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Nickel in PDB 2isy: Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider)

Protein crystallography data

The structure of Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider), PDB code: 2isy was solved by G.Wisedchaisri, C.J.Chou, M.Wu, C.Roach, A.E.Rice, R.K.Holmes, C.Beeson, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.13 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.954, 44.743, 49.641, 110.18, 96.57, 108.29
R / Rfree (%) 17.6 / 21.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider) (pdb code 2isy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider), PDB code: 2isy:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2isy

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Nickel binding site 1 out of 4 in the Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider)


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 Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1001

b:20.9
occ:1.00
OE2 A:GLU83 2.1 15.8 1.0
ND1 A:HIS98 2.2 15.5 1.0
O4 A:PO42001 2.2 22.1 1.0
O A:HOH2020 2.2 18.4 1.0
NE2 A:HIS79 2.2 16.5 1.0
O A:HOH2017 2.4 20.8 1.0
CE1 A:HIS98 3.0 15.2 1.0
CD A:GLU83 3.0 16.1 1.0
CE1 A:HIS79 3.2 14.7 1.0
CD2 A:HIS79 3.2 15.3 1.0
CG A:HIS98 3.2 15.9 1.0
P A:PO42001 3.3 19.1 1.0
OE1 A:GLU83 3.3 17.7 1.0
O1 A:PO42001 3.6 20.0 1.0
CB A:HIS98 3.7 17.6 1.0
O3 A:PO42001 3.7 21.1 1.0
NE2 A:HIS98 4.2 15.7 1.0
O A:HOH2068 4.2 36.2 1.0
CA A:HIS98 4.2 18.4 1.0
ND1 A:HIS79 4.3 16.2 1.0
CD2 A:HIS98 4.3 15.1 1.0
CG A:GLU83 4.3 14.1 1.0
CG A:HIS79 4.3 13.8 1.0
O2 A:PO42001 4.6 18.7 1.0
CE1 A:PHE128 4.8 34.1 1.0
CD1 A:PHE128 4.9 30.9 1.0
O A:HIS98 4.9 18.6 1.0

Nickel binding site 2 out of 4 in 2isy

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Nickel binding site 2 out of 4 in the Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider)


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 Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1002

b:18.7
occ:1.00
OD A:CSO102 1.9 3.8 0.5
OE2 A:GLU105 2.0 18.9 1.0
NE2 A:HIS106 2.1 12.0 1.0
O A:CSO102 2.1 17.0 1.0
O A:HOH2043 2.2 21.9 1.0
SD A:MET10 2.4 19.4 1.0
CD2 A:HIS106 3.0 11.8 1.0
CE1 A:HIS106 3.1 14.1 1.0
CD A:GLU105 3.1 18.0 1.0
SG A:CSO102 3.1 15.0 0.5
SG A:CSO102 3.1 21.1 0.5
C A:CSO102 3.2 16.1 1.0
CG A:MET10 3.4 20.8 1.0
CG A:GLU105 3.5 14.4 1.0
CE A:MET10 3.5 20.3 1.0
CA A:CSO102 3.6 15.8 1.0
CB A:CSO102 3.9 14.6 1.0
NH1 A:ARG13 4.0 36.4 1.0
O A:LEU4 4.1 23.5 1.0
CG A:HIS106 4.2 13.9 1.0
ND1 A:HIS106 4.2 13.2 1.0
OE1 A:GLU105 4.2 20.7 1.0
O A:HOH2049 4.3 31.1 1.0
OD A:CSO102 4.3 14.9 0.5
N A:ARG103 4.3 14.1 1.0
CA A:ARG103 4.8 13.8 1.0
CB A:MET10 4.8 12.4 1.0
N A:CSO102 5.0 15.4 1.0

Nickel binding site 3 out of 4 in 2isy

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Nickel binding site 3 out of 4 in the Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider)


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 Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1001

b:21.1
occ:1.00
O B:HOH2017 2.1 25.2 1.0
NE2 B:HIS79 2.1 19.9 1.0
ND1 B:HIS98 2.1 12.7 1.0
OE2 B:GLU83 2.1 20.0 1.0
O B:HOH2046 2.2 32.6 1.0
O3 B:PO42001 2.3 17.6 1.0
CE1 B:HIS98 3.0 13.7 1.0
CE1 B:HIS79 3.0 19.1 1.0
CD B:GLU83 3.0 19.7 1.0
CD2 B:HIS79 3.1 16.1 1.0
CG B:HIS98 3.2 13.0 1.0
P B:PO42001 3.4 18.1 1.0
OE1 B:GLU83 3.4 19.1 1.0
O1 B:PO42001 3.6 17.4 1.0
O4 B:PO42001 3.6 18.5 1.0
CB B:HIS98 3.6 17.5 1.0
NE2 B:HIS98 4.1 13.0 1.0
ND1 B:HIS79 4.2 19.4 1.0
CA B:HIS98 4.2 17.7 1.0
CG B:HIS79 4.2 19.2 1.0
CD2 B:HIS98 4.3 14.6 1.0
O B:HOH2061 4.3 39.5 1.0
CG B:GLU83 4.3 19.0 1.0
O B:HOH2058 4.5 50.1 1.0
O2 B:PO42001 4.7 18.9 1.0
CE1 B:PHE128 4.8 25.4 1.0
O B:HIS98 4.8 17.4 1.0
CD1 B:PHE128 4.9 25.8 1.0
C B:HIS98 5.0 17.0 1.0

Nickel binding site 4 out of 4 in 2isy

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Nickel binding site 4 out of 4 in the Crystal Structure of the Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider)


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 Nickel-Activated Two-Domain Iron-Dependent Regulator (Ider) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1002

b:19.6
occ:1.00
NE2 B:HIS106 2.0 17.0 1.0
O B:CSO102 2.1 16.0 1.0
OD B:CSO102 2.1 8.3 0.5
OE2 B:GLU105 2.1 23.2 1.0
O B:HOH2013 2.2 29.6 1.0
SD B:MET10 2.5 20.7 1.0
CE1 B:HIS106 2.9 16.4 1.0
CD2 B:HIS106 3.0 14.0 1.0
C B:CSO102 3.1 15.2 1.0
SG B:CSO102 3.1 13.7 0.5
CD B:GLU105 3.2 17.7 1.0
SG B:CSO102 3.4 19.3 0.5
CE B:MET10 3.4 27.0 1.0
CG B:MET10 3.5 24.2 1.0
CA B:CSO102 3.6 16.6 1.0
CG B:GLU105 3.6 15.5 1.0
CB B:CSO102 3.9 14.0 1.0
ND1 B:HIS106 4.0 15.7 1.0
CG B:HIS106 4.1 14.8 1.0
O B:LEU4 4.3 20.1 1.0
N B:ARG103 4.3 15.0 1.0
OE1 B:GLU105 4.3 18.9 1.0
NH1 B:ARG13 4.3 42.1 1.0
O B:HOH2038 4.4 42.2 1.0
OD B:CSO102 4.4 15.5 0.5
CA B:ARG103 4.7 14.7 1.0
CB B:MET10 4.9 20.2 1.0
N B:CSO102 4.9 17.0 1.0

Reference:

G.Wisedchaisri, C.J.Chou, M.Wu, C.Roach, A.E.Rice, R.K.Holmes, C.Beeson, W.G.Hol. Crystal Structures, Metal Activation, and Dna-Binding Properties of Two-Domain Ider From Mycobacterium Tuberculosis Biochemistry V. 46 436 2007.
ISSN: ISSN 0006-2960
PubMed: 17209554
DOI: 10.1021/BI0609826
Page generated: Fri Sep 25 08:10:53 2020
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