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Gold in PDB 5lys: The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative

Protein crystallography data

The structure of The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative, PDB code: 5lys was solved by D.Martinez-Zapien, P.Legrand, A.G.Mcewen, S.Pasquali, A.-C.Dock-Bregeon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.320, 47.830, 69.230, 90.00, 105.54, 90.00
R / Rfree (%) 18.5 / 22.7

Other elements in 5lys:

The structure of The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 1 atom

Gold Binding Sites:

The binding sites of Gold atom in the The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative (pdb code 5lys). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 2 binding sites of Gold where determined in the The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative, PDB code: 5lys:
Jump to Gold binding site number: 1; 2;

Gold binding site 1 out of 2 in 5lys

Go back to Gold Binding Sites List in 5lys
Gold binding site 1 out of 2 in the The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au101

b:64.0
occ:0.35
N3 A:U40 1.0 57.1 0.5
C4 A:U40 1.3 57.4 0.5
O4 A:U40 1.6 56.8 0.5
C2 A:U40 2.3 57.6 0.5
N7 A:G64 2.4 43.1 0.5
C5 A:U40 2.7 58.7 0.5
N7 A:G64 3.0 49.1 0.5
O6 A:G64 3.1 48.7 0.5
O2 A:U40 3.1 57.4 0.5
N1 A:U40 3.2 59.1 0.5
O4' A:U63 3.3 52.3 0.5
C6 A:U40 3.3 59.3 0.5
C8 A:G64 3.4 43.8 0.5
C2 A:C62 3.5 53.9 0.5
C5 A:G64 3.5 42.0 0.5
O2 A:C62 3.5 52.5 0.5
N3 A:C62 3.5 61.8 0.5
O6 A:G64 3.6 42.2 0.5
C2 A:C62 3.6 62.4 0.5
C4' A:U63 3.6 53.3 0.5
C5 A:G64 3.7 48.3 0.5
N3 A:C62 3.7 54.0 0.5
C6 A:G64 3.7 47.8 0.5
O2 A:C62 3.8 61.5 0.5
C2' A:C62 3.9 56.6 0.5
C6 A:G64 3.9 41.4 0.5
N1 A:C62 4.0 56.1 0.5
O4' A:U63 4.0 57.6 0.5
C4 A:C62 4.0 62.8 0.5
C8 A:G64 4.1 49.6 0.5
N1 A:C62 4.2 64.5 0.5
O5' A:U63 4.3 55.9 0.5
N1 A:G46 4.3 44.1 1.0
C4 A:C62 4.3 55.4 0.5
C5' A:U63 4.3 54.4 0.5
C4' A:U63 4.4 58.3 0.5
C1' A:C62 4.5 58.2 0.5
O2' A:C62 4.5 55.8 0.5
N4 A:C62 4.6 62.9 0.5
C6 A:C62 4.6 56.5 0.5
C2' A:C62 4.6 65.8 0.5
C5 A:C62 4.6 64.3 0.5
N9 A:G64 4.6 44.4 0.5
C1' A:U63 4.6 50.7 0.5
C4 A:G64 4.6 42.6 0.5
C6 A:C62 4.6 64.8 0.5
N2 A:G46 4.7 42.8 1.0
C1' A:U40 4.7 61.6 0.5
C5 A:U40 4.7 47.8 0.5
C5 A:C62 4.8 56.6 0.5
O3' A:U63 4.8 52.4 0.5
O A:HOH247 4.8 55.9 1.0
C3' A:C62 4.8 58.9 0.5
O4 A:U40 4.8 45.3 0.5
O5' A:U63 4.8 63.2 0.5
C2 A:G46 4.8 43.0 1.0
C3' A:U63 4.8 52.5 0.5
C1' A:U63 4.9 55.2 0.5
C6 A:G46 5.0 44.6 1.0
C4 A:G64 5.0 48.7 0.5

Gold binding site 2 out of 2 in 5lys

Go back to Gold Binding Sites List in 5lys
Gold binding site 2 out of 2 in the The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au102

b:79.9
occ:0.55
N7 B:G64 2.7 43.6 1.0
O B:HOH296 2.8 50.0 1.0
C2 B:C62 3.4 59.0 1.0
O6 B:G64 3.5 36.8 1.0
N3 B:C62 3.5 58.2 1.0
O2 B:C62 3.5 58.3 1.0
C5 B:G64 3.6 42.1 1.0
O4' B:U63 3.6 49.4 1.0
C8 B:G64 3.7 45.6 1.0
C4' B:U63 3.7 51.5 1.0
O B:HOH220 3.8 36.3 1.0
N1 B:C62 3.9 61.5 1.0
C6 B:G64 3.9 38.6 1.0
C2' B:C62 3.9 62.4 1.0
O5' B:U63 4.0 57.3 1.0
C5' B:U63 4.0 53.6 1.0
C4 B:C62 4.0 58.9 1.0
C6 B:C62 4.4 60.8 1.0
N1 B:G46 4.5 50.5 1.0
C5 B:C62 4.5 60.1 1.0
C1' B:C62 4.5 64.6 1.0
C3' B:C62 4.7 63.7 1.0
O2' B:C62 4.7 62.6 1.0
N4 B:C62 4.8 58.5 1.0
O6 B:G46 4.8 51.9 1.0
C4 B:G64 4.8 44.5 1.0
N9 B:G64 4.9 46.8 1.0
O B:HOH234 4.9 38.5 1.0
C6 B:G46 5.0 51.2 1.0

Reference:

D.Martinez-Zapien, P.Legrand, A.G.Mcewen, F.Proux, T.Cragnolini, S.Pasquali, A.C.Dock-Bregeon. The Crystal Structure of the 5 Functional Domain of the Transcription Riboregulator 7SK. Nucleic Acids Res. V. 45 3568 2017.
ISSN: ESSN 1362-4962
PubMed: 28082395
DOI: 10.1093/NAR/GKW1351
Page generated: Sat Dec 12 01:54:22 2020

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