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Strontium in PDB 3bnq: Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)

Protein crystallography data

The structure of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative), PDB code: 3bnq was solved by J.Kondo, E.Westhof, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.79 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.266, 76.056, 55.912, 90.00, 117.06, 90.00
R / Rfree (%) 22.9 / 26.9

Other elements in 3bnq:

The structure of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Potassium (K) 2 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) (pdb code 3bnq). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 8 binding sites of Strontium where determined in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative), PDB code: 3bnq:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 3bnq

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Strontium binding site 1 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:78.2
occ:0.50
 OP1 A:C16 4.2 40.0 1.0
OP1 A:A18 4.3 39.3 1.0
OP2 A:C16 4.7 32.5 1.0
OP1 A:G15 4.7 54.0 1.0
OP2 A:A18 4.7 38.1 1.0
P A:C16 4.9 38.9 1.0

Strontium binding site 2 out of 8 in 3bnq

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Strontium binding site 2 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr201

b:43.3
occ:1.00
 O B:HOH207 2.6 48.8 1.0
O B:HOH205 2.6 46.1 1.0
O B:HOH203 2.6 45.4 1.0
O B:HOH204 2.6 48.5 1.0
O B:HOH206 2.6 47.9 1.0
O A:HOH302 2.6 50.1 1.0
O6 B:G5 4.1 23.4 1.0
O4 A:U20 4.1 27.2 1.0
N7 B:G5 4.3 28.1 1.0
O B:HOH229 4.6 37.0 1.0
O6 A:G19 4.8 29.8 1.0
C6 B:G5 4.8 25.5 1.0
N4 B:C4 4.8 32.2 1.0
O B:HOH220 4.8 44.0 1.0
O B:HOH223 4.9 45.9 1.0
C5 B:G5 4.9 27.3 1.0
O4 B:U6 5.0 23.7 1.0

Strontium binding site 3 out of 8 in 3bnq

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Strontium binding site 3 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr202

b:60.1
occ:0.94
 O A:HOH304 2.6 60.6 0.9
O B:HOH208 2.6 59.2 0.9
O B:HOH210 2.6 61.8 0.9
O A:HOH303 2.6 61.3 0.9
O B:HOH209 2.6 58.8 0.9
OP2 B:C10 4.1 33.4 1.0
OP2 A:C10 4.3 34.7 1.0
O A:HOH313 4.5 37.1 1.0
OP1 B:C10 4.6 31.9 1.0
P B:C10 4.9 30.6 1.0
OP1 B:C9 5.0 37.4 1.0

Strontium binding site 4 out of 8 in 3bnq

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Strontium binding site 4 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr201

b:75.2
occ:0.79
 O C:HOH305 2.6 75.9 0.8
O C:HOH307 2.6 76.5 0.8
O D:HOH210 2.6 75.8 0.8
O D:HOH209 2.6 76.7 0.8
O C:HOH306 2.6 77.6 0.8
OP2 C:C10 4.0 35.1 1.0
OP2 D:C8 4.4 34.2 1.0
O C:HOH330 4.6 43.6 1.0
OP1 C:C10 4.8 39.7 1.0
OP1 D:C7 4.8 36.6 1.0
P C:C10 4.9 39.0 1.0

Strontium binding site 5 out of 8 in 3bnq

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Strontium binding site 5 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr202

b:88.0
occ:1.00
 O D:HOH215 2.6 87.3 1.0
O C:HOH310 2.6 87.5 1.0
O D:HOH216 2.6 87.0 1.0
O C:HOH309 2.6 87.9 1.0
O C:HOH311 2.6 86.7 1.0
O D:HOH217 2.6 87.1 1.0
O D:HOH221 4.0 58.7 1.0
OP1 C:G5 4.4 69.1 1.0
OP1 C:U6 4.5 46.9 1.0
OP2 C:U6 4.6 48.8 1.0
OP2 D:G13 4.7 44.3 1.0
P C:U6 5.0 51.5 1.0

Strontium binding site 6 out of 8 in 3bnq

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Strontium binding site 6 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr203

b:76.1
occ:0.87
 O C:HOH312 2.6 75.5 0.9
O D:HOH220 2.6 75.8 0.9
O C:HOH313 2.6 75.7 0.9
O D:HOH218 2.6 76.0 0.9
O D:HOH219 2.6 76.8 0.9
O C:HOH314 2.6 75.8 0.9
OP2 D:C14 3.7 44.4 1.0
OP2 C:G5 4.2 67.9 1.0
O C:HOH309 4.5 87.9 1.0

Strontium binding site 7 out of 8 in 3bnq

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Strontium binding site 7 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr201

b:42.4
occ:1.00
 O D:HOH206 2.6 48.6 1.0
O D:HOH207 2.6 44.5 1.0
O D:HOH204 2.6 48.0 1.0
O D:HOH205 2.6 49.4 1.0
O C:HOH304 2.6 46.9 1.0
O D:HOH208 2.6 49.1 1.0
O6 D:G3 4.1 27.1 1.0
O4 C:U20 4.2 27.7 1.0
N7 D:G3 4.4 32.3 1.0
O4 D:U4 4.8 22.2 1.0
C6 D:G3 4.9 30.3 1.0
N4 D:C2 5.0 28.0 1.0

Strontium binding site 8 out of 8 in 3bnq

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Strontium binding site 8 out of 8 in the Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of the Homo Sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SRCL2 (A1555G Mutant, Br-Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr202

b:71.3
occ:1.00
 O D:HOH211 2.6 73.8 1.0
O D:HOH214 2.6 73.0 1.0
O D:HOH212 2.6 72.2 1.0
O C:HOH308 2.6 74.0 1.0
O D:HOH203 2.6 73.4 1.0
O D:HOH213 2.6 73.6 1.0
O6 D:G17 4.2 35.1 1.0
N7 D:G17 4.2 37.1 1.0
OP2 D:A16 4.4 39.1 1.0
O4 C:U6 4.5 43.8 1.0
C6 D:G17 4.9 34.7 1.0
C5 D:G17 4.9 37.1 1.0

Reference:

J.Kondo, E.Westhof. The Bacterial and Mitochondrial Ribosomal A-Site Molecular Switches Possess Different Conformational Substates Nucleic Acids Res. V. 36 2654 2008.
ISSN: ISSN 0305-1048
PubMed: 18346970
DOI: 10.1093/NAR/GKN112
Page generated: Wed Dec 16 02:16:16 2020

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