Atomistry » Strontium » PDB 2hdf-3i5a » 3bnq
Atomistry »
  Strontium »
    PDB 2hdf-3i5a »
      3bnq »

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

Go back to Strontium Binding Sites List in 3bnq
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

Go back to Strontium Binding Sites List in 3bnq
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

Go back to Strontium Binding Sites List in 3bnq
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

Go back to Strontium Binding Sites List in 3bnq
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

Go back to Strontium Binding Sites List in 3bnq
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

Go back to Strontium Binding Sites List in 3bnq
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

Go back to Strontium Binding Sites List in 3bnq
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

Go back to Strontium Binding Sites List in 3bnq
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: Thu Oct 10 21:29:25 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy