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Magnesium in PDB 1dfu: Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution

Protein crystallography data

The structure of Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution, PDB code: 1dfu was solved by M.Lu, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.600, 76.600, 95.100, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution (pdb code 1dfu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution, PDB code: 1dfu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1dfu

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Magnesium binding site 1 out of 5 in the Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution


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 E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg501

b:26.9
occ:1.00
 O M:HOH525 1.8 22.7 1.0
O M:HOH518 2.0 15.7 1.0
O M:HOH529 2.1 18.6 1.0
O4 M:U95 2.2 18.0 1.0
O N:HOH520 2.2 21.2 1.0
O P:HOH131 2.6 28.4 1.0
C4 M:U95 3.3 18.9 1.0
O M:HOH579 3.7 20.4 1.0
O N:HOH512 4.0 22.1 1.0
C5 M:U95 4.0 18.8 1.0
N6 M:A94 4.1 17.3 1.0
N7 M:A94 4.1 20.5 1.0
O P:HOH164 4.1 49.4 1.0
O M:HOH532 4.2 25.2 1.0
O4 N:U80 4.3 15.1 1.0
O M:HOH539 4.4 26.5 1.0
N3 M:U95 4.4 18.1 1.0
O M:HOH517 4.5 24.7 1.0
O6 M:G96 4.6 16.6 1.0
C5 M:A94 4.7 19.2 1.0
C6 M:A94 4.7 18.3 1.0
CD P:LYS14 4.8 24.3 1.0
O M:HOH516 4.9 28.0 1.0

Magnesium binding site 2 out of 5 in 1dfu

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Magnesium binding site 2 out of 5 in the Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution


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 E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg502

b:40.6
occ:1.00
 O M:HOH510 1.6 36.6 1.0
O M:HOH571 2.1 33.6 1.0
OP2 M:G100 2.1 18.1 1.0
O M:HOH552 2.1 30.0 1.0
O M:HOH541 2.5 30.8 1.0
O N:HOH539 2.7 42.6 1.0
MG M:MG505 3.3 35.9 1.0
P M:G100 3.5 18.5 1.0
OP1 M:G100 4.1 16.5 1.0
O5' M:G100 4.1 14.3 1.0
O M:HOH555 4.1 46.1 1.0
O M:HOH535 4.1 34.8 1.0
OP2 M:A101 4.2 17.1 1.0
N7 M:A101 4.2 14.3 1.0
O6 M:G102 4.3 18.3 1.0
O N:HOH528 4.4 34.9 1.0
O M:HOH515 4.5 14.8 1.0
O3' M:A99 4.5 16.0 1.0
O M:HOH588 4.6 40.5 1.0
O M:HOH507 4.8 47.5 1.0
C3' M:A99 4.9 16.8 1.0

Magnesium binding site 3 out of 5 in 1dfu

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Magnesium binding site 3 out of 5 in the Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution


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 E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg503

b:66.0
occ:1.00
 O M:HOH550 1.8 43.6 1.0
O M:HOH583 2.2 23.9 1.0
O M:HOH569 2.3 44.3 1.0
O M:HOH586 2.4 48.6 1.0
O M:HOH573 3.9 42.9 1.0
O M:HOH568 3.9 45.5 1.0
N7 M:G106 4.1 35.4 1.0
O M:HOH578 4.1 52.0 1.0
O M:HOH549 4.2 49.2 1.0
O M:HOH584 4.5 47.2 1.0
N7 M:G107 4.5 41.3 1.0
O6 M:G107 4.6 40.3 1.0
OP2 M:G106 4.6 35.5 1.0
O6 M:G106 4.6 34.0 1.0
O M:HOH585 4.7 23.1 1.0
C5 M:G106 4.8 34.5 1.0
C8 M:G106 4.9 34.9 1.0

Magnesium binding site 4 out of 5 in 1dfu

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Magnesium binding site 4 out of 5 in the Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution


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 E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg505

b:35.9
occ:1.00
 O M:HOH552 2.0 30.0 1.0
O M:HOH535 2.0 34.8 1.0
O M:HOH527 2.5 28.1 1.0
O M:HOH510 2.8 36.6 1.0
N7 M:G102 2.9 18.3 1.0
O6 M:G102 3.0 18.3 1.0
O M:HOH507 3.1 47.5 1.0
MG M:MG502 3.3 40.6 1.0
C5 M:G102 3.5 18.1 1.0
C6 M:G102 3.5 17.7 1.0
O M:HOH541 3.8 30.8 1.0
C8 M:G102 4.0 17.6 1.0
O N:HOH563 4.2 37.8 1.0
N7 M:A101 4.2 14.3 1.0
OP2 M:A101 4.4 17.1 1.0
O M:HOH555 4.5 46.1 1.0
O4 M:U103 4.6 21.2 1.0
C8 M:A101 4.8 13.8 1.0
O M:HOH588 4.8 40.5 1.0
C4 M:G102 4.8 17.8 1.0
O N:HOH539 4.8 42.6 1.0
OP2 M:G102 4.8 19.7 1.0
N1 M:G102 4.9 17.5 1.0

Magnesium binding site 5 out of 5 in 1dfu

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Magnesium binding site 5 out of 5 in the Crystal Structure of E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution


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 E.Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg504

b:54.6
occ:1.00
 O M:HOH536 1.9 38.3 1.0
O N:HOH568 1.9 29.5 1.0
O N:HOH507 2.0 38.7 1.0
O N:HOH527 2.3 40.1 1.0
O N:HOH530 2.3 20.9 1.0
O N:HOH528 2.3 34.9 1.0
O N:HOH529 3.6 28.2 1.0
OP2 M:A99 3.9 20.1 1.0
OP2 N:U74 4.0 25.1 1.0
O N:HOH540 4.0 43.0 1.0
O M:HOH537 4.1 30.4 1.0
N7 N:G75 4.1 15.7 1.0
OP2 N:G75 4.2 23.6 1.0
O N:HOH539 4.4 42.6 1.0
O6 N:G76 4.4 14.2 1.0
O N:HOH508 4.4 24.1 1.0
O M:HOH543 4.4 47.6 1.0
O5' M:A99 4.6 24.2 1.0
C8 N:G75 4.8 17.5 1.0
N7 N:G76 4.9 15.5 1.0
P M:A99 4.9 19.9 1.0

Reference:

M.Lu, T.A.Steitz. Structure of Escherichia Coli Ribosomal Protein L25 Complexed with A 5S Rrna Fragment at 1.8-A Resolution. Proc.Natl.Acad.Sci.Usa V. 97 2023 2000.
ISSN: ISSN 0027-8424
PubMed: 10696113
DOI: 10.1073/PNAS.97.5.2023
Page generated: Sat Aug 9 20:31:07 2025

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