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Nickel in PDB 5t22: WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form

Protein crystallography data

The structure of WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form, PDB code: 5t22 was solved by E.O.Gallimore, M.A.Mcdonough, I.J.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.99 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.948, 80.040, 73.498, 90.00, 96.76, 90.00
R / Rfree (%) 18.9 / 22.1

Nickel Binding Sites:

The binding sites of Nickel atom in the WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form (pdb code 5t22). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form, PDB code: 5t22:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 5t22

Go back to Nickel Binding Sites List in 5t22
Nickel binding site 1 out of 3 in the WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:15.4
occ:1.00
NE2 A:HIS164 2.1 14.6 1.0
O A:HOH504 2.1 14.5 1.0
NE2 A:HIS259 2.1 12.6 1.0
O1 A:AKG303 2.1 11.8 1.0
O A:HOH551 2.1 16.4 1.0
O5 A:AKG303 2.2 14.0 1.0
C1 A:AKG303 2.8 13.3 1.0
C2 A:AKG303 2.8 14.1 1.0
CE1 A:HIS164 2.9 14.4 1.0
CD2 A:HIS259 3.0 13.2 1.0
CE1 A:HIS259 3.1 13.3 1.0
CD2 A:HIS164 3.1 15.0 1.0
O A:HOH575 3.8 36.6 1.0
O2 A:AKG303 4.1 12.9 1.0
ND1 A:HIS164 4.1 14.7 1.0
OG A:SER189 4.1 13.7 1.0
ND1 A:HIS259 4.2 14.3 1.0
CG A:HIS259 4.2 14.2 1.0
CG A:HIS164 4.2 15.0 1.0
O A:HOH607 4.2 19.0 1.0
C3 A:AKG303 4.3 14.6 1.0
O A:HOH614 4.4 18.3 1.0
O A:HOH601 4.4 18.6 1.0
O A:HOH431 4.4 15.9 1.0
CE1 A:PHE276 4.5 13.5 1.0

Nickel binding site 2 out of 3 in 5t22

Go back to Nickel Binding Sites List in 5t22
Nickel binding site 2 out of 3 in the WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:27.7
occ:1.00
OE2 A:GLU202 2.3 16.4 1.0
OE2 B:GLU202 2.3 15.4 1.0
O B:HOH575 2.4 14.0 1.0
O B:HOH440 2.4 14.5 1.0
O A:HOH596 2.4 17.5 1.0
O A:HOH462 2.4 16.8 1.0
CD B:GLU202 3.4 15.7 1.0
CD A:GLU202 3.4 16.1 1.0
CG A:GLU202 4.0 16.0 1.0
CG B:GLU202 4.0 15.5 1.0
N B:GLY200 4.1 14.9 1.0
N A:GLY200 4.2 17.0 1.0
OE1 B:GLU202 4.3 16.2 1.0
O A:HOH623 4.3 33.5 1.0
OE1 A:GLU202 4.3 16.0 1.0
O B:GLY200 4.6 14.0 1.0
O A:HOH493 4.6 22.7 1.0
O A:GLY200 4.7 16.7 1.0
O B:HOH467 4.8 25.2 1.0
CA B:ALA199 4.8 15.6 1.0
CA B:GLY200 4.8 15.1 1.0
CA A:ALA199 4.8 18.2 1.0
O B:HOH574 4.9 38.9 1.0
O B:HOH597 4.9 36.4 1.0
CA A:GLY200 4.9 16.8 1.0
O B:HOH446 4.9 12.7 1.0
C B:ALA199 4.9 15.6 1.0
C A:ALA199 5.0 17.4 1.0

Nickel binding site 3 out of 3 in 5t22

Go back to Nickel Binding Sites List in 5t22
Nickel binding site 3 out of 3 in the WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate P 21 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:19.2
occ:1.00
NE2 B:HIS259 2.1 16.8 1.0
O B:HOH487 2.2 17.2 1.0
O2 B:AKG302 2.2 17.2 1.0
NE2 B:HIS164 2.2 17.8 1.0
O5 B:AKG302 2.2 19.5 1.0
O B:HOH554 2.2 15.0 1.0
C1 B:AKG302 2.9 18.1 1.0
C2 B:AKG302 2.9 18.3 1.0
CD2 B:HIS259 3.1 16.9 1.0
CE1 B:HIS259 3.1 17.3 1.0
CE1 B:HIS164 3.2 18.1 1.0
CD2 B:HIS164 3.2 17.9 1.0
OG B:SER189 4.1 17.8 1.0
O1 B:AKG302 4.1 18.8 1.0
ND1 B:HIS259 4.2 17.5 1.0
CG B:HIS259 4.2 17.3 1.0
O B:HOH589 4.3 31.8 1.0
ND1 B:HIS164 4.3 18.3 1.0
CG B:HIS164 4.3 18.1 1.0
O B:HOH585 4.4 26.4 1.0
O B:HOH430 4.4 18.9 1.0
C3 B:AKG302 4.4 17.5 1.0
O B:HOH576 4.4 23.5 1.0
CE1 B:PHE276 4.6 16.9 1.0

Reference:

E.O.Gallimore, M.A.Mcdonough, I.J.Clifton, C.J.Schofield. WELO5 Small Molecule Halogenase with Ni(II) and 2-Oxoglutarate To Be Published.
Page generated: Wed Dec 16 01:49:09 2020

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