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Nickel in PDB 1ejx: Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K

Enzymatic activity of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K

All present enzymatic activity of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K:
3.5.1.5;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K, PDB code: 1ejx was solved by M.A.Pearson, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 168.960, 168.960, 168.960, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K (pdb code 1ejx). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K, PDB code: 1ejx:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1ejx

Go back to Nickel Binding Sites List in 1ejx
Nickel binding site 1 out of 2 in the Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni4774

b:21.8
occ:1.00
O C:HOH500 1.9 31.7 1.0
OQ1 C:KCX1217 2.0 18.1 1.0
NE2 C:HIS1272 2.1 19.4 1.0
ND1 C:HIS1246 2.1 18.1 1.0
O C:HOH501 2.2 21.8 1.0
CD2 C:HIS1272 3.0 18.3 1.0
CX C:KCX1217 3.0 21.9 1.0
CE1 C:HIS1246 3.1 19.6 1.0
CE1 C:HIS1272 3.1 18.2 1.0
CG C:HIS1246 3.2 17.8 1.0
O C:GLY1277 3.3 21.3 1.0
OQ2 C:KCX1217 3.4 18.5 1.0
CB C:HIS1246 3.5 20.9 1.0
NI C:NI4775 3.5 20.3 1.0
O C:HOH502 3.7 26.7 1.0
NE2 C:HIS1219 3.7 18.4 1.0
O C:HOH170 3.9 24.8 1.0
CD2 C:HIS1219 4.1 18.4 1.0
CE1 C:HIS1134 4.1 18.2 1.0
ND1 C:HIS1272 4.2 17.3 1.0
CG C:HIS1272 4.2 21.9 1.0
NE2 C:HIS1246 4.2 19.1 1.0
NZ C:KCX1217 4.2 22.7 1.0
O C:HOH373 4.3 50.8 1.0
CD2 C:HIS1246 4.3 17.8 1.0
NE2 C:HIS1134 4.3 18.8 1.0
OD2 C:ASP1360 4.4 21.3 1.0
C C:GLY1277 4.4 19.9 1.0
CE C:KCX1217 4.7 19.2 1.0
CE1 C:HIS1219 4.7 21.7 1.0
CA C:HIS1246 4.8 21.7 1.0
OD1 C:ASP1360 4.9 17.5 1.0

Nickel binding site 2 out of 2 in 1ejx

Go back to Nickel Binding Sites List in 1ejx
Nickel binding site 2 out of 2 in the Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni4775

b:20.3
occ:1.00
NE2 C:HIS1134 2.0 18.8 1.0
OD1 C:ASP1360 2.1 17.5 1.0
O C:HOH500 2.1 31.7 1.0
OQ2 C:KCX1217 2.2 18.5 1.0
NE2 C:HIS1136 2.2 20.6 1.0
O C:HOH502 2.5 26.7 1.0
CE1 C:HIS1134 2.9 18.2 1.0
CG C:ASP1360 3.0 20.4 1.0
CD2 C:HIS1134 3.1 19.9 1.0
CX C:KCX1217 3.1 21.9 1.0
CE1 C:HIS1136 3.1 15.9 1.0
CD2 C:HIS1136 3.2 17.3 1.0
OD2 C:ASP1360 3.4 21.3 1.0
OQ1 C:KCX1217 3.4 18.1 1.0
NI C:NI4774 3.5 21.8 1.0
O C:HOH501 3.5 21.8 1.0
CG2 C:THR1169 3.9 16.3 1.0
ND1 C:HIS1134 4.1 20.7 1.0
NZ C:KCX1217 4.2 22.7 1.0
CG C:HIS1134 4.2 21.4 1.0
ND1 C:HIS1136 4.3 16.6 1.0
CB C:ASP1360 4.3 15.4 1.0
CG C:HIS1136 4.3 18.5 1.0
CB C:ALA1363 4.3 17.9 1.0
CA C:ASP1360 4.4 17.5 1.0
O C:ALA1363 4.5 29.9 1.0
O C:HOH170 4.6 24.8 1.0
O C:ALA1167 4.7 21.7 1.0
CD2 C:HIS1272 4.8 18.3 1.0
NE2 C:HIS1272 4.8 19.4 1.0
N C:THR1169 4.9 15.6 1.0

Reference:

M.A.Pearson, P.A.Karplus. Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 100K To Be Published.
Page generated: Fri Sep 25 07:52:00 2020
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