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Nickel in PDB 5nzz: Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1

Enzymatic activity of Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1

All present enzymatic activity of Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1:
2.7.11.24;

Protein crystallography data

The structure of Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1, PDB code: 5nzz was solved by C.E.Nichols, G.F.De Nicola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 140.36 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.879, 107.632, 144.204, 89.26, 76.75, 84.28
R / Rfree (%) 21.9 / 27.1

Other elements in 5nzz:

The structure of Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1 also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1 (pdb code 5nzz). 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 Phosphorylated P38AMAPK in Complex with TAB1, PDB code: 5nzz:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 5nzz

Go back to Nickel Binding Sites List in 5nzz
Nickel binding site 1 out of 6 in the Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1


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 Phosphorylated P38AMAPK in Complex with TAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:84.5
occ:1.00
 OD1 A:ASN69 2.5 41.5 1.0
O A:GLY70 2.5 56.8 1.0
CG A:ASN69 3.6 30.0 1.0
C A:GLY70 3.7 43.0 1.0
OE2 A:GLU50 4.2 43.7 1.0
ND2 A:ASN69 4.2 25.7 1.0
OD2 A:ASP357 4.2 47.0 1.0
OD1 A:ASP51 4.2 39.9 1.0
N A:GLY70 4.2 33.5 1.0
CB A:GLU50 4.5 38.9 1.0
CA A:GLY70 4.5 35.4 1.0
N A:TYR71 4.6 40.3 1.0
CB A:ASP357 4.6 32.7 1.0
OE2 A:GLU356 4.6 64.0 1.0
C A:ASN69 4.7 39.5 1.0
CA A:TYR71 4.7 36.6 1.0
CG A:ASP357 4.8 41.3 1.0
CB A:ASN69 4.8 30.6 1.0
CB A:TYR71 4.9 35.3 1.0
CA A:ASN69 4.9 35.1 1.0

Nickel binding site 2 out of 6 in 5nzz

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Nickel binding site 2 out of 6 in the Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1


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 Phosphorylated P38AMAPK in Complex with TAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni601

b:86.3
occ:0.89
 O B:GLY70 2.1 51.7 1.0
OD1 B:ASN69 2.4 42.5 1.0
C B:GLY70 3.3 43.1 1.0
CG B:ASN69 3.6 39.0 1.0
OD1 B:ASP51 3.9 49.4 1.0
OD2 B:ASP357 4.0 46.0 1.0
OE1 B:GLU356 4.0 64.9 1.0
N B:GLY70 4.0 33.9 1.0
CA B:GLY70 4.2 38.5 1.0
OE1 B:GLU50 4.2 57.2 1.0
ND2 B:ASN69 4.2 51.6 1.0
N B:TYR71 4.3 39.8 1.0
CB B:GLU50 4.4 46.8 1.0
C B:ASN69 4.5 41.4 1.0
CA B:TYR71 4.6 38.6 1.0
O B:HOH701 4.7 52.6 1.0
CB B:ASN69 4.7 38.4 1.0
O B:GLU50 4.7 40.0 1.0
CB B:ASP357 4.8 45.0 1.0
CA B:ASN69 4.8 41.1 1.0
CG B:ASP357 4.8 43.8 1.0
CD B:GLU356 4.8 75.8 1.0
CB B:TYR71 4.9 47.3 1.0
C B:GLU50 5.0 41.6 1.0

Nickel binding site 3 out of 6 in 5nzz

Go back to Nickel Binding Sites List in 5nzz
Nickel binding site 3 out of 6 in the Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1


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 Phosphorylated P38AMAPK in Complex with TAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:97.1
occ:1.00
 O C:GLY70 2.2 49.3 1.0
OD1 C:ASN69 2.3 40.1 1.0
C C:GLY70 3.4 35.6 1.0
CG C:ASN69 3.4 38.4 1.0
OE1 C:GLU50 4.0 41.2 1.0
ND2 C:ASN69 4.0 42.0 1.0
N C:GLY70 4.0 33.5 1.0
OD2 C:ASP357 4.1 46.5 1.0
CB C:GLU50 4.2 33.9 1.0
OD1 C:ASP51 4.3 44.7 1.0
CA C:GLY70 4.3 29.6 1.0
N C:TYR71 4.4 38.2 1.0
C C:ASN69 4.5 39.8 1.0
CA C:TYR71 4.5 41.0 1.0
CB C:ASN69 4.6 35.0 1.0
CB C:TYR71 4.7 42.6 1.0
OE1 C:GLU356 4.8 64.7 1.0
CA C:ASN69 4.8 39.2 1.0
O C:GLU50 4.8 41.5 1.0
CB C:ASP357 4.8 34.5 1.0
C C:GLU50 4.9 37.8 1.0
CG C:ASP357 4.9 47.3 1.0
CD C:GLU50 4.9 43.7 1.0

Nickel binding site 4 out of 6 in 5nzz

Go back to Nickel Binding Sites List in 5nzz
Nickel binding site 4 out of 6 in the Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1


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 Phosphorylated P38AMAPK in Complex with TAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni601

b:98.8
occ:1.00
 O D:GLY70 2.3 46.5 1.0
OD1 D:ASN69 2.4 39.5 1.0
C D:GLY70 3.5 43.2 1.0
CG D:ASN69 3.6 37.5 1.0
OE2 D:GLU50 3.9 55.3 1.0
N D:GLY70 4.0 41.5 1.0
OD1 D:ASP51 4.1 42.6 1.0
ND2 D:ASN69 4.2 42.3 1.0
OD2 D:ASP357 4.2 44.1 1.0
CA D:GLY70 4.3 39.7 1.0
N D:TYR71 4.5 47.5 1.0
CB D:GLU50 4.5 48.4 1.0
OE1 D:GLU356 4.5 60.3 1.0
C D:ASN69 4.6 42.5 1.0
CA D:TYR71 4.7 44.8 1.0
CB D:ASN69 4.8 42.6 1.0
CB D:TYR71 4.9 40.5 1.0
CG D:ASP357 4.9 40.6 1.0
CB D:ASP357 4.9 40.5 1.0
CA D:ASN69 4.9 46.4 1.0
CD D:GLU50 5.0 44.4 1.0

Nickel binding site 5 out of 6 in 5nzz

Go back to Nickel Binding Sites List in 5nzz
Nickel binding site 5 out of 6 in the Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1


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 Phosphorylated P38AMAPK in Complex with TAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni403

b:87.8
occ:1.00
 OD2 E:ASP145 2.3 51.2 1.0
NE2 E:HIS174 2.6 36.7 1.0
CG E:ASP145 3.5 48.4 1.0
CE1 E:HIS174 3.6 36.8 1.0
CD2 E:HIS174 3.6 44.0 1.0
OD2 C:ASP122 3.8 53.6 1.0
CB E:ASP145 4.0 42.2 1.0
O E:TYR323 4.0 42.0 1.0
OE1 E:GLN325 4.0 49.5 1.0
OH C:TYR250 4.3 47.2 1.0
OD1 C:ASP122 4.5 56.0 1.0
OD1 E:ASP145 4.5 47.7 1.0
CG C:ASP122 4.6 49.6 1.0
ND1 E:HIS174 4.7 44.2 1.0
CG E:HIS174 4.7 43.3 1.0
NE2 E:GLN325 4.8 29.7 1.0
CD E:GLN325 4.8 37.9 1.0
O E:ALA144 4.9 46.0 1.0

Nickel binding site 6 out of 6 in 5nzz

Go back to Nickel Binding Sites List in 5nzz
Nickel binding site 6 out of 6 in the Crystal Structure of Phosphorylated P38AMAPK in Complex with TAB1


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 Phosphorylated P38AMAPK in Complex with TAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni403

b:97.1
occ:1.00
 OD2 F:ASP145 2.0 47.0 1.0
NE2 F:HIS174 2.8 37.1 1.0
CG F:ASP145 3.2 38.3 1.0
CE1 F:HIS174 3.6 38.4 1.0
O F:TYR323 3.8 44.6 1.0
CB F:ASP145 3.9 46.1 1.0
CD2 F:HIS174 3.9 41.1 1.0
OD2 B:ASP122 4.1 59.3 1.0
OD1 F:ASP145 4.1 36.2 1.0
OH B:TYR250 4.3 48.8 1.0
OE1 F:GLN325 4.3 46.4 1.0
O F:ALA144 4.6 40.8 1.0
OD1 B:ASP122 4.7 60.3 1.0
CG B:ASP122 4.9 51.6 1.0
ND1 F:HIS174 4.9 45.7 1.0
NE2 F:GLN325 4.9 37.4 1.0
C F:TYR323 5.0 46.0 1.0

Reference:

G.F.De Nicola, R.Bassi, C.Nichols, M.Fernandez-Caggiano, P.A.Golforoush, D.Thapa, R.Anderson, E.D.Martin, S.Verma, J.Kleinjung, A.Laing, J.P.Hutchinson, P.Eaton, J.Clark, M.S.Marber. The TAB1-P38 Alpha Complex Aggravates Myocardial Injury and Can Be Targeted By Small Molecules. Jci Insight V. 3 2018.
ISSN: ISSN 2379-3708
PubMed: 30135318
DOI: 10.1172/JCI.INSIGHT.121144
Page generated: Wed Dec 16 01:42:15 2020

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