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Strontium in PDB 1u3e: Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui

Protein crystallography data

The structure of Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui, PDB code: 1u3e was solved by B.W.Shen, M.Landthaler, D.A.Shub, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.92
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 45.000, 108.300, 248.100, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 24.7

Other elements in 1u3e:

The structure of Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Strontium Binding Sites:

The binding sites of Strontium atom in the Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui (pdb code 1u3e). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 4 binding sites of Strontium where determined in the Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui, PDB code: 1u3e:
Jump to Strontium binding site number: 1; 2; 3; 4;

Strontium binding site 1 out of 4 in 1u3e

Go back to Strontium Binding Sites List in 1u3e
Strontium binding site 1 out of 4 in the Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr414

b:0.4
occ:1.00
O A:HOH424 3.1 73.6 1.0
O2 B:EDO403 3.5 83.5 1.0
C2 B:EDO403 4.0 78.6 1.0
O1 B:EDO403 4.0 73.3 1.0
C5' A:DC27 4.2 67.5 1.0
C4' A:DC27 4.2 66.9 1.0
O2 A:DT26 4.4 46.4 1.0
O4' A:DC27 4.6 66.9 1.0
O4' B:DT14 4.6 60.3 1.0
C1 B:EDO403 4.7 76.4 1.0
C4' B:DT14 4.7 59.1 1.0

Strontium binding site 2 out of 4 in 1u3e

Go back to Strontium Binding Sites List in 1u3e
Strontium binding site 2 out of 4 in the Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr415

b:0.5
occ:0.50
O B:HOH405 3.1 76.4 1.0
O A:HOH418 3.4 78.1 1.0
O6 A:DG36 4.3 0.2 1.0

Strontium binding site 3 out of 4 in 1u3e

Go back to Strontium Binding Sites List in 1u3e
Strontium binding site 3 out of 4 in the Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Sr417

b:96.0
occ:1.00
O M:LYS118 2.8 47.1 1.0
O M:GLN120 3.0 48.2 1.0
O M:HOH425 3.2 77.3 1.0
SR M:SR418 3.2 0.4 1.0
C M:LYS118 3.7 43.1 1.0
C M:GLN120 4.2 47.7 1.0
CA M:LYS118 4.2 40.0 1.0
N M:GLN120 4.5 46.9 1.0
N M:ASN119 4.6 46.5 1.0
C M:ASN119 4.6 47.0 1.0
CA M:ASN119 4.8 46.3 1.0
CB M:LYS118 4.9 36.4 1.0
O M:ILE117 4.9 38.8 1.0
CA M:GLN120 4.9 47.5 1.0

Strontium binding site 4 out of 4 in 1u3e

Go back to Strontium Binding Sites List in 1u3e
Strontium binding site 4 out of 4 in the Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Sr418

b:0.4
occ:1.00
O M:LYS118 2.8 47.1 1.0
O B:HOH404 3.1 67.6 1.0
SR M:SR417 3.2 96.0 1.0
OP1 B:DT18 3.8 45.7 1.0
C M:LYS118 4.0 43.1 1.0
O3' B:DC17 4.5 47.9 1.0
CA M:ASN119 4.6 46.3 1.0
N M:ASN119 4.8 46.5 1.0
P B:DT18 4.8 46.2 1.0
OD1 M:ASN119 4.9 44.4 1.0
CA M:LYS118 5.0 40.0 1.0
CB M:LYS118 5.0 36.4 1.0

Reference:

B.W.Shen, M.Landthaler, D.A.Shub, B.L.Stoddard. Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui. J.Mol.Biol. V. 342 43 2004.
ISSN: ISSN 0022-2836
PubMed: 15313606
DOI: 10.1016/J.JMB.2004.07.032
Page generated: Wed Dec 16 02:10:40 2020

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