Atomistry » Nickel » PDB 1fwc-1j6p » 1h5q
Atomistry »
  Nickel »
    PDB 1fwc-1j6p »
      1h5q »

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

Go back to Nickel Binding Sites List in 1h5q
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

Go back to Nickel Binding Sites List in 1h5q
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

Go back to Nickel Binding Sites List in 1h5q
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

Go back to Nickel Binding Sites List in 1h5q
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

Go back to Nickel Binding Sites List in 1h5q
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

Go back to Nickel Binding Sites List in 1h5q
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy