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Nickel in PDB 7zcy: Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms

Enzymatic activity of Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms

All present enzymatic activity of Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms:
3.5.1.5;

Protein crystallography data

The structure of Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms, PDB code: 7zcy was solved by L.Mazzei, S.Ciurli, M.Cianci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.80 / 1.54
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.612, 131.612, 189.003, 90, 90, 120
R / Rfree (%) 13.7 / 16

Other elements in 7zcy:

The structure of Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms (pdb code 7zcy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms, PDB code: 7zcy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 7zcy

Go back to Nickel Binding Sites List in 7zcy
Nickel binding site 1 out of 2 in the Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:21.9
occ:1.00
OQ2 C:KCX220 2.0 22.3 1.0
NE2 C:HIS275 2.0 22.5 1.0
ND1 C:HIS249 2.0 19.3 1.0
O C:OH603 2.1 21.8 1.0
O C:HOH702 2.1 21.7 1.0
CE1 C:HIS249 2.9 22.8 1.0
CE1 C:HIS275 3.0 24.4 1.0
CD2 C:HIS275 3.0 22.4 1.0
CX C:KCX220 3.1 20.8 1.0
CG C:HIS249 3.1 21.8 1.0
O C:GLY280 3.2 24.8 1.0
OQ1 C:KCX220 3.5 22.0 1.0
CB C:HIS249 3.5 20.4 1.0
O C:HOH709 3.6 25.7 1.0
O C:HOH703 3.7 22.5 1.0
NE2 C:HIS222 3.7 21.4 1.0
NI C:NI602 3.7 21.1 1.0
CD2 C:HIS222 4.0 21.1 1.0
CE1 C:HIS137 4.1 19.9 1.0
ND1 C:HIS275 4.1 20.7 1.0
NE2 C:HIS249 4.1 21.1 1.0
CG C:HIS275 4.1 21.7 1.0
CD2 C:HIS249 4.2 20.3 1.0
NZ C:KCX220 4.2 19.8 1.0
NE2 C:HIS137 4.3 20.6 1.0
C C:GLY280 4.3 23.7 1.0
OD2 C:ASP363 4.3 22.6 1.0
O4 C:SO4606 4.4 41.9 0.8
CE1 C:HIS222 4.7 22.0 1.0
CE C:KCX220 4.7 21.2 1.0
CA C:HIS249 4.8 20.4 1.0
CA C:GLY281 4.9 24.8 1.0
O2 C:SO4606 5.0 37.2 0.8
N C:GLY281 5.0 23.5 1.0

Nickel binding site 2 out of 2 in 7zcy

Go back to Nickel Binding Sites List in 7zcy
Nickel binding site 2 out of 2 in the Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni602

b:21.1
occ:1.00
NE2 C:HIS139 2.1 18.6 1.0
NE2 C:HIS137 2.1 20.6 1.0
O C:OH603 2.1 21.8 1.0
OQ1 C:KCX220 2.1 22.0 1.0
O C:HOH703 2.1 22.5 1.0
OD1 C:ASP363 2.1 22.2 1.0
CE1 C:HIS139 2.9 21.1 1.0
CG C:ASP363 3.0 23.7 1.0
CX C:KCX220 3.0 20.8 1.0
CD2 C:HIS137 3.0 20.8 1.0
CE1 C:HIS137 3.1 19.9 1.0
CD2 C:HIS139 3.2 20.1 1.0
OD2 C:ASP363 3.3 22.6 1.0
OQ2 C:KCX220 3.4 22.3 1.0
O C:HOH702 3.5 21.7 1.0
NI C:NI601 3.7 21.9 1.0
O C:HOH709 3.7 25.7 1.0
ND1 C:HIS139 4.1 19.7 1.0
CG2 C:THR172 4.1 20.3 1.0
CB C:ALA366 4.1 21.9 0.5
CB C:ALA366 4.1 21.8 0.5
NZ C:KCX220 4.2 19.8 1.0
CG C:HIS137 4.2 19.2 1.0
ND1 C:HIS137 4.2 21.0 1.0
CG C:HIS139 4.2 19.7 1.0
O C:ALA170 4.3 21.2 1.0
CB C:ASP363 4.3 21.1 1.0
CA C:ASP363 4.6 20.9 1.0
NE2 C:HIS275 4.8 22.5 1.0
CD2 C:HIS275 4.8 22.4 1.0
N C:THR172 4.9 20.3 1.0

Reference:

L.Mazzei, S.Ciurli, M.Cianci. Sporosarcina Pasteurii Urease (Spu) Co-Crystallized in the Presence of An Ebselen-Derivative and Bound to Se Atoms To Be Published.
Page generated: Thu Oct 10 09:32:56 2024

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