826 4.9 84.8 1.0

Magnesium binding site 7 out of 117 in 1q7y

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Magnesium binding site 7 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8007

b:9.7
occ:1.00
OP2 A:U832 2.0 36.7 1.0
OP2 A:A1840 2.1 31.9 1.0
OP1 A:A1839 2.1 29.4 1.0
O A:HOH9867 2.2 35.4 1.0
O A:HOH7242 2.2 10.7 1.0
O A:HOH8529 2.3 7.9 1.0
P A:A1839 3.4 27.6 1.0
P A:U832 3.4 37.4 1.0
P A:A1840 3.4 31.4 1.0
O A:HOH9153 3.4 10.8 1.0
OP2 A:A1839 3.9 27.8 1.0
OP1 A:U832 4.1 36.5 1.0
OP1 A:A1840 4.1 30.8 1.0
O A:HOH8623 4.1 47.6 1.0
O A:HOH5837 4.2 7.7 1.0
O5' A:U832 4.2 37.7 1.0
O3' A:A1839 4.3 29.3 1.0
O5' A:A1839 4.3 28.9 1.0
O A:HOH9411 4.3 28.5 1.0
O3' A:U1838 4.4 28.4 1.0
O3' A:U831 4.4 37.3 1.0
O5' A:A1840 4.5 31.9 1.0
O A:HOH7328 4.5 39.5 1.0
C5' A:A1839 4.6 28.2 1.0
C3' A:A1839 4.6 28.9 1.0
OP2 A:G833 4.7 40.0 1.0
C3' A:U831 4.8 38.3 1.0
C5' A:U832 4.8 38.1 1.0
O A:HOH7358 4.9 43.8 1.0

Magnesium binding site 8 out of 117 in 1q7y

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Magnesium binding site 8 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8008

b:40.8
occ:1.00
OP1 A:A2465 1.8 34.3 1.0
OP1 A:U919 2.0 26.2 1.0
O A:HOH7246 2.1 5.6 1.0
OP1 A:C2464 2.2 30.3 1.0
O A:HOH7329 2.3 15.1 1.0
O A:HOH3139 2.4 12.0 1.0
P A:U919 3.0 25.5 1.0
P A:A2465 3.0 33.7 1.0
OP2 A:U919 3.4 26.2 1.0
O5' A:A2465 3.4 32.8 1.0
P A:C2464 3.4 32.8 1.0
C5' A:C2464 3.7 29.7 1.0
O5' A:U919 3.8 26.0 1.0
O5' A:C2464 3.8 32.9 1.0
OP2 A:A2465 3.8 34.8 1.0
O A:HOH8964 4.1 0.0 1.0
O A:HOH5385 4.1 42.4 1.0
O A:HOH9438 4.2 18.5 1.0
C5' A:U919 4.3 27.5 1.0
OP2 A:C2464 4.3 33.4 1.0
O3' A:G918 4.3 25.2 1.0
O3' A:C2464 4.3 32.2 1.0
C5' A:A2465 4.4 31.0 1.0
C3' A:A2465 4.4 31.6 1.0
O A:HOH5825 4.4 31.7 1.0
OP1 A:G2466 4.4 32.8 1.0
O3' A:A2463 4.6 32.0 1.0
O A:HOH9858 4.6 10.3 1.0
C4' A:C2464 4.7 28.1 1.0
C3' A:C2464 4.7 29.8 1.0
C2' A:A2465 4.7 30.6 1.0
O A:HOH9063 4.9 8.1 1.0
C5' A:G2466 4.9 33.2 1.0
C4' A:A2465 5.0 30.5 1.0

Magnesium binding site 9 out of 117 in 1q7y

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Magnesium binding site 9 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8009

b:14.0
occ:1.00
O A:HOH6915 1.7 24.7 1.0
OP1 A:A2612 1.8 24.2 1.0
OP1 A:G2611 1.8 29.4 1.0
O A:HOH7247 2.3 0.0 1.0
O A:HOH7248 2.4 56.8 1.0
O A:HOH3250 2.5 4.8 1.0
P A:G2611 3.1 28.5 1.0
P A:A2612 3.2 28.2 1.0
NA A:NA8358 3.4 0.2 1.0
O3' A:U2610 3.5 30.2 1.0
O A:HOH8852 3.5 19.0 1.0
OP2 A:A2612 3.8 28.8 1.0
C5' A:G2611 3.9 26.7 1.0
O5' A:G2611 3.9 26.8 1.0
OP2 A:G2093 4.1 32.8 1.0
O3' A:G2611 4.1 26.9 1.0
O5' A:A2612 4.2 29.1 1.0
OP2 A:G2611 4.3 30.0 1.0
O D:HOH8531 4.3 27.1 1.0
OP2 A:G2094 4.3 27.0 1.0
O A:HOH8823 4.3 15.9 1.0
C3' A:G2611 4.3 26.3 1.0
OP1 A:G2094 4.5 28.4 1.0
C4' A:G2611 4.7 25.9 1.0
O A:HOH7263 4.7 14.7 1.0
C3' A:U2610 4.8 30.7 1.0
P A:G2094 4.8 26.0 1.0
C4' A:U2610 5.0 29.9 1.0

Magnesium binding site 10 out of 117 in 1q7y

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Magnesium binding site 10 out of 117 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8010

b:26.8
occ:1.00
O A:HOH3348 1.5 30.9 1.0
O A:HOH8791 1.6 54.8 1.0
O D:HOH8529 1.9 63.6 1.0
OP1 A:G836 2.0 28.5 1.0
OE1 D:GLN230 2.0 30.1 1.0
OP1 A:U2615 2.1 24.7 1.0
CD D:GLN230 3.2 30.1 1.0
O A:HOH4539 3.4 58.2 1.0
P A:U2615 3.4 26.9 1.0
P A:G836 3.5 29.8 1.0
CG D:GLN230 3.9 30.1 1.0
OP2 A:U2615 4.0 26.6 1.0
CB D:GLN230 4.1 29.9 1.0
NE2 D:GLN230 4.2 28.7 1.0
C5' A:G836 4.2 29.6 1.0
O A:HOH8724 4.3 25.8 1.0
OP2 A:G836 4.3 30.4 1.0
C3' A:U835 4.3 30.4 1.0
O5' A:U2615 4.3 26.6 1.0
O5' A:G836 4.3 30.0 1.0
O3' A:U835 4.4 29.7 1.0
O3' A:C2614 4.4 26.5 1.0
OP2 A:G2616 4.4 31.5 1.0
O A:HOH3498 4.4 37.1 1.0
O A:HOH6310 4.6 42.0 1.0
N2 A:G2616 4.6 32.0 1.0
CA D:GLN230 4.7 30.1 1.0
C5' A:U835 4.7 31.3 1.0
O D:GLN230 4.9 28.3 1.0
C5' A:U2615 4.9 28.7 1.0
O A:HOH9065 5.0 33.5 1.0

Reference:

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz. Structural Insights Into Peptide Bond Formation Proc.Natl.Acad.Sci.Usa V. 99 11670 2002.
ISSN: ISSN 0027-8424
PubMed: 12185246
DOI: 10.1073/PNAS.172404099
Page generated: Mon Dec 14 06:37:26 2020

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