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Nickel in PDB 2qqb: Crystal Structure of Dtxr(M10A C102D) Complexed with Nickel(II)

Protein crystallography data

The structure of Crystal Structure of Dtxr(M10A C102D) Complexed with Nickel(II), PDB code: 2qqb was solved by J.A.D'aquino, J.R.Lattimer, A.Denninger, K.E.D'aquino, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 1.92
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.320, 62.320, 104.582, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 31.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Dtxr(M10A C102D) Complexed with Nickel(II) (pdb code 2qqb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Dtxr(M10A C102D) Complexed with Nickel(II), PDB code: 2qqb:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2qqb

Go back to Nickel Binding Sites List in 2qqb
Nickel binding site 1 out of 2 in the Crystal Structure of Dtxr(M10A C102D) Complexed with Nickel(II)


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 Dtxr(M10A C102D) Complexed with Nickel(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni551

b:21.1
occ:1.00
NE2 A:HIS79 2.1 11.8 1.0
O2 A:PO4600 2.2 16.2 1.0
OE2 A:GLU83 2.3 15.9 1.0
O A:HOH613 2.3 15.7 1.0
ND1 A:HIS98 2.4 12.9 1.0
CD2 A:HIS79 3.0 11.5 1.0
CE1 A:HIS79 3.0 16.0 1.0
CD A:GLU83 3.1 13.1 1.0
CE1 A:HIS98 3.2 8.9 1.0
OE1 A:GLU83 3.3 13.3 1.0
P A:PO4600 3.4 17.0 1.0
CG A:HIS98 3.4 16.8 1.0
O3 A:PO4600 3.6 15.1 1.0
CB A:HIS98 3.8 13.1 1.0
O4 A:PO4600 3.8 18.4 1.0
ND1 A:HIS79 4.2 11.5 1.0
CG A:HIS79 4.2 13.1 1.0
NE2 A:HIS98 4.4 16.5 1.0
CA A:HIS98 4.4 14.7 1.0
CG A:GLU83 4.4 9.3 1.0
CD2 A:HIS98 4.5 13.9 1.0
CD2 A:PHE128 4.5 10.6 1.0
O1 A:PO4600 4.6 14.6 1.0
CE2 A:PHE128 4.6 15.6 1.0
O A:HIS98 4.8 11.3 1.0

Nickel binding site 2 out of 2 in 2qqb

Go back to Nickel Binding Sites List in 2qqb
Nickel binding site 2 out of 2 in the Crystal Structure of Dtxr(M10A C102D) Complexed with Nickel(II)


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 Dtxr(M10A C102D) Complexed with Nickel(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni552

b:24.8
occ:1.00
NE2 A:HIS106 2.1 16.1 1.0
O A:HOH612 2.1 14.8 1.0
O A:ASP102 2.2 12.6 1.0
OE2 A:GLU105 2.3 14.0 1.0
O A:HOH608 2.3 21.1 1.0
OD1 A:ASP102 2.3 13.9 1.0
CD2 A:HIS106 3.0 9.6 1.0
CE1 A:HIS106 3.0 15.7 1.0
C A:ASP102 3.1 12.1 1.0
CD A:GLU105 3.2 12.1 1.0
CG A:ASP102 3.3 17.9 1.0
CG A:GLU105 3.3 7.3 1.0
CA A:ASP102 3.5 13.3 1.0
NH2 A:ARG13 3.9 21.6 1.0
CB A:ASP102 4.0 11.2 1.0
O A:HOH655 4.0 18.6 1.0
ND1 A:HIS106 4.1 10.8 1.0
CG A:HIS106 4.1 16.7 1.0
O A:LEU4 4.2 33.5 1.0
N A:ARG103 4.3 12.8 1.0
OD2 A:ASP102 4.3 21.1 1.0
OE1 A:GLU105 4.3 13.0 1.0
CA A:ARG103 4.8 12.2 1.0
CB A:GLU105 4.8 12.0 1.0
O A:HOH618 4.8 14.5 1.0
N A:ASP102 4.9 13.2 1.0
O A:ALA101 5.0 12.9 1.0
CZ A:ARG13 5.0 20.6 1.0

Reference:

J.A.D'aquino, J.R.Lattimer, A.Denninger, K.E.D'aquino, D.Ringe. Role of the N-Terminal Helix in the Metal Ion-Induced Activation of the Diphtheria Toxin Repressor Dtxr. Biochemistry V. 46 11761 2007.
ISSN: ISSN 0006-2960
PubMed: 17902703
DOI: 10.1021/BI7007883
Page generated: Fri Sep 25 08:13:51 2020
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