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Nickel in PDB 7a9m: Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K

Enzymatic activity of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K

All present enzymatic activity of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K:
3.4.21.64;

Protein crystallography data

The structure of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K, PDB code: 7a9m was solved by J.Breibeck, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.95 / 1.62
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.01, 68.01, 102.58, 90, 90, 90
R / Rfree (%) 14.7 / 19

Other elements in 7a9m:

The structure of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K also contains other interesting chemical elements:

Tungsten (W) 22 atoms
Silicon (Si) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K (pdb code 7a9m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K, PDB code: 7a9m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 7a9m

Go back to Nickel Binding Sites List in 7a9m
Nickel binding site 1 out of 2 in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:11.7
occ:0.30
NI1 A:R5N302 0.0 11.7 0.3
O76 A:R5N302 2.1 8.2 0.3
O77 A:R5N302 2.1 9.0 0.3
O75 A:R5N302 2.1 9.1 0.3
O78 A:R5N302 2.2 14.8 0.3
O61 A:R5N302 2.6 8.6 0.3
O A:HOH410 2.6 34.5 1.0
HG3 A:MET55 3.3 11.0 1.0
W18 A:R5N302 3.4 6.5 0.3
W17 A:R5N302 3.4 7.5 0.3
HG2 A:MET55 3.4 11.0 1.0
HA A:ARG64 3.5 11.3 1.0
SI2 A:R5N302 3.6 6.3 0.3
W13 A:R5N302 3.6 7.6 0.3
W12 A:R5N302 3.6 7.1 0.3
O55 A:R5N302 3.6 9.5 0.3
O41 A:R5N302 3.7 5.8 0.3
CG A:MET55 3.8 9.2 1.0
O53 A:R5N302 3.9 8.2 0.3
O60 A:R5N302 3.9 7.5 0.3
O57 A:R5N302 3.9 7.5 0.3
O59 A:R5N302 3.9 6.0 0.3
O A:ILE42 4.0 6.5 1.0
H A:ALA44 4.0 11.9 1.0
O A:HOH609 4.1 12.3 1.0
HB2 A:SER63 4.3 14.2 1.0
O A:SER63 4.3 8.8 1.0
HB2 A:MET55 4.3 11.7 1.0
CA A:ARG64 4.3 9.4 1.0
HB1 A:ALA44 4.4 13.8 1.0
HB2 A:ARG64 4.4 17.8 1.0
C A:SER63 4.5 12.8 1.0
O45 A:R5N302 4.5 10.9 0.3
O46 A:R5N302 4.5 7.9 0.3
HA A:GLU43 4.5 10.8 1.0
N A:ARG64 4.5 10.2 1.0
HB3 A:SER63 4.5 14.2 1.0
O40 A:R5N302 4.6 0.3 0.3
O42 A:R5N302 4.6 8.8 0.3
CB A:MET55 4.7 9.8 1.0
O56 A:R5N302 4.7 6.9 0.3
O54 A:R5N302 4.7 8.6 0.3
CB A:SER63 4.8 11.9 1.0
N A:ALA44 4.9 9.9 1.0
H A:ASP65 4.9 11.3 1.0
O66 A:R5N302 4.9 6.6 0.3
O67 A:R5N302 4.9 6.9 0.3
H A:ARG64 5.0 12.3 1.0
CB A:ARG64 5.0 14.9 1.0
O62 A:R5N302 5.0 8.1 0.3

Nickel binding site 2 out of 2 in 7a9m

Go back to Nickel Binding Sites List in 7a9m
Nickel binding site 2 out of 2 in the Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:78.1
occ:0.30
NI1 A:R5N303 0.0 78.1 0.3
OD1 A:ASP207 1.3 30.4 1.0
O76 A:R5N303 2.1 100.5 0.3
O77 A:R5N303 2.1 72.8 0.3
O75 A:R5N303 2.1 89.5 0.3
O78 A:R5N303 2.2 58.3 0.3
CG A:ASP207 2.5 19.9 1.0
O61 A:R5N303 2.7 97.8 0.3
OD2 A:ASP207 3.3 20.7 1.0
HB2 A:ASP207 3.4 8.4 1.0
CB A:ASP207 3.5 7.0 1.0
W17 A:R5N303 3.5 52.1 0.3
SI2 A:R5N303 3.5 106.6 0.3
W18 A:R5N303 3.6 30.4 0.3
W12 A:R5N303 3.7 64.6 0.3
HG21 A:THR206 3.7 8.9 1.0
HB3 A:ASP207 3.7 8.4 1.0
W13 A:R5N303 3.7 88.3 0.3
O41 A:R5N303 3.8 125.9 0.3
O55 A:R5N303 3.8 71.7 0.3
O59 A:R5N303 3.8 110.2 0.3
HH22 A:ARG185 3.8 17.2 1.0
HE A:ARG185 3.8 16.6 1.0
O60 A:R5N303 3.9 116.7 0.3
O53 A:R5N303 4.0 107.0 0.3
O57 A:R5N303 4.0 71.8 0.3
O46 A:R5N303 4.3 89.8 0.3
O A:HOH592 4.5 8.1 1.0
O45 A:R5N303 4.5 121.7 0.3
CG2 A:THR206 4.5 7.5 1.0
O40 A:R5N303 4.6 100.6 0.3
HG23 A:THR206 4.6 8.9 1.0
NH2 A:ARG185 4.6 14.4 1.0
NE A:ARG185 4.7 13.8 1.0
O42 A:R5N303 4.7 93.0 0.3
HG22 A:THR206 4.7 8.9 1.0
O54 A:R5N303 4.8 73.2 0.3
CA A:ASP207 4.8 6.3 1.0
O56 A:R5N303 4.9 35.0 0.3
O62 A:R5N303 4.9 109.9 0.3
W19 A:R5N303 5.0 39.8 0.3

Reference:

J.Breibeck, A.Rompel. Ni-Substituted Keggin Silicotungstate with Covalent Bond to Proteinase K To Be Published.
Page generated: Fri Nov 5 16:11:38 2021

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