Nickel in PDB 3t4b: Crystal Structure of the Hcv Ires Pseudoknot Domain

The structure of Crystal Structure of the Hcv Ires Pseudoknot Domain, PDB code: 3t4b was solved by K.E.Berry, S.Waghray, S.A.Mortimer, Y.Bai, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.09 / 3.55
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.390, 113.390, 88.220, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Nickel atom in the Crystal Structure of the Hcv Ires Pseudoknot Domain (pdb code 3t4b). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 17 binding sites of Nickel where determined in the Crystal Structure of the Hcv Ires Pseudoknot Domain, PDB code: 3t4b:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:0.4 occ:1.00 N7 A:G10 1.9 0.5 1.0 C5 A:G10 3.0 0.9 1.0 C8 A:G10 3.0 0.1 1.0 O6 A:G10 3.2 0.5 1.0 C6 A:G10 3.4 0.6 1.0 N7 A:G9 3.5 0.1 1.0 OP2 A:G9 3.5 0.2 1.0 C8 A:G9 3.8 0.3 1.0 OP2 A:G10 3.8 0.9 1.0 N9 A:G10 4.1 0.9 1.0 C4 A:G10 4.2 0.5 1.0 C5 A:G9 4.4 0.7 1.0 O5' A:G9 4.4 0.8 1.0 P A:G9 4.5 0.0 1.0 N9 A:G9 4.8 0.2 1.0 N1 A:G10 4.8 0.6 1.0

Nickel binding site 2 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1002 b:0.9 occ:1.00 N7 A:G7 1.9 0.3 1.0 C8 A:G7 2.9 0.8 1.0 C5 A:G7 3.0 0.7 1.0 O6 A:G7 3.3 0.0 1.0 C6 A:G7 3.5 0.3 1.0 N7 A:G6 3.6 0.9 1.0 OP2 A:G7 3.9 0.8 1.0 OP2 A:G6 3.9 0.1 1.0 C8 A:G6 4.0 0.2 1.0 H8 A:G6 4.0 0.0 1.0 H3' A:G6 4.1 0.0 1.0 N9 A:G7 4.1 0.2 1.0 C4 A:G7 4.2 0.2 1.0 C5 A:G6 4.3 0.4 1.0 O5' A:G6 4.7 0.2 1.0 N9 A:G6 4.8 0.9 1.0 C6 A:G6 4.8 0.4 1.0 N1 A:G7 4.8 0.4 1.0 O6 A:G6 4.9 0.8 1.0 P A:G6 4.9 0.3 1.0 O5' A:G7 4.9 0.8 1.0 C4 A:G6 4.9 0.8 1.0

Nickel binding site 3 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1003 b:0.6 occ:1.00 N7 A:G285 2.1 0.1 1.0 C8 A:G285 3.1 0.4 1.0 C5 A:G285 3.2 0.9 1.0 O6 A:G285 3.5 0.3 1.0 C6 A:G285 3.7 0.4 1.0 C4 A:C21 3.8 0.3 1.0 C5 A:C21 4.0 0.7 1.0 OP2 A:G285 4.0 0.3 1.0 N3 A:C21 4.0 0.2 1.0 N4 A:C21 4.1 0.4 1.0 N9 A:G285 4.3 0.1 1.0 C6 A:C21 4.3 0.7 1.0 C4 A:G285 4.3 0.0 1.0 C2 A:C21 4.4 0.1 1.0 N1 A:C21 4.6 0.4 1.0 O6 A:G286 4.9 0.2 1.0 N7 A:G286 4.9 1.0 1.0

Nickel binding site 4 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1004 b:0.4 occ:1.00 N7 A:G135 2.0 0.7 1.0 C8 A:G135 3.0 0.9 1.0 C5 A:G135 3.0 0.9 1.0 O6 A:G135 3.3 0.6 1.0 C6 A:G135 3.5 0.4 1.0 N7 A:A134 3.9 0.5 1.0 OP2 A:G135 4.0 0.5 1.0 N9 A:G135 4.1 0.4 1.0 C4 A:G135 4.2 0.1 1.0 C8 A:A134 4.3 0.9 1.0 OP2 A:A134 4.7 0.4 1.0 C5 A:A134 4.7 0.2 1.0 N1 A:G135 4.9 0.5 1.0 O5' A:A134 5.0 0.7 1.0

Nickel binding site 5 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1005 b:0.4 occ:1.00 N7 A:G300 2.0 0.2 1.0 C8 A:G300 2.9 0.9 1.0 C5 A:G300 3.0 0.9 1.0 O6 A:G300 3.5 0.7 1.0 C6 A:G300 3.6 0.0 1.0 OP2 A:G300 3.9 0.5 1.0 N7 A:G299 4.0 0.4 1.0 OP2 A:G299 4.1 0.4 1.0 N9 A:G300 4.1 0.4 1.0 C4 A:G300 4.2 0.6 1.0 C8 A:G299 4.4 0.1 1.0 C5 A:G299 4.6 0.7 1.0 N7 A:G301 4.7 0.7 1.0 O5' A:G299 4.8 0.9 1.0 O5' A:G300 4.9 0.5 1.0 N1 A:G300 5.0 0.7 1.0

Nickel binding site 6 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1006 b:0.8 occ:1.00 N7 A:G307 1.8 0.9 1.0 C2 A:U306 2.4 0.5 1.0 N1 A:U306 2.4 0.5 1.0 C8 A:G307 2.7 0.7 1.0 C5 A:G307 2.9 0.5 1.0 C6 A:U306 2.9 0.5 1.0 N3 A:U306 2.9 0.5 1.0 O2 A:U306 2.9 0.5 1.0 C1' A:U306 3.0 0.5 1.0 C2' A:U306 3.3 0.5 1.0 C5 A:U306 3.4 0.5 1.0 N4 A:C308 3.4 0.3 1.0 C4 A:U306 3.4 0.5 1.0 O6 A:G307 3.4 0.3 1.0 O2' A:U306 3.4 0.5 1.0 C6 A:G307 3.5 0.4 1.0 N9 A:G307 3.9 0.9 1.0 C4 A:C308 3.9 0.3 1.0 C4 A:G307 4.0 0.5 1.0 C5 A:C308 4.0 0.7 1.0 N1 A:A330 4.2 0.4 1.0 C2 A:A330 4.3 0.3 1.0 O4 A:U306 4.4 0.5 1.0 O4' A:U306 4.4 0.5 1.0 C3' A:U306 4.8 0.5 1.0 N1 A:G307 4.9 0.4 1.0 N3 A:C308 4.9 0.7 1.0

Nickel binding site 7 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1007 b:0.2 occ:1.00 N7 A:G322 1.9 0.6 1.0 C5 A:G322 2.9 0.7 1.0 C8 A:G322 2.9 0.9 1.0 O6 A:G322 3.3 0.1 1.0 C6 A:G322 3.4 0.9 1.0 OP2 A:G322 3.7 0.3 1.0 N9 A:G322 4.1 0.7 1.0 C4 A:G322 4.1 0.6 1.0 C5 A:A321 4.2 0.8 1.0 N7 A:A321 4.3 0.0 1.0 C6 A:A321 4.5 0.1 1.0 C4 A:A321 4.7 0.5 1.0 C8 A:A321 4.7 0.2 1.0 N6 A:A321 4.7 0.5 1.0 N7 A:G323 4.8 0.5 1.0 N1 A:G322 4.8 0.2 1.0 N9 A:A321 4.9 0.5 1.0 O6 A:G323 5.0 0.2 1.0 P A:G322 5.0 0.5 1.0

Nickel binding site 8 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1008 b:0.6 occ:1.00 N7 A:G319 2.0 0.0 1.0 C8 A:G319 3.0 0.2 1.0 C5 A:G319 3.1 0.4 1.0 O6 A:G319 3.4 0.7 1.0 C6 A:G319 3.6 0.3 1.0 N7 A:G318 3.6 0.7 1.0 C5 A:G318 3.7 0.6 1.0 C6 A:G318 4.0 0.8 1.0 NI A:NI1009 4.0 0.1 1.0 C8 A:G318 4.1 0.9 1.0 N9 A:G319 4.2 0.9 1.0 C4 A:G319 4.2 1.0 1.0 C4 A:G318 4.2 0.5 1.0 O6 A:G318 4.3 0.3 1.0 OP2 A:G319 4.3 0.1 1.0 N9 A:G318 4.5 0.6 1.0 N1 A:G318 4.8 0.7 1.0 N1 A:G319 4.9 0.6 1.0

Nickel binding site 9 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1009 b:0.1 occ:1.00 N7 A:G320 2.0 0.3 1.0 C8 A:G320 3.0 0.0 1.0 C5 A:G320 3.1 0.2 1.0 O6 A:G320 3.4 0.3 1.0 C6 A:G320 3.6 0.1 1.0 C5 A:G319 3.8 0.4 1.0 N7 A:G319 3.8 0.0 1.0 C6 A:G319 3.9 0.3 1.0 NI A:NI1008 4.0 0.6 1.0 O6 A:G319 4.0 0.7 1.0 N9 A:G320 4.2 0.3 1.0 C4 A:G320 4.2 0.3 1.0 C8 A:G319 4.4 0.2 1.0 C4 A:G319 4.4 1.0 1.0 OP2 A:G320 4.5 0.2 1.0 N1 A:G319 4.6 0.6 1.0 N7 A:A321 4.6 0.0 1.0 N9 A:G319 4.7 0.9 1.0 N1 A:G320 5.0 0.7 1.0

Nickel binding site 10 out of 17 in the Crystal Structure of the Hcv Ires Pseudoknot Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of the Hcv Ires Pseudoknot Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1010 b:0.4 occ:1.00 N7 A:G132 2.0 0.8 1.0 C8 A:G132 3.0 0.3 1.0 C5 A:G132 3.1 0.3 1.0 O6 A:G132 3.4 0.2 1.0 NI A:NI1014 3.5 0.7 0.9 C6 A:G132 3.6 0.5 1.0 N7 A:G131 3.8 0.3 1.0 C5 A:G131 4.0 0.4 1.0 C6 A:G131 4.2 0.4 1.0 N9 A:G132 4.2 1.0 1.0 O6 A:G131 4.2 0.7 1.0 C4 A:G132 4.3 0.3 1.0 OP2 A:G132 4.3 0.6 1.0 C8 A:G131 4.4 0.8 1.0 C4 A:G131 4.6 0.2 1.0 N9 A:G131 4.9 0.3 1.0 N1 A:G131 4.9 0.2 1.0 N1 A:G132 5.0 0.1 1.0

K.E.Berry, S.Waghray, S.A.Mortimer, Y.Bai, J.A.Doudna. Crystal Structure of the Hcv Ires Central Domain Reveals Strategy For Start-Codon Positioning. Structure V. 19 1456 2011.
ISSN: ISSN 0969-2126
PubMed: 22000514
DOI: 10.1016/J.STR.2011.08.002