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Nickel in PDB 4gfs: 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site

Enzymatic activity of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site

All present enzymatic activity of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site:
4.2.1.10;

Protein crystallography data

The structure of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site, PDB code: 4gfs was solved by S.H.Light, G.Minasov, S.N.Krishna, L.Shuvalova, K.Kwon, A.Lavie, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.679, 74.468, 63.566, 90.00, 100.17, 90.00
R / Rfree (%) 19.9 / 24.9

Nickel Binding Sites:

The binding sites of Nickel atom in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site (pdb code 4gfs). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site, PDB code: 4gfs:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 4gfs

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Nickel binding site 1 out of 6 in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:77.5
occ:1.00
O A:HOH457 1.9 46.8 1.0
NE2 A:HIS250 2.3 43.4 1.0
O A:HOH432 3.1 52.0 1.0
CE1 A:HIS250 3.2 43.0 1.0
CD2 A:HIS250 3.3 42.7 1.0
ND1 A:HIS250 4.3 46.4 1.0
CG A:HIS250 4.4 43.6 1.0

Nickel binding site 2 out of 6 in 4gfs

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Nickel binding site 2 out of 6 in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:49.7
occ:1.00
O A:HOH461 1.8 42.3 1.0
O A:HOH449 1.8 39.8 1.0
O A:HOH460 2.1 46.9 1.0
NE2 A:HIS134 2.3 47.4 1.0
CD2 A:HIS134 3.0 47.2 1.0
CE1 A:HIS134 3.5 44.5 1.0
OD1 A:ASP106 3.9 47.7 1.0
OH A:TYR130 4.2 42.1 1.0
CG A:HIS134 4.2 47.6 1.0
ND1 A:HIS134 4.4 45.6 1.0
CZ A:TYR130 4.9 43.0 1.0

Nickel binding site 3 out of 6 in 4gfs

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Nickel binding site 3 out of 6 in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:43.1
occ:1.00
O B:HOH497 2.1 39.5 1.0
O B:HOH498 2.1 38.7 1.0
NE2 B:HIS143 2.2 35.8 1.0
NZ B:LYS170 2.2 33.1 1.0
O B:HOH496 2.2 33.1 1.0
O1 B:SIN305 2.3 36.8 1.0
CE1 B:HIS143 3.0 35.2 1.0
CE B:LYS170 3.1 34.5 1.0
C1 B:SIN305 3.2 44.3 1.0
CD2 B:HIS143 3.3 37.2 1.0
O2 B:SIN305 3.4 35.7 1.0
O B:HOH467 3.7 46.6 1.0
O B:HOH465 3.8 41.4 1.0
ND1 B:HIS143 4.2 34.5 1.0
CE2 B:PHE225 4.3 44.9 1.0
CG B:HIS143 4.3 34.6 1.0
CZ B:PHE225 4.4 44.4 1.0
O B:HOH421 4.4 39.7 1.0
NH2 B:ARG82 4.5 32.8 1.0
CD B:LYS170 4.5 31.6 1.0
OE2 B:GLU46 4.5 31.5 1.0
C2 B:SIN305 4.6 45.0 1.0
OE1 B:GLU46 4.6 32.6 1.0
O3 B:SIN305 4.6 43.8 1.0
C4 B:SIN305 4.6 48.4 1.0
O4 B:SIN305 4.7 52.8 1.0
CD2 B:PHE225 4.8 37.5 1.0
NE B:ARG82 4.9 31.7 1.0
CE1 B:PHE225 5.0 45.8 1.0
CD B:GLU46 5.0 32.5 1.0

Nickel binding site 4 out of 6 in 4gfs

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Nickel binding site 4 out of 6 in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni302

b:48.1
occ:0.70
NE2 B:HIS146 2.1 45.6 0.7
CE1 B:HIS146 3.0 49.5 0.7
CD2 B:HIS146 3.1 45.1 0.7
NZ B:LYS147 3.8 55.7 1.0
ND1 B:HIS146 4.1 52.2 0.7
CG B:HIS146 4.2 47.0 0.7
OD1 B:ASP144 4.4 45.8 1.0
OD2 B:ASP144 4.6 41.5 1.0
CD2 B:HIS146 4.6 45.3 0.3
CG B:ASP144 4.7 36.6 1.0

Nickel binding site 5 out of 6 in 4gfs

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Nickel binding site 5 out of 6 in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni303

b:77.8
occ:1.00
O B:HOH523 1.8 53.2 1.0
NE2 B:HIS250 2.3 42.2 1.0
O B:HOH521 2.4 59.3 1.0
O B:HOH522 2.6 61.6 1.0
O B:HOH524 2.7 74.4 1.0
CD2 B:HIS250 3.2 42.2 1.0
CE1 B:HIS250 3.3 44.1 1.0
O B:HOH473 4.1 43.4 1.0
ND1 B:HIS250 4.4 41.2 1.0
CG B:HIS250 4.4 39.9 1.0

Nickel binding site 6 out of 6 in 4gfs

Go back to Nickel Binding Sites List in 4gfs
Nickel binding site 6 out of 6 in the 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni304

b:43.0
occ:1.00
O B:HOH502 1.9 39.6 1.0
O B:HOH501 1.9 36.4 1.0
O B:HOH500 2.0 40.1 1.0
O B:HOH499 2.0 37.0 1.0
NE2 B:HIS134 2.1 30.9 1.0
O B:HOH505 2.2 43.5 1.0
CE1 B:HIS134 3.0 28.4 1.0
CD2 B:HIS134 3.2 29.3 1.0
OD1 B:ASP106 3.9 39.3 1.0
ND1 B:HIS134 4.1 28.7 1.0
CG B:HIS134 4.3 29.9 1.0
O B:HOH526 4.3 52.0 1.0
OH B:TYR130 4.5 36.4 1.0

Reference:

S.H.Light, G.Minasov, S.N.Krishna, L.Shuvalova, K.Kwon, A.Lavie, W.F.Anderson. 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 with Nickel Bound at Active Site To Be Published.
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