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Nickel in PDB 6i9y: The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions

Enzymatic activity of The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions

All present enzymatic activity of The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions:
3.5.1.5;

Protein crystallography data

The structure of The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions, PDB code: 6i9y was solved by L.Mazzei, M.Cianci, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.80 / 2.14
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.291, 132.291, 190.435, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 20.8

Other elements in 6i9y:

The structure of The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions also contains other interesting chemical elements:

Gold (Au) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions (pdb code 6i9y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions, PDB code: 6i9y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6i9y

Go back to Nickel Binding Sites List in 6i9y
Nickel binding site 1 out of 2 in the The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:35.9
occ:1.00
O C:OH603 1.9 40.5 1.0
OQ2 C:KCX220 2.0 35.3 1.0
ND1 C:HIS249 2.1 36.6 1.0
NE2 C:HIS275 2.2 35.9 1.0
O C:HOH713 2.2 36.2 1.0
CE1 C:HIS249 3.0 36.4 1.0
CD2 C:HIS275 3.1 36.5 1.0
CX C:KCX220 3.1 34.6 1.0
CG C:HIS249 3.2 37.0 1.0
CE1 C:HIS275 3.2 37.0 1.0
OQ1 C:KCX220 3.4 34.6 1.0
O C:GLY280 3.4 39.4 1.0
CB C:HIS249 3.6 34.3 1.0
NI C:NI602 3.6 34.3 1.0
O C:HOH771 3.6 46.3 1.0
NE2 C:HIS222 3.6 34.7 1.0
O C:HOH820 3.6 50.9 1.0
CD2 C:HIS222 4.0 33.7 1.0
CE1 C:HIS137 4.1 31.1 1.0
NE2 C:HIS249 4.1 37.6 1.0
CD2 C:HIS249 4.3 37.9 1.0
CG C:HIS275 4.3 36.8 1.0
ND1 C:HIS275 4.3 36.5 1.0
NZ C:KCX220 4.3 33.4 1.0
NE2 C:HIS137 4.3 29.6 1.0
C C:GLY280 4.4 39.8 1.0
OD2 C:ASP363 4.4 38.5 1.0
CE1 C:HIS222 4.6 33.3 1.0
O4 C:SO4615 4.7 83.4 0.8
CE C:KCX220 4.8 32.1 1.0
CA C:HIS249 4.9 32.8 1.0

Nickel binding site 2 out of 2 in 6i9y

Go back to Nickel Binding Sites List in 6i9y
Nickel binding site 2 out of 2 in the The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The 2.14 A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Au(I) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni602

b:34.3
occ:1.00
OQ1 C:KCX220 2.1 34.6 1.0
NE2 C:HIS137 2.1 29.6 1.0
O C:OH603 2.2 40.5 1.0
NE2 C:HIS139 2.2 30.5 1.0
OD1 C:ASP363 2.2 38.1 1.0
O C:HOH771 2.6 46.3 1.0
CX C:KCX220 3.0 34.6 1.0
CE1 C:HIS137 3.1 31.1 1.0
CD2 C:HIS137 3.1 30.5 1.0
CE1 C:HIS139 3.1 29.6 1.0
CG C:ASP363 3.1 37.8 1.0
CD2 C:HIS139 3.3 30.3 1.0
OQ2 C:KCX220 3.4 35.3 1.0
OD2 C:ASP363 3.4 38.5 1.0
NI C:NI601 3.6 35.9 1.0
O C:HOH713 3.7 36.2 1.0
CG2 C:THR172 4.1 32.3 1.0
O C:HOH820 4.1 50.9 1.0
ND1 C:HIS137 4.2 31.4 1.0
NZ C:KCX220 4.2 33.4 1.0
CG C:HIS137 4.2 31.1 1.0
ND1 C:HIS139 4.3 29.9 1.0
CB C:ALA366 4.3 40.0 0.5
CB C:ALA366 4.3 40.0 0.5
CG C:HIS139 4.4 30.8 1.0
CB C:ASP363 4.4 36.4 1.0
O C:ALA170 4.5 31.2 1.0
CA C:ASP363 4.6 35.2 1.0
CD2 C:HIS275 4.9 36.5 1.0
NE2 C:HIS275 4.9 35.9 1.0
N C:THR172 5.0 32.6 1.0

Reference:

L.Mazzei, M.N.Wenzel, M.Cianci, M.Palombo, A.Casini, S.Ciurli. Inhibition Mechanism of Urease By Au(III) Compounds Unveiled By X-Ray Diffraction Analysis. Acs Med.Chem.Lett. V. 10 564 2019.
ISSN: ISSN 1948-5875
PubMed: 30996797
DOI: 10.1021/ACSMEDCHEMLETT.8B00585
Page generated: Wed Dec 16 01:51:53 2020

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