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Strontium in PDB 3ey3: A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution

Protein crystallography data

The structure of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution, PDB code: 3ey3 was solved by M.Egli, P.S.Pallan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.90 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.074, 43.218, 88.712, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 20.7

Strontium Binding Sites:

The binding sites of Strontium atom in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution (pdb code 3ey3). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 7 binding sites of Strontium where determined in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution, PDB code: 3ey3:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7;

Strontium binding site 1 out of 7 in 3ey3

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Strontium binding site 1 out of 7 in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr504

b:11.5
occ:1.00
O B:HOH614 2.6 15.5 1.0
O A:HOH616 2.6 13.5 1.0
O A:HOH617 2.6 14.2 1.0
O B:HOH611 2.6 11.2 1.0
O B:HOH613 2.6 14.1 1.0
O B:HOH610 2.7 9.9 1.0
O A:HOH612 2.7 14.0 1.0
O A:HOH615 2.7 14.0 1.0
O B:HOH684 4.3 15.5 1.0
N2 B:DG204 4.5 9.0 1.0
O B:HOH671 4.5 15.5 1.0
N2 A:DG110 4.6 11.6 1.0
O A:HOH624 4.6 23.2 1.0
O A:HOH947 4.7 56.2 1.0
O B:HOH635 4.8 17.3 1.0
O B:HOH888 4.8 56.2 1.0
O A:HOH925 4.9 47.7 1.0
O4' A:DC111 4.9 14.1 1.0
N3 B:DG204 4.9 9.3 1.0
N3 A:DG110 4.9 11.2 1.0
O A:HOH790 4.9 31.6 1.0

Strontium binding site 2 out of 7 in 3ey3

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Strontium binding site 2 out of 7 in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr506

b:19.4
occ:1.00
O A:HOH930 2.3 45.3 1.0
O A:HOH719 2.5 19.5 1.0
O A:HOH870 2.5 23.9 1.0
O A:HOH623 2.6 19.4 1.0
O A:HOH877 2.6 49.6 1.0
O A:HOH710 2.6 19.2 1.0
O A:HOH931 2.7 34.4 1.0
O B:HOH878 2.8 26.7 1.0
O B:HOH739 4.3 17.1 1.0
O A:HOH736 4.4 25.6 1.0
OP2 A:DC109 4.5 15.4 1.0
O A:HOH791 4.6 34.7 1.0
O B:HOH773 4.8 30.4 1.0
O A:HOH851 4.8 29.7 1.0
O A:HOH693 4.8 20.1 1.0
C5 A:DC109 4.8 10.8 1.0
N7 A:DG110 4.9 10.7 1.0

Strontium binding site 3 out of 7 in 3ey3

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Strontium binding site 3 out of 7 in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr501

b:11.9
occ:1.00
OP1 B:DA205 2.5 11.7 1.0
O B:HOH601 2.6 12.7 1.0
O B:HOH879 2.6 15.2 1.0
O B:HOH604 2.6 14.9 1.0
O B:HOH603 2.7 16.2 1.0
O B:HOH602 2.7 12.7 1.0
P B:DA205 3.8 11.0 1.0
OP2 B:DA205 4.3 11.5 1.0
O B:HOH645 4.4 18.8 1.0
O B:HOH669 4.4 18.1 1.0
O5' B:DA205 4.5 10.2 1.0
C5' B:DA205 4.7 10.3 1.0
O B:HOH712 4.8 24.6 1.0
O3' B:DG204 4.9 10.7 1.0

Strontium binding site 4 out of 7 in 3ey3

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Strontium binding site 4 out of 7 in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr503

b:10.3
occ:1.00
O D:HOH607 2.6 10.9 1.0
O C:HOH665 2.6 11.6 1.0
O C:HOH606 2.6 11.7 1.0
O D:HOH608 2.6 10.6 1.0
O C:HOH605 2.7 12.4 1.0
O D:HOH727 2.7 13.5 1.0
O C:HOH609 2.7 10.8 1.0
O C:HOH728 2.7 11.6 1.0
O D:HOH944 4.2 60.3 1.0
N2 C:DG304 4.4 9.6 1.0
O D:HOH714 4.5 16.5 1.0
O C:HOH681 4.5 25.9 1.0
O C:HOH663 4.6 18.6 1.0
N2 D:DG410 4.6 9.3 1.0
O C:HOH650 4.9 16.9 1.0
N3 C:DG304 4.9 9.6 1.0
N3 D:DG410 4.9 8.7 1.0
O4' D:DC411 5.0 10.6 1.0
O4' C:DA305 5.0 12.4 1.0

Strontium binding site 5 out of 7 in 3ey3

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Strontium binding site 5 out of 7 in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr507

b:22.4
occ:1.00
O C:HOH874 2.4 54.9 1.0
O C:HOH720 2.5 22.2 1.0
O C:HOH876 2.5 34.1 1.0
O C:HOH805 2.6 20.2 1.0
O C:HOH929 2.7 36.5 1.0
O C:HOH642 2.7 17.6 1.0
O C:HOH875 2.9 40.0 1.0
O C:HOH861 4.0 58.7 1.0
O C:HOH838 4.3 24.3 1.0
O C:HOH731 4.9 18.0 1.0
O6 C:DG312 4.9 12.6 1.0

Strontium binding site 6 out of 7 in 3ey3

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Strontium binding site 6 out of 7 in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr502

b:13.7
occ:1.00
O D:HOH724 2.4 18.1 1.0
O D:HOH721 2.5 12.2 1.0
O D:HOH726 2.6 16.7 1.0
OP1 D:DG412 2.6 11.8 1.0
O D:HOH722 2.6 14.3 1.0
O D:HOH723 2.6 14.2 1.0
O D:HOH725 2.7 16.4 1.0
P D:DG412 3.8 10.1 1.0
OP2 D:DG412 4.2 11.7 1.0
O5' D:DG412 4.4 12.0 1.0
O D:HOH703 4.4 14.4 1.0
O D:HOH893 4.5 71.2 1.0
C5' D:DG412 4.6 14.2 1.0
O D:HOH738 4.8 24.8 1.0
O D:HOH636 5.0 11.9 1.0

Strontium binding site 7 out of 7 in 3ey3

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Strontium binding site 7 out of 7 in the A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of A Conformational Transition in the Structure of A 2'-Thiomethyl- Modified Dna Visualized at High Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr505

b:16.6
occ:1.00
O C:HOH618 2.5 25.0 1.0
O D:HOH666 2.6 16.0 1.0
O C:HOH729 2.6 21.3 1.0
O C:HOH871 2.6 30.0 1.0
O C:HOH620 2.6 23.2 1.0
O C:HOH938 2.6 28.2 1.0
O C:HOH730 2.6 30.1 1.0
O D:HOH619 2.7 22.9 1.0
O C:HOH847 4.2 41.7 1.0
O D:HOH628 4.5 20.8 1.0
N2 C:DG310 4.6 12.8 1.0
N2 D:DG404 4.6 11.4 1.0
O C:HOH811 4.6 35.5 1.0
O C:HOH855 4.7 75.7 1.0
O4' C:DC311 4.7 15.5 1.0
C4' C:DC311 4.7 14.0 1.0
O4' D:DA405 4.9 14.0 1.0
O D:HOH747 4.9 24.5 1.0
N3 D:DG404 4.9 10.0 1.0
C4' D:DA405 5.0 13.7 1.0

Reference:

P.S.Pallan, T.P.Prakash, F.Li, R.L.Eoff, M.Manoharan, M.Egli. A Conformational Transition in the Structure of A 2'-Thiomethyl-Modified Dna Visualized at High Resolution. Chem.Commun.(Camb.) V. 15 2017 2009.
ISSN: ISSN 1359-7345
PubMed: 19333476
DOI: 10.1039/B822781K
Page generated: Wed Dec 16 02:20:46 2020

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