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Nickel in PDB 9bkx: Mycobacterium Tuberculosis Encapsulin in Complex with Dyp

Enzymatic activity of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp

All present enzymatic activity of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp:
1.11.1.7;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp, PDB code: 9bkx was solved by B.J.Cuthbert, G.O.Batot, H.Contreras, X.Chen, K.H.Burley, C.W.Goulding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.56 / 3.15
Space group P 21 3 2
Cell size a, b, c (Å), α, β, γ (°) 313.451, 313.451, 313.451, 90, 90, 90
R / Rfree (%) 20.1 / 23.3

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Nickel atom in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp (pdb code 9bkx). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 33 binding sites of Nickel where determined in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp, PDB code: 9bkx:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 33 in 9bkx

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Nickel binding site 1 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni309

b:130.8
occ:1.00
 O T:HIS187 3.7 44.1 1.0
O B:HIS187 3.8 49.0 1.0
O S:HIS187 3.8 46.1 1.0
O R:HIS187 3.8 49.0 1.0
O A:HIS187 3.9 34.5 1.0
C T:HIS187 4.9 40.8 1.0
CB B:HIS187 4.9 46.8 1.0
C B:HIS187 4.9 43.5 1.0
C S:HIS187 5.0 46.1 1.0
CB T:HIS187 5.0 43.0 1.0

Nickel binding site 2 out of 33 in 9bkx

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Nickel binding site 2 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni304

b:95.6
occ:1.00
 O C:SER72 3.6 55.1 1.0
N C:SER72 3.7 42.8 1.0
OG C:SER72 4.2 48.1 1.0
CA C:ALA71 4.2 44.1 1.0
CD1 C:ILE56 4.3 25.4 1.0
C C:ALA71 4.5 41.6 1.0
C C:SER72 4.5 41.3 1.0
O C:ARG70 4.5 43.2 1.0
CA C:SER72 4.6 37.9 1.0
NI C:NI309 4.8 191.9 1.0
CB C:ALA71 4.9 44.9 1.0

Nickel binding site 3 out of 33 in 9bkx

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Nickel binding site 3 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni307

b:88.8
occ:1.00
 OD2 C:ASP238 3.5 54.2 1.0
OG C:SER236 3.5 39.0 1.0
CA C:HIS237 4.0 45.7 1.0
N C:HIS237 4.0 33.8 1.0
OG1 C:THR241 4.1 39.7 1.0
C C:SER236 4.2 35.3 1.0
C C:HIS237 4.2 47.9 1.0
O C:SER236 4.2 48.4 1.0
N C:ASP238 4.2 44.9 1.0
CB C:ARG243 4.4 28.6 1.0
CB C:SER236 4.4 48.5 1.0
CG C:ASP238 4.5 50.4 1.0
O C:THR241 4.7 47.8 1.0
O C:HIS237 4.8 54.7 1.0
N C:ARG243 4.8 31.3 1.0
CB C:ASP238 4.9 41.3 1.0
CA C:SER236 4.9 30.6 1.0

Nickel binding site 4 out of 33 in 9bkx

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Nickel binding site 4 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni308

b:98.6
occ:0.92
 OH C:TYR234 3.7 38.8 1.0
O C:HIS237 3.7 54.7 1.0
N C:HIS237 3.9 33.8 1.0
ND1 C:HIS237 4.3 42.0 1.0
CB C:SER236 4.3 48.5 1.0
CA C:SER236 4.3 30.6 1.0
NE2 B:HIS237 4.3 42.9 1.0
CE1 C:HIS237 4.5 32.7 1.0
C C:SER236 4.6 35.3 1.0
C C:HIS237 4.7 47.9 1.0
CA C:HIS237 4.9 45.7 1.0
CG C:HIS237 4.9 42.8 1.0
CZ C:TYR234 4.9 39.9 1.0
CE1 B:HIS237 5.0 43.2 1.0

Nickel binding site 5 out of 33 in 9bkx

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Nickel binding site 5 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni309

b:191.9
occ:1.00
 CG C:PRO74 4.0 32.5 1.0
CD C:PRO74 4.1 37.4 1.0
OG C:SER127 4.1 52.5 1.0
O A:HOH424 4.7 17.7 1.0
NI C:NI304 4.8 95.6 1.0
CB C:PRO74 4.9 41.4 1.0
CB C:SER127 5.0 35.1 1.0

Nickel binding site 6 out of 33 in 9bkx

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Nickel binding site 6 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni306

b:77.0
occ:0.93
 OG D:SER236 3.4 44.1 1.0
CA D:HIS237 4.0 49.0 1.0
N D:HIS237 4.0 46.4 1.0
C D:SER236 4.1 41.5 1.0
C D:HIS237 4.2 40.1 1.0
OG1 D:THR241 4.2 49.5 1.0
CB D:ARG243 4.2 49.6 1.0
O D:SER236 4.3 45.0 1.0
CB D:SER236 4.3 44.2 1.0
N D:ASP238 4.3 38.1 1.0
OD2 D:ASP238 4.4 40.7 1.0
CG D:ASP238 4.6 46.9 1.0
O D:THR241 4.7 35.4 1.0
N D:ARG243 4.7 41.3 1.0
O D:HIS237 4.8 41.5 1.0
CA D:SER236 4.9 32.1 1.0
CB D:ASP238 5.0 34.9 1.0

Nickel binding site 7 out of 33 in 9bkx

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Nickel binding site 7 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni307

b:99.2
occ:0.95
 O D:GLU93 4.4 40.6 1.0
CB D:ALA14 4.4 29.2 1.0
O D:VAL92 4.5 45.2 1.0
CA D:GLU93 4.7 31.5 1.0
C D:GLU93 4.9 31.1 1.0

Nickel binding site 8 out of 33 in 9bkx

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Nickel binding site 8 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni307

b:81.3
occ:0.94
 OG E:SER236 3.6 42.8 1.0
OG1 E:THR241 3.9 37.1 1.0
CA E:HIS237 4.0 31.5 1.0
N E:HIS237 4.1 32.6 1.0
CB E:ARG243 4.1 39.4 1.0
O E:SER236 4.1 35.1 1.0
C E:SER236 4.1 38.3 1.0
C E:HIS237 4.3 34.4 1.0
N E:ASP238 4.4 39.0 1.0
OD2 E:ASP238 4.4 39.6 1.0
N E:ARG243 4.4 31.8 1.0
O E:THR241 4.5 37.9 1.0
CB E:SER236 4.5 43.1 1.0
CG E:ASP238 4.6 41.2 1.0
C E:THR241 4.8 40.9 1.0
OD1 E:ASP238 4.9 51.0 1.0
CA E:ARG243 4.9 29.9 1.0
CA E:SER236 4.9 29.7 1.0
C E:VAL242 5.0 34.6 1.0
CB E:THR241 5.0 35.4 1.0
O E:HIS237 5.0 48.1 1.0

Nickel binding site 9 out of 33 in 9bkx

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Nickel binding site 9 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni308

b:94.5
occ:0.88
 OD1 E:ASP210 3.2 75.2 1.0
O E:ALA208 3.9 47.2 1.0
CG E:ASP210 4.1 73.0 1.0
OD2 E:ASP210 4.2 73.2 1.0
O E:PRO207 4.4 32.5 1.0
O E:ILE209 4.6 45.3 1.0
C E:ALA208 4.7 44.0 1.0
NH2 E:ARG117 4.9 77.8 1.0
NE E:ARG117 4.9 64.9 1.0
C E:ILE209 5.0 48.1 1.0

Nickel binding site 10 out of 33 in 9bkx

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Nickel binding site 10 out of 33 in the Mycobacterium Tuberculosis Encapsulin in Complex with Dyp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Mycobacterium Tuberculosis Encapsulin in Complex with Dyp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni308

b:104.5
occ:1.00
 N F:SER72 4.4 28.3 1.0
O F:SER72 4.4 35.9 1.0
CD1 F:ILE56 4.5 29.4 1.0
CA F:ALA71 4.6 47.1 1.0
O F:ARG70 4.6 39.9 1.0
OG F:SER72 4.6 32.9 1.0
CB K:PRO74 4.7 35.2 1.0
C F:ALA71 5.0 43.2 1.0

Reference:

B.J.Cuthbert, X.Chen, K.Burley, G.Batot, H.Contreras, S.Dixon, C.W.Goulding. Structural Characterization of Mycobacterium Tuberculosis Encapsulin in Complex with Dye-Decolorizing Peroxide Microorganisms V. 12 2024.
ISSN: ESSN 2076-2607
DOI: 10.3390/MICROORGANISMS12122465
Page generated: Sun Dec 15 11:47:42 2024

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