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Nickel in PDB 5jjt: Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana

Enzymatic activity of Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana

All present enzymatic activity of Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana, PDB code: 5jjt was solved by H.M.Li, H.Pu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.80 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.408, 102.705, 95.290, 90.00, 95.57, 90.00
R / Rfree (%) 18.6 / 23.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana (pdb code 5jjt). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana, PDB code: 5jjt:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 5jjt

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Nickel binding site 1 out of 6 in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana


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 A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:14.6
occ:0.89
 OD1 A:ASN289 2.5 8.3 1.0
ND1 A:HIS413 2.6 9.9 1.0
NE2 A:HIS338 2.6 10.0 1.0
OD2 A:ASP257 2.7 11.4 1.0
O A:HOH601 2.9 22.6 1.0
NI A:NI502 2.9 25.1 0.8
NI A:NI503 3.2 29.2 0.7
CE1 A:HIS413 3.3 12.0 1.0
CG A:ASP257 3.4 11.3 1.0
CG A:ASN289 3.4 9.7 1.0
CD2 A:HIS338 3.5 7.8 1.0
CA A:HIS413 3.7 9.3 1.0
CE1 A:HIS338 3.7 9.6 1.0
CG A:HIS413 3.7 12.3 1.0
ND2 A:ASN289 3.7 10.6 1.0
OD1 A:ASP257 3.8 10.9 1.0
OD2 A:ASP228 3.9 10.0 1.0
O A:HIS413 4.0 13.1 1.0
CB A:HIS413 4.1 10.2 1.0
C A:HIS413 4.3 13.2 1.0
CD2 A:HIS290 4.4 10.7 1.0
CB A:ASP257 4.5 11.1 1.0
NE2 A:HIS413 4.5 11.8 1.0
N A:HIS413 4.6 8.8 1.0
CG A:HIS338 4.7 8.4 1.0
CD2 A:HIS413 4.8 10.7 1.0
ND1 A:HIS338 4.8 8.8 1.0
CB A:ASN289 4.8 10.9 1.0
N A:ASN289 4.8 9.1 1.0
NH1 A:ARG386 4.9 16.2 1.0
O A:LEU371 5.0 10.4 1.0
CG A:ASP228 5.0 9.9 1.0

Nickel binding site 2 out of 6 in 5jjt

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Nickel binding site 2 out of 6 in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana


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 A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni502

b:25.1
occ:0.77
 OD2 A:ASP228 2.6 10.0 1.0
NE2 A:HIS230 2.7 9.4 1.0
OD2 A:ASP257 2.7 11.4 1.0
O A:HOH748 2.7 16.1 1.0
O A:HOH601 2.8 22.6 1.0
NI A:NI501 2.9 14.6 0.9
NI A:NI503 3.1 29.2 0.7
CD2 A:HIS230 3.6 9.6 1.0
CE1 A:HIS230 3.7 10.8 1.0
CG A:ASP257 3.7 11.3 1.0
CG A:ASP228 3.8 9.9 1.0
CB A:ASP257 4.1 11.1 1.0
NH1 A:ARG261 4.1 16.7 1.0
O A:HIS413 4.2 13.1 1.0
CB A:ASP228 4.3 10.0 1.0
CD2 A:HIS290 4.3 10.7 1.0
OH A:TYR437 4.5 14.1 1.0
NE2 A:HIS338 4.5 10.0 1.0
CE1 A:PHE432 4.6 12.5 1.0
C A:HIS413 4.6 13.2 1.0
CA A:HIS413 4.7 9.3 1.0
OD1 A:ASP228 4.8 12.9 1.0
CG A:HIS230 4.8 9.8 1.0
OD1 A:ASP257 4.8 10.9 1.0
ND1 A:HIS230 4.8 9.9 1.0
CE1 A:HIS338 4.9 9.6 1.0
NE2 A:HIS290 4.9 10.3 1.0
OD1 A:ASN289 4.9 8.3 1.0
ND1 A:HIS413 4.9 9.9 1.0
OE1 A:GLU61 4.9 22.6 1.0

Nickel binding site 3 out of 6 in 5jjt

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Nickel binding site 3 out of 6 in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana


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 A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni503

b:29.2
occ:0.65
 O A:HOH601 2.7 22.6 1.0
NI A:NI502 3.1 25.1 0.8
NI A:NI501 3.2 14.6 0.9
NE2 A:HIS290 3.3 10.3 1.0
CD2 A:HIS290 3.3 10.7 1.0
OE1 A:GLU61 3.5 22.6 1.0
ND2 A:ASN289 3.6 10.6 1.0
NH1 A:ARG261 3.6 16.7 1.0
NH1 A:ARG386 3.7 16.2 1.0
NH2 A:ARG261 3.8 19.1 1.0
OD2 A:ASP257 3.9 11.4 1.0
OD1 A:ASN289 4.2 8.3 1.0
CZ A:ARG261 4.2 18.6 1.0
O A:HOH748 4.3 16.1 1.0
CG A:ASN289 4.4 9.7 1.0
ND1 A:HIS413 4.5 9.9 1.0
CE1 A:HIS413 4.5 12.0 1.0
CE1 A:HIS290 4.6 13.0 1.0
CG A:HIS290 4.6 10.7 1.0
CD A:GLU61 4.7 19.5 1.0
NE2 A:HIS230 4.7 9.4 1.0
O A:HIS413 4.7 13.1 1.0
CZ A:ARG386 4.8 16.1 1.0

Nickel binding site 4 out of 6 in 5jjt

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Nickel binding site 4 out of 6 in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:16.0
occ:0.96
 OD1 B:ASN289 2.5 10.4 1.0
ND1 B:HIS413 2.6 12.6 1.0
NE2 B:HIS338 2.7 11.4 1.0
OD2 B:ASP257 2.7 12.9 1.0
NI B:NI502 2.9 32.3 0.9
NI B:NI503 3.0 34.6 0.7
CE1 B:HIS413 3.3 13.1 1.0
CG B:ASP257 3.4 12.3 1.0
CD2 B:HIS338 3.4 9.1 1.0
CG B:ASN289 3.4 12.9 1.0
OD1 B:ASP257 3.7 11.6 1.0
ND2 B:ASN289 3.7 12.9 1.0
CA B:HIS413 3.7 12.0 1.0
CG B:HIS413 3.7 13.7 1.0
CE1 B:HIS338 3.8 10.8 1.0
O B:HIS413 3.9 16.9 1.0
OD2 B:ASP228 4.0 12.3 1.0
CB B:HIS413 4.2 12.5 1.0
C B:HIS413 4.3 13.9 1.0
CD2 B:HIS290 4.4 12.5 1.0
CB B:ASP257 4.5 10.9 1.0
NE2 B:HIS413 4.6 13.0 1.0
CG B:HIS338 4.6 10.0 1.0
N B:HIS413 4.7 10.7 1.0
CD2 B:HIS413 4.8 12.6 1.0
N B:ASN289 4.8 10.8 1.0
ND1 B:HIS338 4.8 11.2 1.0
CB B:ASN289 4.8 11.4 1.0
O B:LEU371 4.9 8.9 1.0
CG B:ASP228 5.0 13.3 1.0

Nickel binding site 5 out of 6 in 5jjt

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Nickel binding site 5 out of 6 in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:32.3
occ:0.90
 OD2 B:ASP228 2.6 12.3 1.0
O B:HOH704 2.7 16.8 1.0
OD2 B:ASP257 2.7 12.9 1.0
NE2 B:HIS230 2.7 13.3 1.0
NI B:NI501 2.9 16.0 1.0
NI B:NI503 3.0 34.6 0.7
CD2 B:HIS230 3.7 10.8 1.0
CE1 B:HIS230 3.7 12.1 1.0
CG B:ASP257 3.8 12.3 1.0
CG B:ASP228 3.8 13.3 1.0
O B:HIS413 3.8 16.9 1.0
CB B:ASP257 4.2 10.9 1.0
CD2 B:HIS290 4.4 12.5 1.0
C B:HIS413 4.4 13.9 1.0
NH1 B:ARG261 4.4 16.1 1.0
CB B:ASP228 4.4 10.2 1.0
NE2 B:HIS338 4.5 11.4 1.0
OH B:TYR437 4.5 15.6 1.0
CA B:HIS413 4.5 12.0 1.0
OE1 B:GLU61 4.6 20.5 1.0
CE1 B:PHE432 4.7 14.1 1.0
OD1 B:ASP228 4.7 12.8 1.0
OD1 B:ASP257 4.8 11.6 1.0
ND1 B:HIS413 4.8 12.6 1.0
ND1 B:HIS230 4.8 11.4 1.0
CG B:HIS230 4.8 12.4 1.0
NE2 B:HIS290 4.9 12.7 1.0
CE1 B:HIS338 4.9 10.8 1.0
OD1 B:ASN289 5.0 10.4 1.0

Nickel binding site 6 out of 6 in 5jjt

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Nickel binding site 6 out of 6 in the Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni503

b:34.6
occ:0.69
 NI B:NI501 3.0 16.0 1.0
NI B:NI502 3.0 32.3 0.9
NE2 B:HIS290 3.6 12.7 1.0
CD2 B:HIS290 3.6 12.5 1.0
NH1 B:ARG386 3.6 18.1 1.0
ND2 B:ASN289 3.6 12.9 1.0
OE1 B:GLU61 3.7 20.5 1.0
OD2 B:ASP257 3.9 12.9 1.0
NH1 B:ARG261 4.0 16.1 1.0
OD1 B:ASN289 4.2 10.4 1.0
ND1 B:HIS413 4.2 12.6 1.0
CE1 B:HIS413 4.2 13.1 1.0
O B:HIS413 4.3 16.9 1.0
CG B:ASN289 4.3 12.9 1.0
O B:HOH704 4.4 16.8 1.0
CZ B:ARG386 4.5 16.6 1.0
NH2 B:ARG261 4.5 18.6 1.0
CD B:GLU61 4.7 18.5 1.0
CZ B:ARG261 4.7 16.6 1.0
NH2 B:ARG386 4.8 14.5 1.0
NE2 B:HIS230 4.8 13.3 1.0
CE1 B:HIS290 4.9 13.7 1.0
O B:HOH678 4.9 14.6 1.0
CG B:HIS290 4.9 11.4 1.0

Reference:

H.M.Li, H.Pu. Crystal Structure of A Type 5 Serine/Threonine Protein Phosphatase From Arabidopsis Thaliana To Be Published.
Page generated: Thu Oct 10 06:31:57 2024

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