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Nickel in PDB 1ejw: Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 298K

Enzymatic activity of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 298K

All present enzymatic activity of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 298K:
3.5.1.5;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 298K, PDB code: 1ejw 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 / 1.90
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 170.800, 170.800, 170.800, 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 298K (pdb code 1ejw). 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 298K, PDB code: 1ejw:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1ejw

Go back to Nickel Binding Sites List in 1ejw
Nickel binding site 1 out of 2 in the Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 298K


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 298K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni4774

b:18.0
occ:1.00
OQ1 C:KCX1217 2.0 15.3 1.0
ND1 C:HIS1246 2.1 14.1 1.0
O C:HOH501 2.1 18.8 1.0
O C:HOH500 2.1 17.4 1.0
NE2 C:HIS1272 2.1 15.4 1.0
CE1 C:HIS1246 2.9 17.7 1.0
CX C:KCX1217 3.0 14.3 1.0
CE1 C:HIS1272 3.1 14.6 1.0
CD2 C:HIS1272 3.1 13.7 1.0
CG C:HIS1246 3.1 14.8 1.0
OQ2 C:KCX1217 3.3 12.7 1.0
O C:GLY1277 3.3 22.0 1.0
CB C:HIS1246 3.5 14.6 1.0
NE2 C:HIS1219 3.6 24.2 1.0
O C:HOH502 3.7 16.0 1.0
O C:HOH170 3.7 30.8 1.0
NI C:NI4775 3.7 16.7 1.0
CD2 C:HIS1219 4.1 16.9 1.0
NE2 C:HIS1246 4.1 17.1 1.0
ND1 C:HIS1272 4.2 17.9 1.0
CE1 C:HIS1134 4.2 17.1 1.0
CD2 C:HIS1246 4.2 14.8 1.0
NZ C:KCX1217 4.2 15.2 1.0
CG C:HIS1272 4.2 17.3 1.0
C C:GLY1277 4.3 24.2 1.0
NE2 C:HIS1134 4.4 16.7 1.0
OD2 C:ASP1360 4.5 18.6 1.0
CE1 C:HIS1320 4.6 62.8 1.0
CE1 C:HIS1219 4.6 19.0 1.0
CA C:HIS1246 4.7 12.9 1.0
CE C:KCX1217 4.8 13.0 1.0
NE2 C:HIS1320 4.8 66.9 1.0
CA C:GLY1278 4.9 17.1 1.0
OD1 C:ASP1360 5.0 14.3 1.0

Nickel binding site 2 out of 2 in 1ejw

Go back to Nickel Binding Sites List in 1ejw
Nickel binding site 2 out of 2 in the Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 298K


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 298K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni4775

b:16.7
occ:1.00
OD1 C:ASP1360 2.0 14.3 1.0
OQ2 C:KCX1217 2.1 12.7 1.0
NE2 C:HIS1136 2.1 15.3 1.0
NE2 C:HIS1134 2.1 16.7 1.0
O C:HOH500 2.2 17.4 1.0
O C:HOH502 2.3 16.0 1.0
CG C:ASP1360 3.0 15.2 1.0
CE1 C:HIS1136 3.0 13.2 1.0
CE1 C:HIS1134 3.1 17.1 1.0
CX C:KCX1217 3.1 14.3 1.0
CD2 C:HIS1134 3.1 12.0 1.0
CD2 C:HIS1136 3.2 11.2 1.0
OD2 C:ASP1360 3.3 18.6 1.0
O C:HOH501 3.5 18.8 1.0
OQ1 C:KCX1217 3.6 15.3 1.0
NI C:NI4774 3.7 18.0 1.0
O C:HOH170 4.1 30.8 1.0
CG2 C:THR1169 4.2 9.9 1.0
ND1 C:HIS1134 4.2 14.4 1.0
ND1 C:HIS1136 4.2 14.2 1.0
NZ C:KCX1217 4.2 15.2 1.0
CG C:HIS1134 4.2 14.2 1.0
CB C:ASP1360 4.2 14.4 1.0
CG C:HIS1136 4.3 12.6 1.0
CB C:ALA1363 4.3 13.6 1.0
O C:ALA1363 4.4 19.2 1.0
CA C:ASP1360 4.4 9.1 1.0
O C:ALA1167 4.6 14.6 1.0
NE2 C:HIS1272 4.8 15.4 1.0
CD2 C:HIS1272 4.9 13.7 1.0

Reference:

M.A.Pearson, P.A.Karplus. Crystal Structure of Wild-Type Klebsiella Aerogenes Urease at 298K To Be Published.
Page generated: Wed Dec 16 01:11:47 2020

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