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Nickel in PDB 2hzy: Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate

Enzymatic activity of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate

All present enzymatic activity of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate:
3.7.1.2;

Protein crystallography data

The structure of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate, PDB code: 2hzy was solved by T.D.Hurley, D.E.Timm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.14 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.144, 109.472, 67.491, 90.00, 102.35, 90.00
R / Rfree (%) 16.8 / 18.8

Other elements in 2hzy:

The structure of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Calcium (Ca) 1 atom
Sodium (Na) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate (pdb code 2hzy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 10 binding sites of Nickel where determined in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate, PDB code: 2hzy:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 10 in 2hzy

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Nickel binding site 1 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1209

b:15.5
occ:0.75
 O A:HOH1285 2.0 24.3 1.0
NE2 A:HIS395 2.1 18.6 1.0
OD1 A:ASP11 2.1 16.0 1.0
O A:HOH1534 2.1 23.5 1.0
O A:HOH1518 2.1 22.8 1.0
O A:HOH1292 2.2 20.9 1.0
CG A:ASP11 3.0 15.0 1.0
CE1 A:HIS395 3.0 18.2 1.0
CD2 A:HIS395 3.1 19.0 1.0
OD2 A:ASP11 3.3 16.4 1.0
O A:HOH1268 3.9 40.7 1.0
O A:HOH1586 4.0 28.3 1.0
ND1 A:HIS395 4.2 19.9 1.0
CG A:HIS395 4.2 18.8 1.0
O A:HOH1636 4.3 40.4 1.0
CB A:ASP11 4.4 15.7 1.0
O A:HOH1438 4.5 17.5 1.0
O A:ASP9 4.6 27.1 1.0
CD A:ARG402 4.6 36.8 1.0
CA A:ASP11 4.8 15.2 1.0
N A:ASP11 4.8 17.9 1.0
O A:HOH1301 5.0 26.1 1.0

Nickel binding site 2 out of 10 in 2hzy

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Nickel binding site 2 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1211

b:24.0
occ:0.50
 O A:HOH1290 2.0 33.5 1.0
NE2 A:HIS154 2.4 19.2 1.0
CE1 A:HIS154 3.3 19.2 1.0
CD2 A:HIS154 3.4 15.9 1.0
O A:PRO150 4.1 18.0 1.0
NH2 B:ARG181 4.3 33.2 1.0
ND1 A:HIS154 4.5 17.5 1.0
CG A:HIS154 4.5 14.1 1.0
NH1 B:ARG181 4.6 26.8 1.0
CZ B:ARG181 4.8 27.9 1.0

Nickel binding site 3 out of 10 in 2hzy

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Nickel binding site 3 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1212

b:17.8
occ:0.50
 O A:HOH1668 1.3 9.9 1.0
O A:HOH1669 1.5 32.9 1.0
O A:HOH1670 2.0 33.8 1.0
O A:HOH1597 2.1 32.0 1.0
OD2 A:ASP399 2.8 35.1 1.0
CG A:ASP399 3.9 31.8 1.0
OD1 A:ASP399 4.2 34.9 1.0
O A:HOH1662 4.9 24.0 1.0

Nickel binding site 4 out of 10 in 2hzy

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Nickel binding site 4 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1213

b:22.6
occ:0.50
 O A:HOH1591 1.3 34.7 1.0
O A:HOH1634 1.4 30.6 1.0
O A:HOH1423 1.9 42.8 1.0
NE2 A:HIS48 2.1 21.1 1.0
O A:HOH1671 2.1 33.8 1.0
CE1 A:HIS48 2.9 24.0 1.0
CD2 A:HIS48 3.2 24.2 1.0
ND1 A:HIS48 4.1 22.7 1.0
CG A:HIS48 4.2 18.6 1.0
O A:HOH1606 4.5 33.4 1.0
CE A:LYS47 4.6 26.9 1.0

Nickel binding site 5 out of 10 in 2hzy

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Nickel binding site 5 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1214

b:24.1
occ:0.25
 NE2 A:HIS58 2.2 28.6 1.0
O A:HOH1646 3.0 44.6 1.0
CE1 A:HIS58 3.1 27.3 1.0
CD2 A:HIS58 3.2 25.1 1.0
O A:HOH1585 3.8 34.2 1.0
O A:HOH1422 4.2 27.0 1.0
O A:HOH1419 4.2 33.4 1.0
ND1 A:HIS58 4.3 28.5 1.0
CG A:HIS58 4.4 24.2 1.0
CB A:LYS57 4.9 23.9 1.0

Nickel binding site 6 out of 10 in 2hzy

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Nickel binding site 6 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1205

b:16.7
occ:1.00
 N B:GLY-1 2.0 18.9 1.0
O B:GLY-1 2.1 14.6 1.0
O B:HOH1447 2.1 20.4 1.0
O B:HOH1448 2.1 21.1 1.0
C B:GLY-1 2.8 17.9 1.0
CA B:GLY-1 2.9 18.5 1.0
N B:SER0 4.1 18.2 1.0
O B:HOH1414 4.2 22.1 1.0
O B:HOH1420 4.2 31.0 1.0
O B:HOH1632 4.7 48.7 1.0
CA B:SER0 4.9 18.9 1.0
O B:HOH1631 5.0 33.3 1.0

Nickel binding site 7 out of 10 in 2hzy

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Nickel binding site 7 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1207

b:16.6
occ:0.75
 O B:HOH1221 2.0 23.2 1.0
O B:HOH1537 2.1 30.9 1.0
NE2 B:HIS154 2.1 14.4 1.0
O B:HOH1677 2.1 27.3 1.0
O B:HOH1520 2.1 27.8 1.0
O B:HOH1506 2.2 26.2 1.0
CE1 B:HIS154 3.1 14.1 1.0
CD2 B:HIS154 3.2 13.1 1.0
O B:PRO150 4.1 14.2 1.0
O A:HOH1559 4.2 43.7 1.0
ND1 B:HIS154 4.2 14.7 1.0
O B:HOH1721 4.2 32.6 1.0
CG B:HIS154 4.3 11.2 1.0
O B:HOH1619 4.3 40.9 1.0
NH2 A:ARG181 4.4 24.7 1.0
O B:HOH1620 4.6 27.1 1.0
O A:HOH1220 4.7 39.4 1.0
CG B:PRO281 4.8 19.1 1.0

Nickel binding site 8 out of 10 in 2hzy

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Nickel binding site 8 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1208

b:12.3
occ:0.75
 OD1 B:ASP11 2.0 13.9 1.0
O B:HOH1468 2.1 19.2 1.0
O B:HOH1714 2.1 16.1 1.0
NE2 B:HIS395 2.1 14.3 1.0
O B:HOH1454 2.1 18.2 1.0
O B:HOH1703 2.1 15.3 1.0
CG B:ASP11 3.0 13.0 1.0
CE1 B:HIS395 3.1 17.3 1.0
CD2 B:HIS395 3.1 14.6 1.0
OD2 B:ASP11 3.2 13.5 1.0
O B:HOH1331 3.8 29.8 1.0
O B:HOH1518 4.0 31.8 1.0
O B:HOH1347 4.2 18.1 1.0
ND1 B:HIS395 4.2 15.0 1.0
CG B:HIS395 4.2 15.1 1.0
O B:HOH1701 4.2 30.8 1.0
CB B:ASP11 4.4 11.8 1.0
O B:HOH1314 4.5 13.9 1.0
O B:ASP9 4.5 19.1 1.0
NH1 B:ARG402 4.6 32.0 1.0
N B:ASP11 4.7 12.1 1.0
CA B:ASP11 4.8 12.0 1.0
CD B:ARG402 4.9 25.1 1.0

Nickel binding site 9 out of 10 in 2hzy

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Nickel binding site 9 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1210

b:16.3
occ:0.50
 O B:HOH1642 1.5 11.7 0.5
O B:HOH1723 1.7 29.6 1.0
O B:HOH1642 1.9 22.2 0.5
O B:HOH1282 1.9 24.4 1.0
O B:HOH1676 1.9 25.6 1.0
OD2 B:ASP296 2.2 18.6 1.0
O B:HOH1709 2.3 27.6 1.0
CG B:ASP296 3.1 14.6 1.0
OD1 B:ASP296 3.2 14.5 1.0
O B:HOH1604 4.1 23.6 1.0
O B:HOH1386 4.2 19.0 1.0
O B:HOH1657 4.2 27.0 1.0
NZ B:LYS320 4.3 30.9 1.0
CB B:ASP296 4.5 12.1 1.0
ND2 B:ASN298 4.6 26.7 1.0
OD1 B:ASN298 4.8 27.8 1.0

Nickel binding site 10 out of 10 in 2hzy

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Nickel binding site 10 out of 10 in the Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Mouse Fumarylacetoacetate Hydrolase Complexes with A Transition-State Mimic of the Complete Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1215

b:28.7
occ:0.25
 O B:HOH1499 1.9 45.4 1.0
NE2 B:HIS58 2.3 33.3 1.0
CD2 B:HIS58 3.2 31.1 1.0
CE1 B:HIS58 3.3 34.0 1.0
O B:HOH1498 4.0 31.8 1.0
O B:HOH1698 4.3 39.1 1.0
CG B:HIS58 4.4 27.6 1.0
ND1 B:HIS58 4.4 31.4 1.0
CB B:LYS57 4.8 26.8 1.0

Reference:

R.L.Bateman, J.Ashworth, J.F.Witte, L.J.Baker, P.Bhanumoorthy, D.E.Timm, T.D.Hurley, M.Grompe, R.W.Mcclard. Slow-Onset Inhibition of Fumarylacetoacetate Hydrolase By Phosphinate Mimics of the Tetrahedral Intermediate: Kinetics, Crystal Structure and Pharmacokinetics. Biochem.J. V. 402 251 2007.
ISSN: ISSN 0264-6021
PubMed: 17064256
DOI: 10.1042/BJ20060961
Page generated: Wed Dec 16 01:18:50 2020

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