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Nickel in PDB 8bnw: X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form

Protein crystallography data

The structure of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form, PDB code: 8bnw was solved by E.V.Blagova, M.Bennett, R.Booth, E.J.Dodson, A.-K.Duhme-Klair, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.62 / 2.13
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 35.369, 118.433, 141.046, 90, 90, 90
R / Rfree (%) 22.2 / 26.6

Nickel Binding Sites:

The binding sites of Nickel atom in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form (pdb code 8bnw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form, PDB code: 8bnw:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 8bnw

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Nickel binding site 1 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:53.5
occ:0.50
O4 A:SO4306 1.9 63.7 0.5
OD2 A:ASP88 2.0 61.9 1.0
O A:HOH403 2.0 53.3 1.0
O2 A:SO4306 2.2 70.6 0.5
S A:SO4306 2.5 61.4 0.5
CG A:ASP88 2.8 52.7 1.0
OD1 A:ASP88 2.9 61.5 1.0
O3 A:SO4306 3.5 76.7 0.5
O1 A:SO4306 3.6 53.2 0.5
HB2 A:LYS91 3.9 52.9 1.0
HB3 A:GLU90 4.2 63.6 1.0
CB A:ASP88 4.2 50.3 1.0
HB3 A:LYS91 4.3 52.9 1.0
H A:LYS91 4.4 57.5 1.0
HB2 A:ASP88 4.4 51.3 1.0
CB A:LYS91 4.6 50.1 1.0
HB3 A:ASP88 4.6 51.3 1.0
N A:LYS91 4.9 55.7 1.0
NI A:NI304 5.0 58.3 0.5

Nickel binding site 2 out of 5 in 8bnw

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Nickel binding site 2 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:68.8
occ:0.50
OE1 A:GLU151 1.9 92.7 1.0
OE2 A:GLU151 1.9 99.6 1.0
OE2 A:GLU155 2.0 82.6 1.0
CD A:GLU151 2.1 98.2 1.0
CD A:GLU155 3.2 76.5 1.0
CG A:GLU151 3.6 85.2 1.0
HG2 A:GLU151 4.0 85.1 1.0
OE1 A:GLU155 4.0 74.5 1.0
HG3 A:GLU155 4.0 74.6 1.0
HG3 A:GLU151 4.0 85.2 1.0
CG A:GLU155 4.2 76.0 1.0
HB3 A:GLU151 4.2 74.2 1.0
HG2 A:GLU155 4.4 74.6 1.0
CB A:GLU151 4.5 73.8 1.0

Nickel binding site 3 out of 5 in 8bnw

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Nickel binding site 3 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:75.2
occ:1.00
OE1 A:GLU111 1.9 89.4 1.0
CD A:GLU111 3.2 88.9 1.0
HG3 A:GLU111 3.7 88.5 1.0
OE2 A:GLU111 4.0 108.5 1.0
CG A:GLU111 4.0 91.3 1.0
HG2 A:GLU111 4.6 88.4 1.0
HB3 A:GLU111 4.9 81.2 1.0

Nickel binding site 4 out of 5 in 8bnw

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Nickel binding site 4 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni304

b:58.3
occ:0.50
O1 A:SO4306 1.9 53.2 0.5
OE2 A:GLU94 2.0 74.1 1.0
OE1 A:GLU94 2.1 66.3 1.0
OE2 A:GLU90 2.2 82.2 1.0
O3 A:SO4306 2.2 76.7 0.5
CD A:GLU94 2.3 67.2 1.0
S A:SO4306 2.5 61.4 0.5
HG2 A:GLU90 3.0 74.6 1.0
CD A:GLU90 3.1 84.4 1.0
O2 A:SO4306 3.4 70.6 0.5
CG A:GLU90 3.5 77.5 1.0
O4 A:SO4306 3.6 63.7 0.5
CG A:GLU94 3.8 60.8 1.0
HA A:LYS91 4.0 56.0 1.0
HG3 A:GLU94 4.1 61.6 1.0
HB3 A:GLU90 4.1 63.6 1.0
OE1 A:GLU90 4.1 75.7 1.0
HG3 A:GLU90 4.3 74.7 1.0
HG2 A:GLU94 4.3 61.6 1.0
CB A:GLU90 4.4 60.7 1.0
HE3 A:LYS91 4.6 59.2 1.0
HB2 A:GLU94 4.6 58.1 1.0
C A:GLU90 4.6 60.3 1.0
N A:LYS91 4.7 55.7 1.0
HB2 A:LYS91 4.7 52.9 1.0
O A:GLU90 4.7 61.9 1.0
CA A:LYS91 4.8 59.0 1.0
CB A:GLU94 4.8 58.3 1.0
NI A:NI301 5.0 53.5 0.5

Nickel binding site 5 out of 5 in 8bnw

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Nickel binding site 5 out of 5 in the X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of X-Ray Structure of the Ceue Homologue From Parageobacillus Thermoglucosidasius - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni305

b:101.2
occ:0.50
HZ1 A:LYS294 1.6 84.8 0.0
HZ2 A:LYS294 1.6 84.8 0.0
NZ A:LYS294 1.9 82.7 1.0
HZ3 A:LYS294 2.5 84.8 0.0
OE1 A:GLU297 2.6 66.2 1.0
OE2 A:GLU297 3.0 75.6 1.0
HD2 A:LYS294 3.1 84.6 1.0
CE A:LYS294 3.2 84.1 1.0
CD A:GLU297 3.2 88.9 1.0
CD A:LYS294 3.5 87.6 1.0
OE1 A:GLU293 3.5 110.4 1.0
HD3 A:LYS294 3.5 84.5 1.0
HE3 A:LYS294 3.8 84.6 1.0
HE2 A:LYS294 3.8 84.6 1.0
CD A:GLU293 4.4 105.5 1.0
HG2 A:GLU293 4.6 97.0 1.0
CG A:GLU297 4.7 87.3 1.0
CG A:LYS294 5.0 78.6 1.0

Reference:

E.V.Blagova, A.Miller, M.Bennett, R.Booth, E.J.Dodson, A.-K.Duhme-Klair, K.S.Wilson. Thermostable Homologues of the Periplasmic Siderophore-Binding Protein Ceue From and Acta Crystallogr.,Sect.D 2023.
ISSN: ESSN 1399-0047
Page generated: Thu Oct 10 09:36:47 2024

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