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Nickel in PDB 3a1f: The Crystal Structure of Nadph Binding Domain of GP91(Phox)

Protein crystallography data

The structure of The Crystal Structure of Nadph Binding Domain of GP91(Phox), PDB code: 3a1f was solved by K.Honbou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.48 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 60.022, 60.022, 90.398, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 27.7

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of Nadph Binding Domain of GP91(Phox) (pdb code 3a1f). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 7 binding sites of Nickel where determined in the The Crystal Structure of Nadph Binding Domain of GP91(Phox), PDB code: 3a1f:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7;

Nickel binding site 1 out of 7 in 3a1f

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Nickel binding site 1 out of 7 in the The Crystal Structure of Nadph Binding Domain of GP91(Phox)


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 Nadph Binding Domain of GP91(Phox) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni187

b:63.4
occ:1.00
NE2 A:HIS178 2.1 44.7 1.0
O A:HOH231 2.2 31.2 1.0
O A:HOH247 2.3 54.8 1.0
CD2 A:HIS178 3.0 43.0 1.0
O A:HOH248 3.1 60.2 1.0
O A:HOH239 3.1 54.6 1.0
CE1 A:HIS178 3.1 43.5 1.0
O A:GLY173 3.9 56.4 1.0
CG A:HIS178 4.2 42.4 1.0
ND1 A:HIS178 4.2 42.6 1.0
O A:GLU171 4.2 53.1 1.0
O A:GLY176 4.3 42.7 1.0
O A:HOH258 4.6 51.5 1.0
ND2 A:ASN145 4.8 46.5 1.0
C A:GLY176 4.9 42.6 1.0
C A:GLY173 4.9 56.2 1.0
O A:SER172 4.9 55.5 1.0

Nickel binding site 2 out of 7 in 3a1f

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Nickel binding site 2 out of 7 in the The Crystal Structure of Nadph Binding Domain of GP91(Phox)


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 Nadph Binding Domain of GP91(Phox) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni188

b:0.5
occ:1.00
O A:HOH252 2.4 59.3 1.0
NE2 A:HIS65 2.5 50.0 1.0
O A:HOH256 2.9 40.8 1.0
CD2 A:HIS65 3.1 48.0 1.0
O A:HOH253 3.5 53.4 1.0
CE1 A:HIS65 3.6 49.2 1.0
O A:HOH213 3.9 52.8 1.0
CG A:HIS65 4.4 47.1 1.0
ND1 A:HIS65 4.6 49.7 1.0

Nickel binding site 3 out of 7 in 3a1f

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Nickel binding site 3 out of 7 in the The Crystal Structure of Nadph Binding Domain of GP91(Phox)


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 Nadph Binding Domain of GP91(Phox) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni189

b:39.8
occ:1.00
OE2 A:GLU12 2.4 36.3 1.0
CD A:GLU12 2.9 35.1 1.0
OE1 A:GLU12 3.0 34.8 1.0
O A:HOH246 3.1 27.1 1.0
O A:HOH259 4.1 53.6 1.0
O A:PHE7 4.2 28.2 1.0
CG A:GLU12 4.3 34.0 1.0
O A:HOH245 4.5 53.1 1.0

Nickel binding site 4 out of 7 in 3a1f

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Nickel binding site 4 out of 7 in the The Crystal Structure of Nadph Binding Domain of GP91(Phox)


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 Nadph Binding Domain of GP91(Phox) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni190

b:46.9
occ:1.00
O A:HOH225 2.2 33.9 1.0
O A:HOH235 2.2 47.6 1.0
O A:HOH233 2.3 41.4 1.0
O A:ILE1 2.3 33.0 1.0
N A:ILE1 2.3 29.0 1.0
O A:HOH227 2.4 33.0 1.0
C A:ILE1 2.9 31.2 1.0
CA A:ILE1 3.1 28.1 1.0
CB A:ILE1 3.9 28.8 1.0
N A:ALA2 4.1 30.3 1.0
CA A:ALA2 4.7 30.1 1.0
CG2 A:ILE1 4.9 25.9 1.0
CG1 A:ILE1 4.9 27.4 1.0

Nickel binding site 5 out of 7 in 3a1f

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Nickel binding site 5 out of 7 in the The Crystal Structure of Nadph Binding Domain of GP91(Phox)


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 Nadph Binding Domain of GP91(Phox) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni191

b:56.4
occ:0.50
O A:HOH249 1.6 43.7 0.5
O A:HOH250 1.8 43.7 0.5
O A:HOH221 2.3 39.7 1.0
O A:HOH251 2.4 57.7 1.0
OE2 A:GLU18 3.7 40.4 1.0
OE1 A:GLU18 3.9 38.5 1.0
O A:ASN145 4.2 38.1 1.0
CD A:GLU18 4.3 37.5 1.0
OG1 A:THR146 4.3 34.9 1.0
O A:HOH210 4.7 38.2 1.0
O A:PRO144 4.9 38.7 1.0

Nickel binding site 6 out of 7 in 3a1f

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Nickel binding site 6 out of 7 in the The Crystal Structure of Nadph Binding Domain of GP91(Phox)


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 Nadph Binding Domain of GP91(Phox) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni192

b:0.9
occ:1.00
O A:GLY98 4.5 44.6 1.0

Nickel binding site 7 out of 7 in 3a1f

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Nickel binding site 7 out of 7 in the The Crystal Structure of Nadph Binding Domain of GP91(Phox)


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 Nadph Binding Domain of GP91(Phox) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni193

b:53.6
occ:1.00
N A:PHE7 3.4 27.6 1.0
N A:ALA2 3.5 30.3 1.0
CD A:PRO6 3.5 28.3 1.0
N A:PRO6 3.5 28.3 1.0
CA A:GLY5 3.6 28.1 1.0
C A:GLY5 3.6 27.9 1.0
CA A:ILE1 3.7 28.1 1.0
CG2 A:ILE1 3.8 25.9 1.0
O A:ALA2 3.9 29.5 1.0
CB A:ILE1 4.1 28.8 1.0
C A:ILE1 4.1 31.2 1.0
CG1 A:ILE1 4.1 27.4 1.0
CB A:PHE7 4.2 26.8 1.0
CA A:PHE7 4.2 28.5 1.0
O A:GLY5 4.3 27.9 1.0
N A:GLY8 4.3 28.2 1.0
CD1 A:PHE7 4.3 29.2 1.0
CA A:PRO6 4.3 28.7 1.0
C A:PRO6 4.4 29.6 1.0
N A:GLY5 4.5 29.6 1.0
CA A:ALA2 4.5 30.1 1.0
C A:PHE7 4.5 27.8 1.0
CB A:PRO6 4.5 27.8 1.0
CG A:PRO6 4.6 27.7 1.0
C A:ALA2 4.7 29.0 1.0
CG A:PHE7 4.8 26.3 1.0
CB A:ALA2 4.8 29.3 1.0
N A:ILE1 4.9 29.0 1.0

Reference:

K.Honbou, N.N.Noda, H.Sumimoto, F.Inagaki. Crystal Structure of Nadph Binding Domain of GP91(Phox) To Be Published.
Page generated: Thu Oct 29 06:19:06 2020
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