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Nickel in PDB 3toy: Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound

Enzymatic activity of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound

All present enzymatic activity of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound:
5.1.2.2; 5.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound, PDB code: 3toy was solved by Y.Patskovsky, J.Kim, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammond, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative(Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.389, 131.838, 108.825, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.9

Other elements in 3toy:

The structure of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound (pdb code 3toy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound, PDB code: 3toy:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3toy

Go back to Nickel Binding Sites List in 3toy
Nickel binding site 1 out of 3 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni363

b:81.7
occ:0.50
 O A:HOH1213 2.1 33.7 0.5
O A:HOH1440 2.1 31.5 0.5
NE2 A:HIS64 2.3 74.4 1.0
CD2 A:HIS64 3.2 70.4 1.0
CE1 A:HIS64 3.4 76.9 1.0
O A:HOH850 4.2 45.1 1.0
CG A:HIS64 4.4 64.4 1.0
ND1 A:HIS64 4.4 72.0 1.0
O A:HOH1222 4.9 57.1 1.0

Nickel binding site 2 out of 3 in 3toy

Go back to Nickel Binding Sites List in 3toy
Nickel binding site 2 out of 3 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni363

b:37.3
occ:1.00
 NE2 B:HIS64 2.1 35.4 1.0
O B:HOH1265 2.1 39.0 1.0
O B:HOH1266 2.1 31.9 1.0
NE2 C:HIS64 2.2 31.3 1.0
O B:HOH1532 2.2 20.3 0.5
O B:HOH1532 2.3 28.1 0.5
CE1 B:HIS64 3.0 41.3 1.0
CE1 C:HIS64 3.1 38.5 1.0
CD2 C:HIS64 3.1 39.2 1.0
CD2 B:HIS64 3.2 41.0 1.0
O B:HOH444 4.0 37.9 1.0
ND1 B:HIS64 4.2 40.5 1.0
O B:HOH471 4.2 43.9 1.0
ND1 C:HIS64 4.3 41.1 1.0
CG B:HIS64 4.3 41.7 1.0
CG C:HIS64 4.3 43.2 1.0
O C:HOH497 4.4 31.3 1.0
O C:HOH1329 5.0 47.0 1.0
O B:HOH1392 5.0 48.2 1.0

Nickel binding site 3 out of 3 in 3toy

Go back to Nickel Binding Sites List in 3toy
Nickel binding site 3 out of 3 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni363

b:59.2
occ:0.50
 NE2 D:HIS64 2.3 64.6 1.0
O D:HOH411 2.3 27.7 0.5
CD2 D:HIS64 3.0 57.0 1.0
CE1 D:HIS64 3.5 68.4 1.0
O D:HOH383 4.3 35.6 1.0
CG D:HIS64 4.3 57.1 1.0
ND1 D:HIS64 4.5 68.2 1.0
CB D:LYS60 5.0 31.6 1.0

Reference:

Y.Patskovsky, J.Kim, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammond, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo. Crystal Structure of Mandelate Racemase From Bradyrhizobium Sp. ORS278 To Be Published.
Page generated: Wed Oct 9 17:50:17 2024

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