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Magnesium in PDB 6xef: Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 4 Bound to Vanadate

Enzymatic activity of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 4 Bound to Vanadate

All present enzymatic activity of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 4 Bound to Vanadate:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 4 Bound to Vanadate, PDB code: 6xef 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) 44.19 / 2.05
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.384, 88.384, 104.879, 90, 90, 120
R / Rfree (%) 18.1 / 20.3

Other elements in 6xef:

The structure of Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 4 Bound to Vanadate also contains other interesting chemical elements:

Vanadium (V) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 6xef

Go back to Magnesium Binding Sites List in 6xef
Magnesium binding site 1 out of 2 in the Crystal Structure of the PTP1B Yoph Wpd Loop Chimera 4 Bound to Vanadate


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 4 Bound to Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:53.3
occ:1.00
O A:PRO89 2.5 43.7 1.0
N A:CYS92 3.0 41.9 1.0
O A:HOH613 3.1 55.1 1.0
C A:ASN90 3.2 45.6 1.0
C A:PRO89 3.4 48.1 1.0
N A:THR91 3.5 38.1 1.0
CA A:ASN90 3.5 42.9 1.0
CB A:CYS92 3.5 38.3 1.0
N A:GLY93 3.5 36.0 1.0
O A:HOH551 3.5 41.0 1.0
C3 A:BEN405 3.6 67.5 0.9
O A:ASN90 3.6 44.0 1.0
CA A:CYS92 3.7 36.9 1.0
N A:ASN90 3.8 42.2 1.0
C2 A:BEN405 3.9 67.3 0.9
C A:THR91 3.9 40.6 1.0
C A:CYS92 4.1 37.3 1.0
CA A:THR91 4.1 37.9 1.0
SG A:CYS92 4.2 42.4 1.0
O A:LEU88 4.3 37.9 1.0
C4 A:BEN405 4.5 67.3 0.9
CA A:PRO89 4.6 40.0 1.0
CA A:GLY93 4.7 40.8 1.0
C1 A:BEN405 4.9 66.7 0.9
CB A:ASN90 4.9 45.5 1.0
O A:THR91 5.0 37.0 1.0

Magnesium binding site 2 out of 2 in 6xef

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


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 4 Bound to Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:73.6
occ:1.00
OD1 A:ASN90 2.6 45.2 1.0
O A:HOH622 2.8 54.7 1.0
CG A:ASN90 3.4 48.4 1.0
CB A:LEU88 3.6 35.8 1.0
CD A:PRO89 3.7 40.2 1.0
O A:ASN42 4.1 45.8 1.0
ND2 A:ASN90 4.1 44.5 1.0
N A:ASN90 4.2 42.2 1.0
CD2 A:LEU88 4.2 37.7 1.0
N A:PRO89 4.2 44.2 1.0
CG A:LEU88 4.3 40.4 1.0
CB A:ASN90 4.3 45.5 1.0
CD1 A:LEU88 4.3 41.4 1.0
CG A:PRO89 4.5 43.3 1.0
CA A:LEU88 4.7 38.2 1.0
CB A:PRO89 4.8 42.0 1.0
C A:LEU88 4.8 40.5 1.0
CA A:ASN90 4.9 42.9 1.0
CA A:PRO89 4.9 40.0 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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