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Magnesium in PDB 3hy4: Structure of Human Mthfs with N5-Iminium Phosphate

Enzymatic activity of Structure of Human Mthfs with N5-Iminium Phosphate

All present enzymatic activity of Structure of Human Mthfs with N5-Iminium Phosphate:
6.3.3.2;

Protein crystallography data

The structure of Structure of Human Mthfs with N5-Iminium Phosphate, PDB code: 3hy4 was solved by D.Wu, Y.Li, G.Song, C.Cheng, N.Shaw, Z.-J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.32 / 2.79
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.065, 144.583, 60.149, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 30

Other elements in 3hy4:

The structure of Structure of Human Mthfs with N5-Iminium Phosphate also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Mthfs with N5-Iminium Phosphate (pdb code 3hy4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Human Mthfs with N5-Iminium Phosphate, PDB code: 3hy4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3hy4

Go back to Magnesium Binding Sites List in 3hy4
Magnesium binding site 1 out of 3 in the Structure of Human Mthfs with N5-Iminium Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Mthfs with N5-Iminium Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:42.0
occ:1.00
CE1 A:HIS142 2.7 38.0 1.0
NE2 A:HIS142 2.8 41.2 1.0
ND1 A:HIS142 3.8 42.3 1.0
CD2 A:HIS142 4.0 40.7 1.0
CG A:HIS142 4.5 39.6 1.0
CD2 A:LEU181 4.6 38.2 1.0

Magnesium binding site 2 out of 3 in 3hy4

Go back to Magnesium Binding Sites List in 3hy4
Magnesium binding site 2 out of 3 in the Structure of Human Mthfs with N5-Iminium Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Mthfs with N5-Iminium Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:32.5
occ:1.00
O A:HOH233 2.7 32.7 1.0
N A:LEU181 3.4 34.5 1.0
CB A:CYS180 3.9 31.4 1.0
CB A:LEU181 4.0 38.1 1.0
CA A:CYS180 4.0 33.8 1.0
C A:CYS180 4.3 33.7 1.0
CA A:LEU181 4.3 34.2 1.0
CD1 A:LEU13 4.6 32.1 1.0
SG A:CYS180 4.6 31.1 1.0
NH2 A:ARG20 4.7 38.0 1.0
N A:GLN182 4.8 35.8 1.0
O A:GLN182 5.0 32.6 1.0

Magnesium binding site 3 out of 3 in 3hy4

Go back to Magnesium Binding Sites List in 3hy4
Magnesium binding site 3 out of 3 in the Structure of Human Mthfs with N5-Iminium Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Mthfs with N5-Iminium Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:19.3
occ:1.00
OH A:TYR156 3.0 22.5 1.0
N A:LEU124 3.4 25.5 1.0
N A:MET92 3.4 23.7 1.0
CE1 A:TYR156 3.5 23.9 1.0
N A:ALA123 3.6 25.6 1.0
CG A:LEU124 3.7 25.8 1.0
CZ A:TYR156 3.7 22.8 1.0
O A:MET92 3.8 21.8 1.0
CB A:LEU124 3.8 24.7 1.0
CB A:ASP91 3.9 24.1 1.0
CD1 A:LEU124 3.9 28.4 1.0
CA A:ASP91 3.9 22.9 1.0
CB A:ALA123 4.0 23.1 1.0
CB A:GLU122 4.1 23.7 1.0
NH2 A:ARG159 4.1 22.2 1.0
C A:GLU122 4.1 24.4 1.0
CA A:ALA123 4.1 23.6 1.0
C A:ASP91 4.2 24.4 1.0
CA A:LEU124 4.2 25.8 1.0
C A:ALA123 4.3 25.1 1.0
CA A:MET92 4.3 20.0 1.0
CB A:MET92 4.4 21.1 1.0
CG A:ASP91 4.4 26.7 1.0
CA A:GLU122 4.4 23.1 1.0
C A:MET92 4.4 20.9 1.0
OD1 A:ASP91 4.6 26.8 1.0
CD1 A:TYR156 4.8 23.1 1.0
CZ A:ARG159 4.8 24.2 1.0
O A:GLU122 4.8 24.1 1.0
CG A:MET92 4.9 20.7 1.0

Reference:

D.Wu, Y.Li, G.Song, C.Cheng, R.Zhang, A.Joachimiak, N.Shaw, Z.-J.Liu. Structural Basis For the Inhibition of Human 5,10-Methenyltetrahydrofolate Synthetase By N10-Substituted Folate Analogues Cancer Res. V. 69 7294 2009.
ISSN: ISSN 0008-5472
PubMed: 19738041
DOI: 10.1158/0008-5472.CAN-09-1927
Page generated: Mon Dec 14 08:15:08 2020

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