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Nickel in PDB 1qco: Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate

Enzymatic activity of Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate

All present enzymatic activity of Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate:
3.7.1.2;

Protein crystallography data

The structure of Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate, PDB code: 1qco was solved by D.E.Timm, H.A.Mueller, P.Bhanumoorthy, J.M.Harp, G.J.Bunick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.90 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.640, 110.940, 67.810, 90.00, 102.52, 90.00
R / Rfree (%) 15.9 / 19.2

Other elements in 1qco:

The structure of Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate (pdb code 1qco). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate, PDB code: 1qco:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 1qco

Go back to Nickel Binding Sites List in 1qco
Nickel binding site 1 out of 5 in the Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate


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 Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1006

b:8.7
occ:0.40
 O A:HOH1121 2.3 25.2 1.0
O A:HOH1260 2.3 46.0 1.0
OD1 A:ASP11 2.3 21.5 1.0
O A:HOH1270 2.3 32.9 1.0
O A:HOH1238 2.3 45.9 1.0
NE2 A:HIS395 2.5 29.2 1.0
CG A:ASP11 3.0 23.3 1.0
OD2 A:ASP11 3.1 24.0 1.0
CD2 A:HIS395 3.2 29.2 1.0
CE1 A:HIS395 3.6 29.0 1.0
CB A:ASP11 4.4 22.2 1.0
CG A:HIS395 4.4 28.1 1.0
O A:HOH1217 4.4 47.2 1.0
O A:HOH1267 4.4 25.6 1.0
ND1 A:HIS395 4.6 29.6 1.0
O A:ASP9 4.6 32.9 1.0
O A:HOH1177 4.7 37.9 1.0
NH1 A:ARG402 4.8 58.1 1.0
CA A:ASP11 4.9 20.9 1.0
N A:ASP11 4.9 22.3 1.0

Nickel binding site 2 out of 5 in 1qco

Go back to Nickel Binding Sites List in 1qco
Nickel binding site 2 out of 5 in the Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate


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 Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1003

b:27.3
occ:0.40
 O B:HOH1203 2.2 58.2 1.0
O B:HOH1226 2.3 59.5 1.0
O B:HOH1202 2.4 52.9 1.0
O A:HOH1250 2.4 57.5 1.0
NE2 B:HIS654 2.7 20.8 1.0
CD2 B:HIS654 3.5 18.8 1.0
CE1 B:HIS654 3.7 18.4 1.0
O B:PRO650 4.3 20.0 1.0
NH2 A:ARG181 4.6 37.1 1.0
CG B:HIS654 4.7 17.5 1.0
ND1 B:HIS654 4.8 19.3 1.0

Nickel binding site 3 out of 5 in 1qco

Go back to Nickel Binding Sites List in 1qco
Nickel binding site 3 out of 5 in the Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1004

b:8.9
occ:0.40
 O B:HOH1260 2.3 35.6 1.0
O B:HOH1150 2.3 28.1 1.0
OD1 B:ASP511 2.3 22.7 1.0
O B:HOH1277 2.3 36.7 1.0
O B:HOH1250 2.3 54.7 1.0
NE2 B:HIS895 2.4 26.4 1.0
CG B:ASP511 3.0 23.5 1.0
CD2 B:HIS895 3.1 23.0 1.0
OD2 B:ASP511 3.1 22.6 1.0
CE1 B:HIS895 3.6 24.5 1.0
O B:HOH1246 3.8 44.9 1.0
CB B:ASP511 4.4 19.9 1.0
CG B:HIS895 4.4 22.7 1.0
O B:HOH1183 4.4 25.2 1.0
O B:ASP509 4.5 40.9 1.0
O B:HOH1172 4.6 46.3 1.0
ND1 B:HIS895 4.6 23.6 1.0
O B:HOH1182 4.6 44.3 1.0
N B:ASP511 4.8 22.4 1.0
CA B:ASP511 4.8 20.8 1.0

Nickel binding site 4 out of 5 in 1qco

Go back to Nickel Binding Sites List in 1qco
Nickel binding site 4 out of 5 in the Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1005

b:22.4
occ:0.40
 O B:HOH1280 2.3 38.9 1.0
O B:HOH1013 2.3 62.7 1.0
O B:HOH1274 2.3 44.8 1.0
O B:HOH1012 2.3 46.3 1.0
NE2 B:HIS722 2.5 24.6 1.0
CE1 B:HIS722 3.2 24.6 1.0
CD2 B:HIS722 3.7 23.9 1.0
OE2 B:GLU723 3.7 36.4 1.0
CG B:GLU723 4.2 29.4 1.0
NE2 B:GLN575 4.3 40.5 1.0
ND1 B:HIS722 4.4 24.8 1.0
OE1 B:GLN575 4.4 42.9 1.0
CD B:GLU723 4.5 33.1 1.0
CG B:HIS722 4.7 24.5 1.0
CD B:GLN575 4.8 38.8 1.0

Nickel binding site 5 out of 5 in 1qco

Go back to Nickel Binding Sites List in 1qco
Nickel binding site 5 out of 5 in the Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Fumarylacetoacetate Hydrolase Complexed with Fumarate and Acetoacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1007

b:32.8
occ:1.00
 O B:GLY499 2.1 42.6 1.0
O B:HOH1271 2.3 25.1 1.0
O B:HOH1035 2.3 50.8 1.0
O B:HOH1278 2.3 28.3 1.0
C B:GLY499 3.2 44.3 1.0
N B:GLY499 3.2 45.3 1.0
CA B:GLY499 3.7 44.7 1.0
O B:HOH1275 4.0 39.4 1.0
OG B:SER500 4.4 50.1 1.0
N B:SER500 4.4 44.2 1.0
CA B:SER500 4.9 43.0 1.0

Reference:

D.E.Timm, H.A.Mueller, P.Bhanumoorthy, J.M.Harp, G.J.Bunick. Crystal Structure and Mechanism of A Carbon-Carbon Bond Hydrolase. Structure Fold.Des. V. 7 1023 1999.
ISSN: ISSN 0969-2126
PubMed: 10508789
DOI: 10.1016/S0969-2126(99)80170-1
Page generated: Wed Oct 9 16:19:30 2024

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