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Magnesium in PDB 357d: 3.5 A Structure of Fragment I From E. Coli 5S Rrna

Protein crystallography data

The structure of 3.5 A Structure of Fragment I From E. Coli 5S Rrna, PDB code: 357d was solved by C.C.Correll, B.Freeborn, 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) 10.00 / 3.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.670, 58.670, 248.840, 90.00, 90.00, 120.00
R / Rfree (%) 31.2 / 26.5

Other elements in 357d:

The structure of 3.5 A Structure of Fragment I From E. Coli 5S Rrna also contains other interesting chemical elements:

Mercury (Hg) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna (pdb code 357d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna, PDB code: 357d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 357d

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Magnesium binding site 1 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg62

b:25.1
occ:1.00
 OP2 B:G75 2.2 57.8 1.0
OP2 C:A99 2.6 65.1 1.0
P B:G75 3.5 58.2 1.0
O5' C:A99 3.5 64.6 1.0
P C:A99 3.6 64.2 1.0
O5' B:G75 3.8 59.3 1.0
N7 B:G76 4.1 73.2 1.0
C3' C:G98 4.2 62.2 1.0
N7 B:G75 4.2 52.6 1.0
C8 B:G75 4.2 52.9 1.0
O3' C:G98 4.3 63.4 1.0
O4 B:U77 4.4 67.5 1.0
O6 B:G76 4.5 76.1 1.0
OP1 B:G75 4.5 57.2 1.0
O3' B:U74 4.5 55.7 1.0
O5' B:U74 4.7 55.5 1.0
C3' B:U74 4.7 53.4 1.0
C5' C:A99 4.8 64.1 1.0
OP2 B:U74 4.8 56.5 1.0
OP1 C:A99 4.9 63.6 1.0
C2' C:G98 4.9 61.3 1.0
OP2 B:G76 4.9 65.4 1.0
C5 B:G76 4.9 73.0 1.0
C8 B:G76 5.0 71.6 1.0

Magnesium binding site 2 out of 8 in 357d

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Magnesium binding site 2 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg63

b:25.4
occ:1.00
 OP1 B:U74 2.2 55.5 1.0
OP1 C:A99 2.9 63.6 1.0
OP2 C:A99 3.3 65.1 1.0
P C:A99 3.6 64.2 1.0
P B:U74 3.7 55.5 1.0
C5' C:G98 3.8 63.4 1.0
C5' B:U74 4.1 55.0 1.0
O5' B:U74 4.2 55.5 1.0
O3' B:A73 4.5 53.4 1.0
OP1 C:G98 4.5 67.0 1.0
O5' C:G98 4.6 65.1 1.0
O3' C:G98 4.6 63.4 1.0
OP2 B:U74 4.7 56.5 1.0
O5' C:A99 4.8 64.6 1.0
OP2 B:G75 4.9 57.8 1.0
C4' C:G98 4.9 62.6 1.0

Magnesium binding site 3 out of 8 in 357d

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Magnesium binding site 3 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg64

b:23.5
occ:1.00
 OP2 C:G100 2.4 63.7 1.0
P C:G100 3.7 62.9 1.0
OP2 B:A73 4.0 60.0 1.0
OP1 C:G100 4.1 63.6 1.0
C5' B:A73 4.3 53.9 1.0
O6 C:G102 4.4 83.9 1.0
OP2 B:U74 4.5 56.5 1.0
N7 C:G102 4.6 80.6 1.0
O5' C:G100 4.6 64.5 1.0
O3' C:A99 4.8 61.5 1.0
C5' C:A99 4.8 64.1 1.0
O5' B:A73 4.9 58.3 1.0
P B:A73 5.0 60.6 1.0

Magnesium binding site 4 out of 8 in 357d

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Magnesium binding site 4 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg65

b:31.9
occ:1.00
 O6 C:G98 2.8 62.5 1.0
C6 C:G98 3.6 61.1 1.0
N7 C:G98 3.9 61.7 1.0
C5 C:G98 4.1 61.5 1.0
OP2 B:G76 4.1 65.4 1.0
OP1 B:G76 4.4 64.4 1.0
OP2 C:C97 4.5 68.9 1.0
P B:G76 4.8 64.5 1.0
N1 C:G98 4.8 60.4 1.0

Magnesium binding site 5 out of 8 in 357d

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Magnesium binding site 5 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg66

b:59.9
occ:1.00
 OP2 B:A78 2.3 70.9 1.0
P B:A78 3.2 70.7 1.0
OP1 B:A78 3.3 71.2 1.0
OP2 B:G79 3.6 80.7 1.0
O5' B:A78 3.9 71.3 1.0
N7 B:G79 4.5 81.5 1.0
O3' B:U77 4.6 69.1 1.0
O4 B:U80 4.8 83.0 1.0

Magnesium binding site 6 out of 8 in 357d

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Magnesium binding site 6 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg67

b:80.9
occ:1.00
 N2 C:G100 4.3 73.6 1.0
N1 C:G100 4.5 67.3 1.0
O2 B:U77 4.8 65.3 1.0
N2 B:G76 4.9 73.7 1.0
C2 C:G100 5.0 69.2 1.0

Magnesium binding site 7 out of 8 in 357d

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Magnesium binding site 7 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg68

b:69.4
occ:1.00
 OP2 C:A119 2.4 0.4 1.0
P C:A119 3.7 0.6 1.0
OP1 C:A119 4.3 0.9 1.0
C5' C:C118 4.3 95.0 1.0
O3' C:C118 4.4 99.9 1.0
C3' C:C118 4.7 97.5 1.0
O5' C:A119 4.9 0.7 1.0

Magnesium binding site 8 out of 8 in 357d

Go back to Magnesium Binding Sites List in 357d
Magnesium binding site 8 out of 8 in the 3.5 A Structure of Fragment I From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 3.5 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg69

b:61.1
occ:1.00
 O6 A:G6 3.7 98.5 1.0
O6 A:G7 4.1 88.7 1.0
N7 A:G6 4.4 99.5 1.0
O4 A:SSU5 4.6 98.9 1.0
C6 A:G6 4.6 98.4 1.0
C5 A:SSU5 4.7 99.5 1.0
C5 A:G6 4.9 98.6 1.0
C4 A:SSU5 4.9 99.5 1.0
N4 A:C8 5.0 93.4 1.0

Reference:

C.C.Correll, B.Freeborn, P.B.Moore, T.A.Steitz. Metals, Motifs, and Recognition in the Crystal Structure of A 5S Rrna Domain. Cell(Cambridge,Mass.) V. 91 705 1997.
ISSN: ISSN 0092-8674
PubMed: 9393863
DOI: 10.1016/S0092-8674(00)80457-2
Page generated: Wed Aug 14 08:11:07 2024

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