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

Protein crystallography data

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

Nickel Binding Sites:

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 1r6z

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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 1r6z

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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 1r6z

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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 1r6z

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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 1r6z

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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 1r6z

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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 1r6z

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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 1r6z

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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 1r6z

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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

Reference:

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
Page generated: Fri Sep 25 08:00:45 2020
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