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Barium in PDB 5ip8: Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg)

Protein crystallography data

The structure of Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg), PDB code: 5ip8 was solved by J.E.Souter, J.P.Hall, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.73 / 1.76
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 47.450, 47.450, 35.130, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22

Other elements in 5ip8:

The structure of Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg) also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg) (pdb code 5ip8). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg), PDB code: 5ip8:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in 5ip8

Go back to Barium Binding Sites List in 5ip8
Barium binding site 1 out of 2 in the Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:40.6
occ:1.00
O B:HOH219 2.7 39.6 1.0
O B:HOH222 2.8 43.4 1.0
O B:HOH207 2.8 41.4 1.0
O B:HOH215 2.8 40.3 1.0
O6 B:DG4 2.8 39.9 1.0
O A:HOH202 2.9 40.1 1.0
O B:HOH239 2.9 41.0 1.0
N7 B:DG3 3.0 39.0 1.0
N7 B:DG4 3.1 40.4 1.0
C6 B:DG4 3.6 37.2 1.0
C5 B:DG4 3.7 36.3 1.0
C8 B:DG3 3.7 37.9 1.0
C5 B:DG3 4.2 37.0 1.0
C8 B:DG4 4.3 37.4 1.0
O6 B:DG3 4.5 35.9 1.0
C6 B:DG3 4.7 35.4 1.0
OP2 B:DG3 4.7 44.4 1.0
O4 A:DT6 4.9 51.4 1.0
O A:HOH222 4.9 50.0 1.0
N1 B:DG4 4.9 38.6 1.0

Barium binding site 2 out of 2 in 5ip8

Go back to Barium Binding Sites List in 5ip8
Barium binding site 2 out of 2 in the Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:40.1
occ:1.00
O A:HOH210 2.6 42.9 1.0
O A:HOH203 2.7 41.4 1.0
O A:HOH213 2.7 40.5 1.0
O A:HOH217 2.7 46.5 1.0
O B:HOH205 2.8 40.2 1.0
O6 A:DG4 2.9 40.8 1.0
O A:HOH229 2.9 43.9 1.0
N7 A:DG3 3.0 39.7 1.0
N7 A:DG4 3.1 40.3 1.0
C6 A:DG4 3.6 36.8 1.0
C8 A:DG3 3.7 35.3 1.0
C5 A:DG4 3.7 36.1 1.0
C5 A:DG3 4.2 36.1 1.0
C8 A:DG4 4.3 40.9 1.0
O6 A:DG3 4.5 37.6 1.0
OP2 A:DG3 4.7 43.3 1.0
C6 A:DG3 4.7 34.5 1.0
O A:HOH227 4.7 50.2 1.0
O6 B:DG6 4.9 46.2 1.0
N1 A:DG4 5.0 39.7 1.0
N4 B:DC7 5.0 44.8 1.0
N9 A:DG3 5.0 40.8 1.0

Reference:

J.P.Hall, J.E.Souter, S.P.Gurung, C.J.Cardin. Sequence Specific Binding of Light Activated Ru-Polypyridyls To Be Published.
Page generated: Sat Dec 12 01:57:32 2020

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