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Nickel in PDB 1e9y: Crystal Structure of Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid

Enzymatic activity of Crystal Structure of Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid

All present enzymatic activity of Crystal Structure of Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid:
3.5.1.5;

Protein crystallography data

The structure of Crystal Structure of Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid, PDB code: 1e9y was solved by N.-C.Ha, S.-T.Oh, B.-H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 3.00
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 178.160, 178.160, 178.160, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 28.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid (pdb code 1e9y). 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 Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid, PDB code: 1e9y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1e9y

Go back to Nickel Binding Sites List in 1e9y
Nickel binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid


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 Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni3001

b:55.6
occ:1.00
NE2 B:HIS274 2.4 53.1 1.0
ND1 B:HIS248 2.4 36.6 1.0
O B:HAE800 2.4 60.2 1.0
OQ1 B:KCX219 2.4 53.2 1.0
O2 B:HAE800 2.5 61.4 1.0
OQ2 B:KCX219 2.6 50.6 1.0
CX B:KCX219 2.9 49.6 1.0
CE1 B:HIS248 2.9 38.5 1.0
NI B:NI3002 3.0 42.7 1.0
CD2 B:HIS274 3.1 51.4 1.0
C2 B:HAE800 3.2 61.5 1.0
N B:HAE800 3.2 60.9 1.0
O B:GLY279 3.5 53.6 1.0
CE1 B:HIS274 3.5 51.8 1.0
CG B:HIS248 3.6 38.3 1.0
NE2 B:HIS136 3.9 40.5 1.0
NE2 B:HIS221 4.0 33.5 1.0
CD2 B:HIS221 4.0 33.2 1.0
CE1 B:HIS136 4.1 41.7 1.0
NE2 B:HIS248 4.1 38.8 1.0
NZ B:KCX219 4.2 46.2 1.0
CB B:HIS248 4.2 37.7 1.0
CG B:HIS274 4.4 50.7 1.0
C B:GLY279 4.5 53.9 1.0
CD2 B:HIS248 4.5 38.5 1.0
ND1 B:HIS274 4.5 52.0 1.0
OD2 B:ASP362 4.7 42.2 1.0
C1 B:HAE800 4.7 61.0 1.0
OD1 B:ASP362 4.7 40.0 1.0
NE2 B:HIS138 5.0 31.9 1.0
CG B:ASP362 5.0 39.5 1.0
O B:ALA169 5.0 38.4 1.0

Nickel binding site 2 out of 2 in 1e9y

Go back to Nickel Binding Sites List in 1e9y
Nickel binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid


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 Helicobacter Pylori Urease in Complex with Acetohydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni3002

b:42.7
occ:1.00
NE2 B:HIS138 2.2 31.9 1.0
NE2 B:HIS136 2.3 40.5 1.0
OD2 B:ASP362 2.4 42.2 1.0
OQ2 B:KCX219 2.4 50.6 1.0
O B:HAE800 2.6 60.2 1.0
CX B:KCX219 2.9 49.6 1.0
CE1 B:HIS138 3.0 32.7 1.0
NI B:NI3001 3.0 55.6 1.0
OQ1 B:KCX219 3.2 53.2 1.0
CD2 B:HIS136 3.2 39.4 1.0
CD2 B:HIS138 3.2 33.1 1.0
CG B:ASP362 3.3 39.5 1.0
CE1 B:HIS136 3.3 41.7 1.0
N B:HAE800 3.3 60.9 1.0
OD1 B:ASP362 3.7 40.0 1.0
CG2 B:THR171 3.8 29.0 1.0
NZ B:KCX219 3.8 46.2 1.0
O2 B:HAE800 3.9 61.4 1.0
C2 B:HAE800 3.9 61.5 1.0
ND1 B:HIS138 4.2 34.5 1.0
CG B:HIS138 4.3 34.2 1.0
CB B:ASP362 4.4 38.8 1.0
ND1 B:HIS136 4.4 41.1 1.0
CG B:HIS136 4.4 39.3 1.0
CA B:ASP362 4.7 37.1 1.0
O B:ALA169 4.7 38.4 1.0
O B:ALA365 4.8 47.2 1.0
CD2 B:HIS274 4.8 51.4 1.0
NE2 B:HIS274 4.8 53.1 1.0

Reference:

N.-C.Ha, S.-T.Oh, J.Y.Sung, K.-A.Cha, M.Hyung Lee, B.-H.Oh. Supramolecular Assembly and Acid Resistance of Helicobacter Pylori Urease Nat.Struct.Biol. V. 8 480 2001.
ISSN: ISSN 1072-8368
PubMed: 11373617
DOI: 10.1038/88563
Page generated: Wed Dec 16 01:11:28 2020

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