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Magnesium in PDB 6xed: Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate

Enzymatic activity of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate

All present enzymatic activity of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate, PDB code: 6xed was solved by K.J.Olsen, R.Shen, S.J.Johnson, A.C.Hengge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.44 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.871, 88.871, 104.351, 90, 90, 120
R / Rfree (%) 15.7 / 17.9

Other elements in 6xed:

The structure of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate also contains other interesting chemical elements:

Tungsten (W) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate (pdb code 6xed). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate, PDB code: 6xed:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6xed

Go back to Magnesium Binding Sites List in 6xed
Magnesium binding site 1 out of 4 in the Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:53.6
occ:1.00
OD2 A:ASP265 2.5 42.5 1.0
N A:ALA184 2.9 28.7 1.0
O A:HOH519 3.3 42.9 1.0
CG A:ASP265 3.5 42.5 1.0
CA A:THR183 3.5 26.4 1.0
O A:HOH533 3.7 46.0 1.0
C A:THR183 3.7 27.0 1.0
CB A:ALA184 3.8 28.9 1.0
CB A:ASP265 3.8 32.3 1.0
CB A:THR183 3.8 28.7 1.0
O A:HOH668 3.9 49.7 1.0
CA A:ALA184 3.9 25.9 1.0
O A:ALA184 4.5 32.5 1.0
OD1 A:ASP265 4.6 45.4 1.0
O A:GLN182 4.6 32.7 1.0
CG2 A:THR183 4.7 31.7 1.0
C A:ALA184 4.7 29.2 1.0
N A:THR183 4.8 28.2 1.0
O A:THR183 4.9 25.9 1.0
OG1 A:THR183 4.9 33.1 1.0

Magnesium binding site 2 out of 4 in 6xed

Go back to Magnesium Binding Sites List in 6xed
Magnesium binding site 2 out of 4 in the Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:46.0
occ:1.00
OD1 A:ASP181 2.5 41.9 1.0
O A:HOH774 2.7 34.7 1.0
N A:ASP181 2.9 27.5 1.0
OE2 A:GLU115 3.2 26.8 1.0
CG A:ASP181 3.4 38.3 1.0
CD A:GLU115 3.5 28.0 1.0
CA A:PRO180 3.6 27.3 1.0
CB A:ASP181 3.6 28.7 1.0
CB A:GLU115 3.6 25.0 1.0
C A:PRO180 3.7 27.0 1.0
CB A:PRO180 3.8 29.6 1.0
CA A:ASP181 3.8 29.3 1.0
CE A:LYS116 3.9 39.5 1.0
O A:HOH692 4.0 53.0 1.0
OE1 A:GLU115 4.1 25.5 1.0
CG A:GLU115 4.1 26.5 1.0
NH1 A:ARG221 4.2 22.3 1.0
CG A:LYS116 4.3 33.2 1.0
NZ A:LYS116 4.3 43.7 1.0
CD A:LYS116 4.4 36.8 1.0
O A:ASP181 4.5 27.6 1.0
OD2 A:ASP181 4.6 38.1 1.0
O A:HOH790 4.6 34.6 1.0
O A:HOH757 4.6 42.5 1.0
C A:ASP181 4.7 25.4 1.0
NH2 A:ARG221 4.7 22.9 1.0
CZ A:ARG221 4.7 21.5 1.0
CA A:GLU115 4.9 27.0 1.0
O A:PRO180 4.9 24.2 1.0
O A:HOH535 4.9 42.1 1.0
N A:PRO180 5.0 27.1 1.0
O A:HOH554 5.0 30.2 1.0

Magnesium binding site 3 out of 4 in 6xed

Go back to Magnesium Binding Sites List in 6xed
Magnesium binding site 3 out of 4 in the Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:63.0
occ:1.00
OE1 A:GLU6 2.4 48.5 1.0
O A:HOH632 2.6 37.9 1.0
OE2 A:GLU2 2.9 57.7 1.0
CD A:GLU6 3.5 48.8 1.0
CA A:MET3 3.8 38.1 1.0
CB A:GLU6 3.9 36.8 1.0
CD A:GLU2 4.0 59.0 1.0
N A:MET3 4.2 38.3 1.0
CG A:GLU6 4.2 42.4 1.0
O A:GLU2 4.2 44.3 1.0
OH A:TYR271 4.2 34.4 1.0
CB A:MET3 4.3 41.1 1.0
OE2 A:GLU6 4.3 53.4 1.0
OD1 A:ASP245 4.3 41.4 1.0
NZ A:LYS247 4.4 41.4 1.0
C A:GLU2 4.4 45.3 1.0
OE1 A:GLU2 4.4 62.0 1.0
CE2 A:TYR271 4.5 34.3 1.0
O A:VAL244 4.6 35.6 1.0
CA A:ASP245 4.6 28.3 1.0
N A:ILE246 4.7 28.0 1.0
CZ A:TYR271 4.9 33.9 1.0
CG A:ASP245 4.9 39.2 1.0
C A:MET3 5.0 38.9 1.0

Magnesium binding site 4 out of 4 in 6xed

Go back to Magnesium Binding Sites List in 6xed
Magnesium binding site 4 out of 4 in the Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 3 Bound to Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:55.2
occ:1.00
OE1 A:GLU167 2.2 55.1 1.0
OG1 A:THR165 2.7 43.9 1.0
O A:HOH635 2.9 47.4 1.0
CB A:GLU167 3.1 35.4 1.0
CD A:GLU167 3.3 51.2 1.0
CB A:THR165 3.5 46.0 1.0
CZ2 A:TRP100 3.6 30.5 1.0
CG A:GLU167 3.8 40.8 1.0
CG2 A:THR165 3.8 46.2 1.0
ND2 A:ASN162 4.2 40.8 1.0
OE2 A:GLU167 4.3 42.0 1.0
CA A:GLU167 4.4 33.6 1.0
CE2 A:TRP100 4.5 28.4 1.0
CH2 A:TRP100 4.5 27.2 1.0
N A:GLU167 4.6 35.3 1.0
NE1 A:TRP100 4.6 25.6 1.0
CB A:ASN162 4.7 36.5 1.0
CG A:ASN162 4.8 43.5 1.0
CA A:THR165 4.9 43.1 1.0

Reference:

R.Shen, K.J.Olsen, S.J.Johnson, A.C.Hengge. Insights From PTP1B Yoph Chimeras Into the Importance of Wpd-Loop Sequence For Activity and Structure in Protein Tyrosine Phosphatases To Be Published.
Page generated: Fri Dec 17 10:03:57 2021

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