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Strontium in PDB 1f1t: Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine

Protein crystallography data

The structure of Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine, PDB code: 1f1t was solved by C.Baugh, D.Grate, C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.00 / 2.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 55.297, 55.297, 143.920, 90.00, 90.00, 120.00
R / Rfree (%) 26.1 / 28.2

Other elements in 1f1t:

The structure of Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine also contains other interesting chemical elements:

Bromine (Br) 5 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine (pdb code 1f1t). 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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine, PDB code: 1f1t:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 1f1t

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Strontium binding site 1 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:44.5
occ:1.00
 OP1 A:G34 2.6 34.6 1.0
O2 A:5BU32 2.8 40.5 1.0
C2 A:5BU32 3.9 40.6 1.0
P A:G34 4.1 34.9 1.0
O2' A:5BU32 4.5 39.5 1.0
O3' A:G33 4.7 34.9 1.0
N3 A:5BU32 4.7 40.9 1.0
C2' A:5BU32 4.8 39.2 1.0
C1' A:5BU32 4.8 39.6 1.0
N1 A:5BU32 4.9 40.3 1.0
C5' A:G34 4.9 33.7 1.0
O5' A:G34 5.0 34.2 1.0

Strontium binding site 2 out of 8 in 1f1t

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Strontium binding site 2 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr202

b:0.0
occ:1.00
 O6 A:G34 4.5 32.0 1.0
N6 A:A35 4.7 30.3 1.0
N7 A:A35 4.7 31.5 1.0

Strontium binding site 3 out of 8 in 1f1t

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Strontium binding site 3 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr203

b:0.0
occ:0.77
 OP1 A:C28 4.2 47.7 1.0
N7 A:G24 4.3 46.8 1.0
OP2 A:G29 4.4 45.4 1.0
O6 A:G24 4.7 47.1 1.0
C23 A:ROS101 4.9 22.9 1.0
OP2 A:C28 5.0 47.5 1.0

Strontium binding site 4 out of 8 in 1f1t

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Strontium binding site 4 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr204

b:0.0
occ:0.96
 O A:HOH302 3.6 35.2 1.0
O6 A:G23 4.4 37.3 1.0
N7 A:A22 4.7 35.3 1.0
N7 A:G23 4.8 37.8 1.0

Strontium binding site 5 out of 8 in 1f1t

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Strontium binding site 5 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr205

b:70.9
occ:0.54
 OP2 A:G33 3.2 38.0 1.0
OP2 A:A31 3.2 40.2 1.0
OP1 A:G33 4.0 38.3 1.0
P A:G33 4.1 38.2 1.0
OP2 A:A30 4.1 42.4 1.0
P A:A31 4.4 40.0 1.0
O5' A:A31 4.4 39.9 1.0
C8 A:A31 4.7 38.4 1.0
C5' A:A30 4.7 41.2 1.0
N7 A:A31 4.8 38.3 1.0
OP2 A:5BU32 4.8 38.3 1.0
O A:HOH304 4.8 18.6 1.0

Strontium binding site 6 out of 8 in 1f1t

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Strontium binding site 6 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr206

b:71.3
occ:0.66
 OP1 A:G33 2.6 38.3 1.0
O A:HOH304 2.7 18.6 1.0
P A:G33 3.8 38.2 1.0
C5' A:G33 3.9 36.8 1.0
O3' A:5BU32 4.1 38.1 1.0
O5' A:G33 4.2 37.6 1.0

Strontium binding site 7 out of 8 in 1f1t

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Strontium binding site 7 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr208

b:99.0
occ:0.73
 O A:HOH301 3.7 60.8 1.0
N7 A:G13 4.5 44.4 1.0
OP2 A:G13 4.5 45.8 1.0
N4 A:C14 4.6 41.2 1.0
O6 A:G15 4.7 39.2 1.0
C5 A:C14 5.0 41.4 1.0

Strontium binding site 8 out of 8 in 1f1t

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Strontium binding site 8 out of 8 in the Crystal Structure of the Malachite Green Aptamer Complexed with Tetramethyl-Rosamine


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 Malachite Green Aptamer Complexed with Tetramethyl-Rosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr209

b:78.3
occ:0.52
 OP2 A:G19 4.1 33.4 1.0

Reference:

C.Baugh, D.Grate, C.Wilson. 2.8 A Crystal Structure of the Malachite Green Aptamer. J.Mol.Biol. V. 301 117 2000.
ISSN: ISSN 0022-2836
PubMed: 10926496
DOI: 10.1006/JMBI.2000.3951
Page generated: Thu Oct 10 14:03:40 2024

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