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Nickel in PDB 9ayo: Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+

Protein crystallography data

The structure of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+, PDB code: 9ayo was solved by C.J.Presloid, J.Jiang, P.C.Beardslee, H.R.Anderson, T.M.Swayne, K.R.Schmitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.05 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.04, 52.51, 54.098, 90, 90, 90
R / Rfree (%) 16.2 / 18.9

Other elements in 9ayo:

The structure of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ (pdb code 9ayo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+, PDB code: 9ayo:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 9ayo

Go back to Nickel Binding Sites List in 9ayo
Nickel binding site 1 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni203

b:20.9
occ:1.00
 NE2 A:HIS65 1.9 13.3 1.0
O A:HOH324 1.9 18.5 1.0
O A:PHE201 2.0 17.8 1.0
O A:HOH326 2.1 22.1 1.0
N A:PHE201 2.2 16.6 1.0
O A:HOH337 2.2 20.0 1.0
H2 A:PHE201 2.7 19.9 1.0
H A:PHE201 2.7 19.9 1.0
C A:PHE201 2.8 17.0 1.0
CD2 A:HIS65 2.8 16.0 1.0
CE1 A:HIS65 2.9 22.7 1.0
HD2 A:HIS65 3.0 19.1 1.0
CA A:PHE201 3.0 10.3 1.0
HE1 A:HIS65 3.2 27.2 1.0
HB2 A:PHE201 3.4 15.2 1.0
HA A:PHE201 3.8 12.3 1.0
CB A:PHE201 3.8 12.7 1.0
CG A:HIS65 4.0 15.4 1.0
ND1 A:HIS65 4.0 22.0 1.0
N A:ALA202 4.1 16.0 1.0
OD1 A:ASP33 4.2 16.4 1.0
HA A:PRO35 4.2 20.5 1.0
OD2 A:ASP33 4.2 20.1 1.0
O A:HOH372 4.3 25.9 1.0
O A:HOH327 4.3 24.5 1.0
HA A:ALA202 4.3 17.2 1.0
O A:HOH302 4.4 29.0 1.0
HB3 A:PHE201 4.5 15.2 1.0
O A:HOH344 4.5 27.3 1.0
O A:ASP34 4.6 12.9 1.0
CG A:ASP33 4.7 23.3 1.0
H A:ALA202 4.7 19.1 1.0
CG A:PHE201 4.7 13.4 1.0
CA A:ALA202 4.8 14.4 1.0
HD1 A:HIS65 4.8 26.4 1.0

Nickel binding site 2 out of 5 in 9ayo

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Nickel binding site 2 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni203

b:16.8
occ:1.00
 OE1 B:GLU78 2.0 10.1 1.0
OE1 B:GLU81 2.1 14.7 1.0
O B:HOH305 2.1 10.3 1.0
O B:HOH344 2.1 12.0 1.0
O B:HOH303 2.2 12.3 1.0
CD B:GLU78 3.0 14.3 1.0
CD B:GLU81 3.0 18.5 1.0
OE2 B:GLU81 3.3 19.4 1.0
OE2 B:GLU78 3.4 15.4 1.0
HA B:GLU78 3.9 18.8 1.0
O B:HOH373 4.0 30.8 1.0
O B:HOH363 4.1 30.8 1.0
O B:HOH369 4.3 28.6 1.0
HB2 B:GLU81 4.4 20.1 1.0
CG B:GLU78 4.4 19.3 1.0
CG B:GLU81 4.4 13.7 1.0
HB3 B:GLU81 4.6 20.1 1.0
HB3 B:GLU78 4.6 17.2 1.0
HG2 B:GLU78 4.7 23.1 1.0
CB B:GLU81 4.7 16.8 1.0
CA B:GLU78 4.7 15.7 1.0
CB B:GLU78 4.8 14.4 1.0
HG3 B:GLU81 4.8 16.4 1.0
HG2 B:GLU81 5.0 16.4 1.0

Nickel binding site 3 out of 5 in 9ayo

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Nickel binding site 3 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni204

b:50.4
occ:1.00
 HE2 B:HIS88 1.6 40.0 1.0
O B:HOH308 2.1 21.2 1.0
NE2 B:HIS88 2.2 33.4 1.0
HE1 B:HIS88 2.5 38.2 1.0
CE1 B:HIS88 2.6 31.9 1.0
CD2 B:HIS88 3.5 36.6 1.0
ND1 B:HIS88 3.9 29.0 1.0
O B:HOH355 4.0 35.3 1.0
HD2 B:HIS88 4.0 43.8 1.0
CG B:HIS88 4.4 26.9 1.0

Nickel binding site 4 out of 5 in 9ayo

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Nickel binding site 4 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni205

b:28.9
occ:1.00
 O B:HOH325 1.9 27.0 1.0
OD1 B:ASP99 2.0 24.6 1.0
OD1 A:ASP99 2.0 24.5 1.0
O A:HOH314 2.0 23.8 1.0
O B:HOH314 2.1 22.1 1.0
O A:HOH303 2.4 29.0 1.0
CG B:ASP99 3.0 30.1 1.0
CG A:ASP99 3.1 27.4 1.0
H B:ARG100 3.2 41.6 1.0
OD2 B:ASP99 3.4 27.3 1.0
OD2 A:ASP99 3.5 27.9 1.0
H A:ARG100 3.7 38.0 1.0
HA A:ASP99 4.0 24.2 1.0
N B:ARG100 4.0 34.7 1.0
HA B:ASP99 4.1 31.3 1.0
O A:HOH366 4.2 34.8 1.0
O A:ARG100 4.2 32.1 1.0
N A:ARG100 4.3 31.8 1.0
CB B:ASP99 4.3 27.4 1.0
CB A:ASP99 4.4 20.9 1.0
OXT B:ARG100 4.4 35.2 1.0
CA A:ASP99 4.6 20.2 1.0
C B:ARG100 4.6 42.0 1.0
HG11 A:VAL28 4.6 17.7 1.0
CA B:ASP99 4.6 26.1 1.0
HB2 B:ARG100 4.7 52.1 1.0
HB2 A:ARG100 4.7 48.8 1.0
HB2 B:ASP99 4.8 32.9 1.0
HG11 B:VAL28 4.8 22.3 1.0
C A:ASP99 4.8 26.8 1.0
CA B:ARG100 4.8 47.0 1.0
HB2 A:ASP99 4.8 25.0 1.0
C B:ASP99 4.9 29.7 1.0
HB3 B:ASP99 4.9 32.9 1.0

Nickel binding site 5 out of 5 in 9ayo

Go back to Nickel Binding Sites List in 9ayo
Nickel binding site 5 out of 5 in the Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Mycolicibacterium Smegmatis Clps with Bound Pheala and NI2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni206

b:20.4
occ:1.00
 O B:HOH311 2.1 16.5 1.0
NE2 B:HIS65 2.1 16.1 1.0
O B:PHE201 2.1 15.8 1.0
O B:HOH354 2.1 20.8 1.0
O B:HOH338 2.2 19.9 1.0
N B:PHE201 2.2 17.5 1.0
H B:PHE201 2.6 20.9 1.0
H2 B:PHE201 2.8 20.9 1.0
C B:PHE201 2.9 16.8 1.0
CD2 B:HIS65 2.9 17.9 1.0
HD2 B:HIS65 3.0 21.4 1.0
CA B:PHE201 3.0 18.1 1.0
CE1 B:HIS65 3.2 23.0 1.0
HB2 B:PHE201 3.5 18.7 1.0
HE1 B:HIS65 3.5 27.6 1.0
HA B:PHE201 3.8 21.7 1.0
CB B:PHE201 3.8 15.6 1.0
CG B:HIS65 4.2 17.8 1.0
N B:ALA202 4.2 17.3 1.0
OD2 B:ASP33 4.2 13.4 1.0
OD1 B:ASP33 4.2 11.8 1.0
O B:HOH335 4.2 28.0 1.0
ND1 B:HIS65 4.3 16.0 1.0
HA B:ALA202 4.4 18.6 1.0
HA B:PRO35 4.5 22.3 1.0
HB3 B:PHE201 4.6 18.7 1.0
O B:ASP34 4.6 16.6 1.0
CG B:ASP33 4.7 14.8 1.0
CG B:PHE201 4.8 14.3 1.0
H B:ALA202 4.8 20.7 1.0
CA B:ALA202 4.9 15.6 1.0

Reference:

C.J.Presloid, J.Jiang, P.Kandel, H.R.Anderson, P.C.Beardslee, T.M.Swayne, K.R.Schmitz. Clps Directs Degradation of N-Degron Substrates with Primary Destabilizing Residues in Mycolicibacterium Smegmatis. Mol.Microbiol. 2024.
ISSN: ESSN 1365-2958
PubMed: 39626090
DOI: 10.1111/MMI.15334
Page generated: Sun Dec 15 11:47:32 2024

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