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Magnesium in PDB 430d: Structure of Sarcin/Ricin Loop From Rat 28S Rrna

Protein crystallography data

The structure of Structure of Sarcin/Ricin Loop From Rat 28S Rrna, PDB code: 430d was solved by C.C.Correll, A.Munishkin, Y.L.Chan, Z.Ren, I.G.Wool, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.830, 56.830, 107.960, 90.00, 90.00, 120.00
R / Rfree (%) 28 / 33

Other elements in 430d:

The structure of Structure of Sarcin/Ricin Loop From Rat 28S Rrna also contains other interesting chemical elements:

Bromine (Br) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna (pdb code 430d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna, PDB code: 430d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 430d

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Magnesium binding site 1 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg31

b:56.5
occ:1.00
 OP2 A:C23 3.2 71.6 1.0
OP1 A:C23 3.4 71.9 1.0
OP2 A:G24 3.6 72.8 1.0
P A:C23 3.6 71.8 1.0
O5' A:C23 3.9 72.6 1.0

Magnesium binding site 2 out of 9 in 430d

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Magnesium binding site 2 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg32

b:67.5
occ:1.00
 O A:HOH107 2.2 63.8 1.0
N1 A:G16 3.6 67.1 1.0
N2 A:G16 3.7 66.8 1.0
C2 A:G16 4.2 66.9 1.0
C2 A:A17 4.4 67.9 1.0
O6 A:G16 4.6 67.2 1.0
C6 A:G16 4.6 66.5 1.0
N6 A:A15 4.7 66.4 1.0
N3 A:A17 4.9 68.2 1.0
N1 A:A17 5.0 67.6 1.0

Magnesium binding site 3 out of 9 in 430d

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Magnesium binding site 3 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg33

b:64.3
occ:1.00
 OP1 A:G24 2.2 72.6 1.0
P A:G24 2.7 72.6 1.0
O5' A:G24 2.9 72.4 1.0
OP2 A:G24 2.9 72.8 1.0
C5' A:G24 3.5 71.0 1.0
C3' A:G24 3.9 69.1 1.0
OP2 A:C25 3.9 67.3 1.0
C4' A:G24 4.2 70.0 1.0
O3' A:G24 4.3 68.0 1.0
O3' A:C23 4.3 73.2 1.0
P A:C25 4.7 67.5 1.0

Magnesium binding site 4 out of 9 in 430d

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Magnesium binding site 4 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg34

b:71.5
occ:1.00
 N4 A:C28 3.4 52.0 1.0
BR A:CBV27 4.2 92.7 1.0
MG A:MG36 4.3 70.5 1.0
C4 A:C28 4.6 51.9 1.0
O6 A:G2 4.6 46.3 1.0
N4 A:CBV27 4.6 51.9 1.0
C5 A:C28 4.9 52.1 1.0

Magnesium binding site 5 out of 9 in 430d

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Magnesium binding site 5 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg35

b:66.1
occ:1.00
 OP2 A:A12 2.3 71.2 1.0
N4 A:C13 2.8 72.5 1.0
C5 A:C13 3.4 72.4 1.0
OP2 A:U11 3.5 67.8 1.0
C4 A:C13 3.5 72.4 1.0
O5' A:U11 3.5 67.8 1.0
P A:A12 3.6 72.3 1.0
N2 A:G19 3.8 57.3 1.0
P A:U11 4.0 67.3 1.0
C3' A:U11 4.1 69.8 1.0
O3' A:U11 4.2 71.2 1.0
O5' A:A12 4.2 72.0 1.0
N7 A:A12 4.5 73.1 1.0
O6 A:G14 4.5 68.3 1.0
C5' A:U11 4.6 68.5 1.0
OP1 A:U11 4.7 67.5 1.0
C6 A:C13 4.7 72.0 1.0
C8 A:A12 4.7 72.8 1.0
N3 A:C13 4.8 72.3 1.0
OP1 A:A12 4.9 72.2 1.0
C2 A:G19 4.9 58.3 1.0
C4' A:U11 5.0 69.2 1.0

Magnesium binding site 6 out of 9 in 430d

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Magnesium binding site 6 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg36

b:70.5
occ:1.00
 N4 A:C29 3.2 50.1 1.0
N4 A:C28 4.0 52.0 1.0
C4 A:C29 4.1 50.5 1.0
C5 A:C29 4.1 50.2 1.0
MG A:MG34 4.3 71.5 1.0
C5 A:C28 4.4 52.1 1.0
C4 A:C28 4.4 51.9 1.0

Magnesium binding site 7 out of 9 in 430d

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Magnesium binding site 7 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg37

b:66.5
occ:1.00
 C8 A:G10 3.8 64.5 1.0
C2' A:G10 4.2 65.0 1.0
C5' A:G10 4.3 63.8 1.0
N7 A:G10 4.7 64.2 1.0
N9 A:G10 4.7 64.5 1.0
O4' A:G10 4.8 64.8 1.0
C1' A:G10 4.9 64.8 1.0
C4' A:G10 4.9 64.7 1.0
C3' A:G10 5.0 65.3 1.0
O2' A:G10 5.0 65.3 1.0

Magnesium binding site 8 out of 9 in 430d

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Magnesium binding site 8 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg38

b:56.0
occ:1.00
 N4 A:C25 3.4 59.3 1.0
N6 A:A26 3.8 53.5 1.0
C4 A:C25 4.3 60.4 1.0
C5 A:C25 4.6 60.2 1.0

Magnesium binding site 9 out of 9 in 430d

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Magnesium binding site 9 out of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg39

b:68.9
occ:1.00
 O2 A:CBV27 3.7 53.3 1.0
O2 A:U4 3.8 48.7 1.0
C2 A:CBV27 4.2 53.4 1.0
C1' A:CBV27 4.4 55.9 1.0
N1 A:CBV27 4.6 54.5 1.0
O2' A:U4 4.7 48.2 1.0
C2 A:A26 4.7 55.5 1.0
N2 A:G3 4.8 47.4 1.0
O4' A:G5 4.9 52.1 1.0
C1' A:G5 4.9 51.5 1.0
N3 A:CBV27 4.9 52.8 1.0

Reference:

C.C.Correll, A.Munishkin, Y.L.Chan, Z.Ren, I.G.Wool, T.A.Steitz. Crystal Structure of the Ribosomal Rna Domain Essential For Binding Elongation Factors. Proc.Natl.Acad.Sci.Usa V. 95 13436 1998.
ISSN: ISSN 0027-8424
PubMed: 9811818
DOI: 10.1073/PNAS.95.23.13436
Page generated: Mon Dec 14 09:05:12 2020

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