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Nickel in PDB 1h5q: Mannitol Dehydrogenase From Agaricus Bisporus

Enzymatic activity of Mannitol Dehydrogenase From Agaricus Bisporus

All present enzymatic activity of Mannitol Dehydrogenase From Agaricus Bisporus:
1.1.1.138;

Protein crystallography data

The structure of Mannitol Dehydrogenase From Agaricus Bisporus, PDB code: 1h5q was solved by S.Horer, J.Stoop, H.Mooibroek, U.Baumann, J.Sassoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 227.250, 124.850, 132.690, 90.00, 118.54, 90.00
R / Rfree (%) 19.3 / 20.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Mannitol Dehydrogenase From Agaricus Bisporus (pdb code 1h5q). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Mannitol Dehydrogenase From Agaricus Bisporus, PDB code: 1h5q:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 1h5q

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Nickel binding site 1 out of 6 in the Mannitol Dehydrogenase From Agaricus Bisporus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Mannitol Dehydrogenase From Agaricus Bisporus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni2263

b:32.9
occ:1.00
 OXT A:TRP262 2.3 26.9 1.0
O A:HOH2125 2.3 26.3 1.0
OXT C:TRP262 2.3 27.1 1.0
O C:HOH2243 2.4 29.9 1.0
O A:HOH2127 2.4 26.0 1.0
O C:HOH2241 2.5 25.2 1.0
C C:TRP262 3.3 27.5 1.0
C A:TRP262 3.4 26.7 1.0
O C:TRP262 3.7 28.1 1.0
O A:TRP262 3.7 26.9 1.0
CG2 C:ILE154 3.9 24.1 1.0
CG2 A:ILE154 4.0 28.7 1.0
O C:LEU260 4.4 25.9 1.0
O A:LEU260 4.5 25.6 1.0
O A:HOH2021 4.5 37.1 1.0
CA C:TRP262 4.7 28.1 1.0
O A:HOH2022 4.7 33.4 1.0
CA A:TRP262 4.7 27.0 1.0
O A:HOH2126 4.7 31.8 1.0
O C:HOH2244 4.8 31.9 1.0
C A:LEU260 4.9 26.5 1.0
C C:LEU260 4.9 25.6 1.0
O A:GLN259 4.9 28.3 1.0
N A:TRP262 4.9 26.6 1.0
N C:TRP262 4.9 27.2 1.0
O C:GLN259 4.9 26.0 1.0
CA A:LEU260 5.0 27.2 1.0

Nickel binding site 2 out of 6 in 1h5q

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Nickel binding site 2 out of 6 in the Mannitol Dehydrogenase From Agaricus Bisporus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Mannitol Dehydrogenase From Agaricus Bisporus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni2263

b:78.8
occ:1.00
 O D:HOH2183 2.1 28.9 1.0
OXT B:TRP262 2.3 21.3 1.0
O B:HOH2195 2.3 20.5 1.0
O B:HOH2193 2.4 23.8 1.0
OXT D:TRP262 2.4 25.3 1.0
O D:HOH2184 2.4 22.4 1.0
C B:TRP262 3.3 23.3 1.0
C D:TRP262 3.4 26.6 1.0
O B:TRP262 3.7 24.2 1.0
O D:TRP262 3.7 26.8 1.0
CG2 D:ILE154 3.9 22.6 1.0
CG2 B:ILE154 3.9 23.5 1.0
O B:LEU260 4.3 22.6 1.0
O D:LEU260 4.6 26.2 1.0
O B:HOH2196 4.6 28.8 1.0
CA B:TRP262 4.6 23.1 1.0
O D:HOH2185 4.7 29.3 1.0
CA D:TRP262 4.7 28.0 1.0
C B:LEU260 4.8 21.8 1.0
O B:HOH2051 4.8 32.7 1.0
CA B:LEU260 4.9 21.6 1.0
N B:TRP262 4.9 22.3 1.0
C D:LEU260 4.9 26.7 1.0
O B:GLN259 4.9 22.2 1.0
O D:GLN259 5.0 26.8 1.0
CA D:LEU260 5.0 26.0 1.0
CB D:ILE154 5.0 22.2 1.0

Nickel binding site 3 out of 6 in 1h5q

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Nickel binding site 3 out of 6 in the Mannitol Dehydrogenase From Agaricus Bisporus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Mannitol Dehydrogenase From Agaricus Bisporus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni3263

b:20.0
occ:1.00
 OXT G:TRP262 2.3 16.9 1.0
OXT E:TRP262 2.4 17.2 1.0
O E:HOH2329 2.4 19.0 1.0
O E:HOH2333 2.4 16.9 1.0
O G:HOH2278 2.4 20.0 1.0
O G:HOH2281 2.5 16.9 1.0
C G:TRP262 3.4 16.7 1.0
C E:TRP262 3.4 17.2 1.0
O G:TRP262 3.7 16.9 1.0
O E:TRP262 3.8 17.2 1.0
CG2 E:ILE154 3.9 15.4 1.0
CG2 G:ILE154 3.9 15.9 1.0
O E:LEU260 4.4 16.0 1.0
O G:LEU260 4.4 16.4 1.0
O E:HOH2113 4.7 32.3 1.0
CA E:TRP262 4.7 17.4 1.0
CA G:TRP262 4.7 17.3 1.0
O E:HOH2114 4.7 27.8 1.0
O G:HOH2280 4.8 22.3 1.0
C G:LEU260 4.9 16.5 1.0
C E:LEU260 4.9 16.0 1.0
N E:TRP262 4.9 16.8 1.0
N G:TRP262 4.9 16.9 1.0
O E:HOH2332 4.9 24.3 1.0
O G:GLN259 5.0 16.7 1.0
CA G:LEU260 5.0 16.3 1.0
CA E:LEU260 5.0 15.6 1.0
O E:GLN259 5.0 16.1 1.0

Nickel binding site 4 out of 6 in 1h5q

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Nickel binding site 4 out of 6 in the Mannitol Dehydrogenase From Agaricus Bisporus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Mannitol Dehydrogenase From Agaricus Bisporus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni3263

b:20.3
occ:1.00
 OXT H:TRP262 2.2 15.4 1.0
OXT F:TRP262 2.3 14.8 1.0
O F:HOH2304 2.3 15.3 1.0
O H:HOH2291 2.3 19.1 1.0
O F:HOH2306 2.4 16.2 1.0
O H:HOH2290 2.4 18.1 1.0
C H:TRP262 3.3 15.6 1.0
C F:TRP262 3.4 15.3 1.0
O H:TRP262 3.7 15.6 1.0
O F:TRP262 3.7 15.0 1.0
CG2 F:ILE154 3.9 14.6 1.0
CG2 H:ILE154 4.0 15.0 1.0
O F:LEU260 4.4 15.0 1.0
O H:LEU260 4.4 15.2 1.0
O F:HOH2095 4.6 30.8 1.0
O F:HOH2094 4.6 29.0 1.0
CA H:TRP262 4.7 16.0 1.0
CA F:TRP262 4.7 16.0 1.0
O F:HOH2305 4.8 22.8 1.0
O H:HOH2292 4.8 20.6 1.0
O F:GLN259 4.9 15.4 1.0
C F:LEU260 4.9 15.6 1.0
N F:TRP262 4.9 15.2 1.0
C H:LEU260 4.9 15.1 1.0
N H:TRP262 4.9 15.2 1.0
O H:GLN259 4.9 14.8 1.0
CA F:LEU260 5.0 15.2 1.0
CA H:LEU260 5.0 14.8 1.0

Nickel binding site 5 out of 6 in 1h5q

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Nickel binding site 5 out of 6 in the Mannitol Dehydrogenase From Agaricus Bisporus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Mannitol Dehydrogenase From Agaricus Bisporus within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni3263

b:21.1
occ:1.00
 OXT I:TRP262 2.3 14.8 1.0
OXT K:TRP262 2.3 16.4 1.0
O K:HOH2273 2.3 19.9 1.0
O I:HOH2299 2.4 19.2 1.0
O I:HOH2300 2.5 17.1 1.0
O K:HOH2275 2.5 18.4 1.0
C K:TRP262 3.3 16.4 1.0
C I:TRP262 3.4 16.2 1.0
O K:TRP262 3.7 16.4 1.0
O I:TRP262 3.8 15.8 1.0
CG2 I:ILE154 3.9 15.1 1.0
CG2 K:ILE154 3.9 15.5 1.0
O I:LEU260 4.3 15.2 1.0
O K:LEU260 4.4 15.9 1.0
O I:HOH2100 4.6 26.8 1.0
CA K:TRP262 4.7 16.9 1.0
CA I:TRP262 4.7 16.4 1.0
O I:HOH2099 4.7 29.1 1.0
O K:HOH2274 4.8 20.3 1.0
C I:LEU260 4.8 15.5 1.0
O I:HOH2301 4.9 22.4 1.0
O I:GLN259 4.9 16.5 1.0
CA I:LEU260 4.9 15.1 1.0
N I:TRP262 4.9 15.7 1.0
C K:LEU260 4.9 15.9 1.0
N K:TRP262 4.9 16.2 1.0

Nickel binding site 6 out of 6 in 1h5q

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Nickel binding site 6 out of 6 in the Mannitol Dehydrogenase From Agaricus Bisporus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Mannitol Dehydrogenase From Agaricus Bisporus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni3263

b:16.9
occ:1.00
 OXT J:TRP262 2.3 17.7 1.0
OXT L:TRP262 2.4 18.3 1.0
O J:HOH2260 2.4 20.9 1.0
O L:HOH2297 2.4 17.3 1.0
O J:HOH2257 2.5 21.5 1.0
O L:HOH2295 2.6 20.6 1.0
C J:TRP262 3.2 17.6 1.0
C L:TRP262 3.4 17.8 1.0
O J:TRP262 3.6 18.9 1.0
O L:TRP262 3.8 17.6 1.0
CG2 L:ILE154 3.8 16.2 1.0
CG2 J:ILE154 4.0 17.0 1.0
O J:LEU260 4.4 17.1 1.0
O L:LEU260 4.5 16.8 1.0
CA J:TRP262 4.6 18.2 1.0
O J:HOH2079 4.6 26.7 1.0
CA L:TRP262 4.7 18.1 1.0
O J:HOH2259 4.7 21.6 1.0
O J:HOH2080 4.7 28.9 1.0
O L:HOH2298 4.7 24.7 1.0
N J:TRP262 4.9 17.5 1.0
O L:GLN259 4.9 17.0 1.0
C J:LEU260 4.9 17.3 1.0
N L:TRP262 4.9 17.5 1.0
C L:LEU260 4.9 16.5 1.0
O J:GLN259 5.0 17.2 1.0

Reference:

S.Horer, J.Stoop, H.Mooibroek, U.Baumann, J.Sassoon. The Crystallographic Structure of the Mannitol 2- Dehydrogenase Nadp+ Binary Complex From Agaricus Bisporus J.Biol.Chem. V. 276 27555 2001.
ISSN: ISSN 0021-9258
PubMed: 11335726
DOI: 10.1074/JBC.M102850200
Page generated: Wed Oct 9 14:55:09 2024

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