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Gold 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:

Nickel (Ni) 2 atoms

Gold Binding Sites:

The binding sites of Gold 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 Gold atom.
In total 3 binding sites of Gold 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 Gold binding site number: 1; 2; 3;

Gold binding site 1 out of 3 in 6i9y

Go back to Gold Binding Sites List in 6i9y
Gold binding site 1 out of 3 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 Gold with other atoms in the Au 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:Au612

b:61.7
occ:0.85
O3 C:SO4615 2.2 78.2 0.8
SG C:CYS322 2.7 64.3 1.0
ND1 C:HIS323 2.8 55.6 1.0
CB C:CYS322 3.2 55.2 1.0
AU C:AU613 3.3 54.1 0.8
C C:CYS322 3.3 55.8 1.0
O C:CYS322 3.4 55.0 1.0
S C:SO4615 3.4 82.4 0.8
N C:HIS323 3.5 54.7 1.0
CG C:HIS323 3.6 56.2 1.0
CB C:HIS323 3.6 55.1 1.0
O2 C:SO4615 3.7 82.6 0.8
CA C:HIS323 3.7 54.2 1.0
CE1 C:HIS323 3.8 56.2 1.0
CA C:CYS322 3.9 54.8 1.0
CD1 C:LEU319 4.0 49.0 1.0
O4 C:SO4615 4.0 83.4 0.8
O2 C:EDO616 4.2 63.5 1.0
O C:LEU319 4.5 47.3 1.0
O1 C:SO4615 4.6 79.5 0.8
C2 C:EDO616 4.7 66.3 1.0
NH2 C:ARG339 4.7 52.5 1.0
CD2 C:HIS323 4.8 57.6 1.0
C1 C:EDO616 4.9 65.9 1.0
NE2 C:HIS323 4.9 58.1 1.0
NH1 C:ARG339 5.0 51.6 1.0

Gold binding site 2 out of 3 in 6i9y

Go back to Gold Binding Sites List in 6i9y
Gold binding site 2 out of 3 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 Gold with other atoms in the Au 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:Au613

b:54.1
occ:0.85
SD C:MET367 2.4 47.5 1.0
SG C:CYS322 2.6 64.3 1.0
AU C:AU612 3.3 61.7 0.8
CG C:MET367 3.3 44.1 1.0
CB C:CYS322 3.4 55.2 1.0
CE C:MET367 3.6 49.1 1.0
CB C:MET367 3.7 41.5 1.0
O3 C:SO4615 3.7 78.2 0.8
NH2 C:ARG339 4.2 52.5 1.0
O4 C:SO4615 4.2 83.4 0.8
O C:ALA366 4.3 43.1 0.5
O C:ALA366 4.3 43.1 0.5
CD1 C:LEU319 4.3 49.0 1.0
O C:HOH820 4.4 50.9 1.0
S C:SO4615 4.6 82.4 0.8
CA C:MET367 4.8 41.4 1.0
CA C:LEU319 4.9 48.8 1.0
CA C:CYS322 4.9 54.8 1.0

Gold binding site 3 out of 3 in 6i9y

Go back to Gold Binding Sites List in 6i9y
Gold binding site 3 out of 3 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 Gold with other atoms in the Au binding site number 3 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:Au614

b:60.5
occ:0.85
SG C:CYS555 2.7 69.5 1.0
CB C:CYS555 3.4 63.8 1.0
OE1 C:GLN387 3.5 60.9 1.0
CA C:CYS555 3.6 61.7 1.0
O C:THR554 3.7 64.1 1.0
CB C:GLN387 4.0 50.0 1.0
CD C:GLN387 4.0 58.5 1.0
CE C:MET384 4.3 38.1 1.0
CD1 C:ILE350 4.3 43.0 1.0
N C:GLU556 4.4 59.3 1.0
CG1 C:ILE350 4.4 41.8 1.0
CG C:GLN387 4.5 53.0 1.0
C C:THR554 4.6 65.1 1.0
N C:CYS555 4.6 63.5 1.0
C C:CYS555 4.6 61.4 1.0
CG C:ARG388 4.6 53.1 1.0
NE2 C:GLN387 4.7 59.9 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: Sat Dec 12 01:54:33 2020

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