Nickel in PDB 1r6z: The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)

The structure of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion), PDB code: 1r6z was solved by J.J.Song, J.Liu, N.H.Tolia, J.Schneiderman, S.K.Smith, R.A.Martienssen, G.J.Hannon, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.91 / 2.80
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	89.811, 89.811, 380.326, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 28.1

The binding sites of Nickel atom in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) (pdb code 1r6z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion), PDB code: 1r6z:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ P:Ni728 b:40.0 occ:1.00 NE2 P:HIS671 2.0 44.5 1.0 CE1 P:HIS671 2.6 44.5 1.0 OD2 P:ASP672 2.8 68.2 1.0 CD2 P:HIS671 3.2 44.5 1.0 OD1 P:ASP672 3.3 68.2 1.0 CG P:ASP672 3.4 68.2 1.0 ND1 P:HIS671 3.8 44.5 1.0 CG P:HIS671 4.1 44.5 1.0 CB P:ASP672 4.9 68.2 1.0

Nickel binding site 2 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ P:Ni729 b:0.3 occ:1.00 CE1 P:HIS38 2.6 52.3 1.0 NI P:NI730 3.1 91.9 1.0 ND1 P:HIS38 3.4 52.3 1.0 NE2 P:HIS38 3.6 52.3 1.0 OH P:TYR16 4.2 35.6 1.0 CG P:HIS38 4.6 52.3 1.0 CD2 P:HIS38 4.7 52.3 1.0 CZ P:TYR16 4.9 35.6 1.0

Nickel binding site 3 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ P:Ni730 b:91.9 occ:1.00 ND1 P:HIS38 2.3 52.3 1.0 O P:HIS38 2.5 49.0 1.0 CE1 P:HIS38 2.8 52.3 1.0 NI P:NI729 3.1 0.3 1.0 CG P:HIS38 3.6 52.3 1.0 C P:HIS38 3.7 49.0 1.0 NE2 P:HIS38 4.0 52.3 1.0 CB P:HIS38 4.3 52.3 1.0 OD1 P:ASP40 4.4 55.8 1.0 CD2 P:HIS38 4.4 52.3 1.0 CA P:HIS38 4.5 49.0 1.0 N P:PRO39 4.6 31.3 1.0 CA P:PRO39 4.8 31.3 1.0 C P:PRO39 5.0 31.3 1.0

Nickel binding site 4 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni728 b:61.1 occ:1.00 NE2 A:HIS671 2.4 44.9 1.0 CE1 A:HIS671 3.0 44.9 1.0 OD2 A:ASP672 3.5 0.4 1.0 CD2 A:HIS671 3.6 44.9 1.0 OD1 A:ASP672 3.6 0.4 1.0 CG A:ASP672 4.0 0.4 1.0 ND1 A:HIS671 4.3 44.9 1.0 CG A:HIS671 4.6 44.9 1.0

Nickel binding site 5 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni729 b:77.8 occ:1.00 CE1 A:HIS38 2.9 47.6 1.0 ND1 A:HIS38 3.7 47.6 1.0 NE2 A:HIS38 3.9 47.6 1.0 NI A:NI730 4.1 0.7 1.0 OH A:TYR16 4.4 51.9 1.0 CG A:HIS38 4.9 47.6 1.0 CD2 A:HIS38 5.0 47.6 1.0

Nickel binding site 6 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni730 b:0.7 occ:1.00 O A:HIS38 2.6 38.4 1.0 ND1 A:HIS38 3.2 47.6 1.0 CE1 A:HIS38 3.6 47.6 1.0 C A:HIS38 3.7 38.4 1.0 NI A:NI729 4.1 77.8 1.0 OD1 A:ASP40 4.1 72.9 1.0 CA A:PRO39 4.2 38.0 1.0 CG A:HIS38 4.3 47.6 1.0 N A:PRO39 4.3 38.0 1.0 N A:ASP40 4.5 34.0 1.0 C A:PRO39 4.5 38.0 1.0 CG A:ASP40 4.7 72.9 1.0 CA A:HIS38 4.8 38.4 1.0 NE2 A:HIS38 4.8 47.6 1.0 OD2 A:ASP40 4.8 72.9 1.0 CB A:HIS38 4.9 47.6 1.0

Nickel binding site 7 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ni728 b:67.1 occ:1.00 NE2 Z:HIS671 2.0 59.4 1.0 OD2 Z:ASP672 2.7 71.1 1.0 CE1 Z:HIS671 2.7 59.4 1.0 OD1 Z:ASP672 2.9 71.1 1.0 CD2 Z:HIS671 3.1 59.4 1.0 CG Z:ASP672 3.1 71.1 1.0 ND1 Z:HIS671 3.9 59.4 1.0 CG Z:HIS671 4.1 59.4 1.0 CB Z:ASP672 4.6 71.1 1.0

Nickel binding site 8 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ni729 b:58.8 occ:1.00 O Z:HIS38 2.4 42.5 1.0 ND1 Z:HIS38 2.5 37.3 1.0 NI Z:NI730 2.9 0.3 1.0 CE1 Z:HIS38 2.9 37.3 1.0 C Z:HIS38 3.6 42.5 1.0 CG Z:HIS38 3.7 37.3 1.0 NE2 Z:HIS38 4.2 37.3 1.0 CB Z:HIS38 4.3 37.3 1.0 OD1 Z:ASP40 4.3 48.5 1.0 N Z:PRO39 4.4 43.0 1.0 CA Z:HIS38 4.5 42.5 1.0 CA Z:PRO39 4.5 43.0 1.0 CD2 Z:HIS38 4.6 37.3 1.0 C Z:PRO39 4.7 43.0 1.0 N Z:ASP40 4.8 34.8 1.0 N Z:HIS38 5.0 42.5 1.0

Nickel binding site 9 out of 9 in the The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of The Crystal Structure of the ARGONAUTE2 Paz Domain (As A Mbp Fusion) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ni730 b:0.3 occ:1.00 CE1 Z:HIS38 2.7 37.3 1.0 ND1 Z:HIS38 2.7 37.3 1.0 NI Z:NI729 2.9 58.8 1.0 NE2 Z:HIS38 3.8 37.3 1.0 CG Z:HIS38 3.8 37.3 1.0 O Z:HIS38 4.4 42.5 1.0 CD2 Z:HIS38 4.4 37.3 1.0 OH Z:TYR16 4.4 51.4 1.0 CA Z:GLY12 4.4 28.7 1.0 CE2 Z:TYR16 4.6 51.4 1.0 CB Z:HIS38 4.7 37.3 1.0 CZ Z:TYR16 4.8 51.4 1.0

J.J.Song, J.Liu, N.H.Tolia, J.Schneiderman, S.K.Smith, R.A.Martienssen, G.J.Hannon, L.Joshua-Tor. The Crystal Structure of the ARGONAUTE2 Paz Domain Reveals An Rna Binding Motif in Rnai Effector Complexes. Nat.Struct.Biol. V. 10 1026 2003.
ISSN: ISSN 1072-8368
PubMed: 14625589
DOI: 10.1038/NSB1016