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Nickel in PDB 1ejr: Crystal Structure of the D221A Variant of Klebsiella Aerogenes Urease

Enzymatic activity of Crystal Structure of the D221A Variant of Klebsiella Aerogenes Urease

All present enzymatic activity of Crystal Structure of the D221A Variant of Klebsiella Aerogenes Urease:
3.5.1.5;

Protein crystallography data

The structure of Crystal Structure of the D221A Variant of Klebsiella Aerogenes Urease, PDB code: 1ejr was solved by M.A.Pearson, I.S.Park, R.A.Schaller, L.O.Michel, P.A.Karplus, R.P.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 170.600, 170.600, 170.600, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / n/a

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the D221A Variant of Klebsiella Aerogenes Urease (pdb code 1ejr). 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 the D221A Variant of Klebsiella Aerogenes Urease, PDB code: 1ejr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1ejr

Go back to Nickel Binding Sites List in 1ejr
Nickel binding site 1 out of 2 in the Crystal Structure of the D221A Variant of Klebsiella Aerogenes Urease


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 the D221A Variant of Klebsiella Aerogenes Urease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni4774

b:37.0
occ:1.00
OQ1 C:KCX1217 2.0 27.4 1.0
O C:HOH500 2.1 36.0 1.0
ND1 C:HIS1246 2.1 25.5 1.0
NE2 C:HIS1272 2.2 25.8 1.0
O C:HOH501 2.5 37.9 1.0
CE1 C:HIS1246 2.9 27.3 1.0
CX C:KCX1217 3.0 23.6 1.0
CG C:HIS1246 3.2 22.6 1.0
CD2 C:HIS1272 3.2 26.7 1.0
CE1 C:HIS1272 3.2 24.5 1.0
OQ2 C:KCX1217 3.3 24.8 1.0
O C:GLY1277 3.4 31.4 1.0
NI C:NI4775 3.6 33.2 1.0
NE2 C:HIS1219 3.6 26.1 1.0
O C:HOH502 3.6 38.4 1.0
CB C:HIS1246 3.6 19.6 1.0
CD2 C:HIS1219 3.8 22.6 1.0
NE2 C:HIS1246 4.1 24.4 1.0
O C:HOH170 4.2 37.6 1.0
CE1 C:HIS1134 4.2 28.0 1.0
CD2 C:HIS1246 4.2 22.0 1.0
NZ C:KCX1217 4.2 22.4 1.0
NE2 C:HIS1134 4.3 28.0 1.0
ND1 C:HIS1272 4.3 28.3 1.0
CG C:HIS1272 4.4 28.4 1.0
C C:GLY1277 4.5 32.0 1.0
OD2 C:ASP1360 4.6 24.7 1.0
CE1 C:HIS1219 4.7 24.3 1.0
CE C:KCX1217 4.8 19.6 1.0
CA C:HIS1246 4.8 19.5 1.0

Nickel binding site 2 out of 2 in 1ejr

Go back to Nickel Binding Sites List in 1ejr
Nickel binding site 2 out of 2 in the Crystal Structure of the D221A Variant of Klebsiella Aerogenes Urease


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 the D221A Variant of Klebsiella Aerogenes Urease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni4775

b:33.2
occ:1.00
O C:HOH500 2.1 36.0 1.0
NE2 C:HIS1136 2.1 21.6 1.0
OD1 C:ASP1360 2.1 21.7 1.0
OQ2 C:KCX1217 2.2 24.8 1.0
NE2 C:HIS1134 2.2 28.0 1.0
O C:HOH502 2.4 38.4 1.0
CG C:ASP1360 3.0 23.5 1.0
CE1 C:HIS1136 3.0 16.9 1.0
CD2 C:HIS1134 3.2 24.2 1.0
CE1 C:HIS1134 3.2 28.0 1.0
CD2 C:HIS1136 3.2 16.2 1.0
CX C:KCX1217 3.2 23.6 1.0
OD2 C:ASP1360 3.3 24.7 1.0
OQ1 C:KCX1217 3.5 27.4 1.0
O C:HOH501 3.6 37.9 1.0
NI C:NI4774 3.6 37.0 1.0
CG2 C:THR1169 4.2 15.0 1.0
ND1 C:HIS1136 4.2 17.7 1.0
ND1 C:HIS1134 4.2 26.6 1.0
CB C:ASP1360 4.3 21.4 1.0
CG C:HIS1136 4.3 16.7 1.0
CG C:HIS1134 4.3 23.1 1.0
NZ C:KCX1217 4.3 22.4 1.0
O C:ALA1363 4.3 32.1 1.0
CB C:ALA1363 4.4 20.2 1.0
O C:ALA1167 4.4 20.6 1.0
CA C:ASP1360 4.5 20.3 1.0
O C:HOH170 4.6 37.6 1.0
NE2 C:HIS1272 4.9 25.8 1.0
CD2 C:HIS1272 5.0 26.7 1.0

Reference:

M.A.Pearson, I.S.Park, R.A.Schaller, L.O.Michel, P.A.Karplus, R.P.Hausinger. Kinetic and Structural Characterization of Urease Active Site Variants. Biochemistry V. 39 8575 2000.
ISSN: ISSN 0006-2960
PubMed: 10913264
DOI: 10.1021/BI000613O
Page generated: Fri Sep 25 07:51:36 2020
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