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Nickel in PDB 2c9w: Crystal Structure of Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution

Protein crystallography data

The structure of Crystal Structure of Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution, PDB code: 2c9w was solved by J.E.Debreczeni, A.Bullock, A.Amos, P.Savitsky, A.Barr, N.Burgess, M.Sundstrom, J.Weigelt, C.Arrowsmith, A.Edwards, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.29 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.290, 105.290, 70.200, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 22.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution (pdb code 2c9w). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution, PDB code: 2c9w:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 2c9w

Go back to Nickel Binding Sites List in 2c9w
Nickel binding site 1 out of 3 in the Crystal Structure of Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution


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 Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1202

b:74.0
occ:1.00
ND1 A:HIS124 3.3 44.3 1.0
N A:ASP120 3.6 32.2 1.0
CB A:ASP120 3.9 35.8 1.0
CE1 A:HIS124 3.9 46.3 1.0
O A:HOH2053 4.1 41.4 1.0
N A:SER121 4.2 35.6 1.0
CA A:ASP120 4.3 35.6 1.0
CA A:PHE119 4.3 35.7 1.0
C A:PHE119 4.4 35.0 1.0
CG A:HIS124 4.5 38.9 1.0
CB A:PHE119 4.6 36.8 1.0
CG A:ASP120 4.7 46.6 1.0
CD2 A:PHE119 4.7 34.9 1.0
C A:ASP120 4.8 34.3 1.0
CB A:SER121 4.8 33.5 1.0
CB A:HIS124 4.8 31.1 1.0

Nickel binding site 2 out of 3 in 2c9w

Go back to Nickel Binding Sites List in 2c9w
Nickel binding site 2 out of 3 in the Crystal Structure of Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution


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 Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1203

b:33.8
occ:0.75
SG A:CYS111 2.1 37.0 1.0
CB A:CYS111 3.1 40.3 1.0
CA A:CYS111 3.8 43.6 1.0
N A:CYS111 4.4 41.4 1.0
CG2 A:ILE110 4.7 41.0 1.0
NE2 A:HIS149 4.7 72.9 1.0
O A:ILE110 4.7 43.3 1.0
C A:ILE110 4.8 40.5 1.0
O A:HOH2049 4.9 47.6 1.0
CD2 A:LEU95 5.0 39.0 1.0

Nickel binding site 3 out of 3 in 2c9w

Go back to Nickel Binding Sites List in 2c9w
Nickel binding site 3 out of 3 in the Crystal Structure of Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution


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 Socs-2 in Complex with Elongin-B and Elongin-C at 1.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1105

b:47.2
occ:0.50
SG B:CYS89 2.3 48.4 1.0
CB B:CYS89 3.1 39.9 1.0
C B:CYS89 3.7 37.4 1.0
O B:CYS89 3.8 35.8 1.0
CA B:CYS89 3.9 36.7 1.0
N B:ILE90 4.0 34.0 1.0
CA B:HIS10 4.1 32.6 1.0
N B:GLU91 4.2 32.4 1.0
CD2 B:HIS10 4.2 34.2 1.0
C B:ILE90 4.3 33.2 1.0
CG B:HIS10 4.3 32.7 1.0
CA B:ILE90 4.5 33.2 1.0
OE1 B:GLU91 4.5 49.6 1.0
CA B:GLU91 4.6 36.0 1.0
CB B:HIS10 4.6 31.9 1.0
O B:ILE90 4.7 33.2 1.0
NE2 B:HIS10 4.7 28.8 1.0
CB B:GLU91 4.7 36.4 1.0
ND1 B:HIS10 4.8 33.7 1.0
N B:HIS10 4.9 32.4 1.0
C B:HIS10 5.0 32.2 1.0

Reference:

A.N.Bullock, J.E.Debreczeni, A.M.Edwards, M.Sundstrom, S.Knapp. Crystal Structure of the SOCS2-Elongin C-Elongin B Complex Defines A Prototypical Socs Box Ubiquitin Ligase. Proc. Natl. Acad. Sci. V. 103 7637 2006U.S.A..
ISSN: ISSN 0027-8424
PubMed: 16675548
DOI: 10.1073/PNAS.0601638103
Page generated: Fri Sep 25 08:07:32 2020
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