Atomistry » Strontium » PDB 1cs7-2grb » 1nvy
Atomistry »
  Strontium »
    PDB 1cs7-2grb »
      1nvy »

Strontium in PDB 1nvy: Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4

Protein crystallography data

The structure of Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4, PDB code: 1nvy was solved by C.J.Cardin, J.H.Thorpe, B.C.Gale, S.C.M.Teixeira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.30 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 63.734, 25.320, 36.493, 90.00, 110.11, 90.00
R / Rfree (%) 20.7 / 26.3

Strontium Binding Sites:

The binding sites of Strontium atom in the Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4 (pdb code 1nvy). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 5 binding sites of Strontium where determined in the Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4, PDB code: 1nvy:
Jump to Strontium binding site number: 1; 2; 3; 4; 5;

Strontium binding site 1 out of 5 in 1nvy

Go back to Strontium Binding Sites List in 1nvy
Strontium binding site 1 out of 5 in the Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr103

b:30.7
occ:1.00
O B:HOH638 2.4 30.9 1.0
O A:HOH490 2.5 32.5 1.0
O B:HOH492 2.5 58.6 1.0
O A:HOH491 2.6 22.3 1.0
O B:HOH493 2.6 28.6 1.0
O B:HOH488 2.6 20.9 1.0
O A:HOH489 2.9 33.8 1.0
N2 A:DG3 4.4 18.2 1.0
O A:HOH502 4.4 25.7 1.0
N2 A:DG4 4.4 18.9 1.0
O B:HOH512 4.5 31.0 1.0
O2 B:DC8 4.5 18.1 1.0
O B:HOH501 4.5 25.2 1.0
O A:HOH523 4.8 23.4 1.0
O4' A:DT5 4.8 25.7 1.0
O4' B:DG9 4.8 26.4 1.0
O B:HOH539 4.9 22.6 1.0
N3 A:DG4 5.0 20.3 1.0

Strontium binding site 2 out of 5 in 1nvy

Go back to Strontium Binding Sites List in 1nvy
Strontium binding site 2 out of 5 in the Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr104

b:36.5
occ:1.00
O B:HOH495 2.5 29.5 1.0
O A:HOH497 2.5 23.3 1.0
O A:HOH500 2.6 38.1 1.0
O A:HOH496 2.7 39.5 1.0
O B:HOH498 2.7 27.4 1.0
O B:HOH494 2.7 29.8 1.0
O A:HOH499 2.8 24.6 1.0
O B:HOH561 4.1 20.8 0.5
N2 B:DG9 4.3 17.4 1.0
O A:HOH514 4.4 30.0 1.0
O2 A:DC2 4.4 18.4 1.0
O A:HOH540 4.6 28.3 1.0
O4' A:DG3 4.8 32.6 1.0
N3 B:DA10 4.9 19.0 1.0
O4' A:DC2 4.9 21.4 1.0

Strontium binding site 3 out of 5 in 1nvy

Go back to Strontium Binding Sites List in 1nvy
Strontium binding site 3 out of 5 in the Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr101

b:22.8
occ:1.00
O B:HOH472 2.5 24.2 1.0
O B:HOH476 2.5 23.1 1.0
O B:HOH473 2.6 17.9 1.0
O B:HOH478 2.6 17.5 1.0
O B:HOH477 2.6 21.0 1.0
O B:HOH474 2.7 21.8 1.0
O B:HOH475 2.7 19.5 1.0
O B:HOH479 2.7 21.3 1.0
O B:HOH519 4.5 24.9 1.0
O2 B:DC2 4.5 17.4 1.0
O B:HOH516 4.5 23.9 1.0
O B:HOH521 4.8 40.5 0.5
O4' B:DG3 4.8 19.3 1.0
O B:HOH555 4.8 31.0 0.5
O4' B:DC2 4.9 18.0 1.0

Strontium binding site 4 out of 5 in 1nvy

Go back to Strontium Binding Sites List in 1nvy
Strontium binding site 4 out of 5 in the Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr102

b:27.7
occ:1.00
O B:HOH484 2.5 27.0 1.0
O B:HOH480 2.6 20.8 1.0
O B:HOH482 2.6 29.3 1.0
O B:HOH483 2.6 20.6 1.0
O B:HOH481 2.7 24.2 1.0
O B:HOH486 2.7 24.1 1.0
O B:HOH485 2.7 26.7 1.0
O B:HOH487 2.7 28.7 1.0
O B:HOH522 4.3 31.2 1.0
N2 B:DG4 4.5 18.6 1.0
O B:HOH515 4.6 22.0 1.0
N2 B:DG3 4.7 17.4 1.0
O4' B:DT5 4.7 22.9 1.0
O B:HOH544 4.9 33.2 1.0
O B:HOH556 4.9 30.5 1.0
C4' B:DT5 5.0 27.0 1.0

Strontium binding site 5 out of 5 in 1nvy

Go back to Strontium Binding Sites List in 1nvy
Strontium binding site 5 out of 5 in the Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Strontium Bound to the Holliday Junction Sequence D(Tcggtaccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr105

b:31.2
occ:1.00
O B:HOH466 2.4 23.8 1.0
O B:HOH639 2.4 33.2 1.0
O B:HOH468 2.5 28.2 1.0
O B:HOH470 2.6 26.7 1.0
O B:HOH471 2.6 45.4 1.0
O B:HOH469 2.7 34.2 1.0
O B:HOH467 2.8 33.5 1.0
O B:HOH506 4.4 25.2 1.0
OP1 B:DC7 4.4 23.2 1.0
O B:HOH536 4.5 32.1 1.0
O B:HOH542 4.8 26.9 1.0
OP2 B:DC8 4.9 21.9 1.0
OP1 B:DC8 4.9 22.4 1.0
O B:HOH518 4.9 20.5 1.0
O3' B:DA6 4.9 22.0 1.0

Reference:

C.J.Cardin, J.H.Thorpe, B.C.Gale, S.C.M.Teixeira. Strontium, A Mad Taerget For the Dna Holliday Junction To Be Published.
Page generated: Wed Dec 16 02:10:37 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy