Nickel in PDB 3hxt: Structure of Human Mthfs

All present enzymatic activity of Structure of Human Mthfs:
6.3.3.2;

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

Resolution Low / High (Å)	30.94 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.705, 145.122, 59.218, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25

The structure of Structure of Human Mthfs also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Nickel atom in the Structure of Human Mthfs (pdb code 3hxt). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of Human Mthfs, PDB code: 3hxt:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Human Mthfs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni204 b:29.3 occ:1.00 O A:HOH215 3.0 15.4 1.0 OH A:TYR156 3.1 9.0 1.0 N A:MET92 3.3 10.4 1.0 N A:LEU124 3.4 11.3 1.0 CE1 A:TYR156 3.6 9.0 1.0 N A:ALA123 3.6 10.5 1.0 O A:MET92 3.6 9.0 1.0 CZ A:TYR156 3.8 8.7 1.0 CG A:LEU124 3.8 11.9 1.0 CB A:GLU122 3.8 10.2 1.0 CB A:LEU124 3.9 11.7 1.0 CB A:ASP91 4.0 11.5 1.0 CA A:ASP91 4.0 11.4 1.0 C A:GLU122 4.0 10.5 1.0 OD1 A:ASP91 4.1 13.1 1.0 CD1 A:LEU124 4.1 11.8 1.0 CA A:ALA123 4.1 10.7 1.0 CB A:ALA123 4.1 10.7 1.0 C A:ASP91 4.2 11.0 1.0 CA A:MET92 4.2 9.3 1.0 C A:ALA123 4.2 10.7 1.0 CA A:LEU124 4.2 12.1 1.0 CA A:GLU122 4.2 10.4 1.0 CB A:MET92 4.3 8.6 1.0 C A:MET92 4.3 9.0 1.0 CG A:ASP91 4.5 12.1 1.0 NH1 A:ARG159 4.5 16.6 1.0 NH2 A:ARG159 4.5 14.7 1.0 CG A:GLU122 4.8 11.2 1.0 O A:GLU122 4.8 10.7 1.0 CG A:MET92 4.9 7.5 1.0 OE1 A:GLU122 4.9 11.6 1.0 CD1 A:TYR156 4.9 9.9 1.0 CZ A:ARG159 4.9 15.8 1.0

Nickel binding site 2 out of 4 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Human Mthfs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni205 b:20.1 occ:1.00 O A:HOH339 1.9 12.1 1.0 NE2 A:HIS89 2.1 12.0 1.0 O A:HOH237 2.1 17.3 1.0 O A:HOH223 2.2 19.2 1.0 OD2 A:ASP91 2.2 13.7 1.0 CD2 A:HIS89 2.9 13.9 1.0 CG A:ASP91 3.0 12.1 1.0 CE1 A:HIS89 3.1 12.8 1.0 OD1 A:ASP91 3.2 13.1 1.0 O A:HOH220 4.0 17.8 1.0 NH2 A:ARG82 4.1 9.7 1.0 CG A:HIS89 4.1 15.0 1.0 OE2 A:GLU122 4.2 11.7 1.0 ND1 A:HIS89 4.2 13.8 1.0 O A:HOH228 4.2 23.1 1.0 CB A:ASP91 4.4 11.5 1.0 MG A:MG213 4.6 48.1 1.0 OE1 A:GLU122 4.7 11.6 1.0 CD A:GLU122 4.8 12.0 1.0

Nickel binding site 3 out of 4 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Human Mthfs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni207 b:45.6 occ:1.00 NE2 A:HIS142 2.1 33.5 1.0 O A:HOH306 2.2 47.0 1.0 O A:HOH300 2.2 36.0 1.0 O A:HOH303 2.5 34.3 1.0 CD2 A:HIS142 3.1 33.0 1.0 CE1 A:HIS142 3.1 33.0 1.0 O A:LEU181 4.1 31.2 1.0 CG A:HIS142 4.2 31.4 1.0 ND1 A:HIS142 4.2 32.3 1.0 CG A:GLN182 4.4 37.7 1.0 NE2 A:GLN182 4.6 46.0 1.0 O A:HOH311 4.7 45.0 1.0 O A:HOH321 4.9 34.6 1.0

Nickel binding site 4 out of 4 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Human Mthfs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni209 b:55.2 occ:1.00 N A:TYR152 3.3 19.4 1.0 N A:TYR153 3.3 17.2 1.0 NH2 A:ARG145 3.3 29.8 1.0 NH1 A:ARG145 3.7 27.1 1.0 O A:HOH225 3.7 22.0 1.0 CD1 A:TYR153 3.8 14.3 1.0 CB A:TYR152 3.9 17.0 1.0 C A:GLY151 3.9 22.3 1.0 CA A:TYR152 3.9 17.5 1.0 CB A:TYR153 3.9 17.6 1.0 CZ A:ARG145 3.9 28.0 1.0 N A:GLY151 4.0 28.5 1.0 CA A:GLY151 4.0 25.2 1.0 C A:TYR152 4.1 17.1 1.0 CA A:TYR153 4.2 18.1 1.0 CG A:TYR153 4.4 15.4 1.0 OD2 A:ASP154 4.4 32.5 1.0 CD1 A:TYR152 4.6 18.3 1.0 CG A:TYR152 4.7 17.8 1.0 O A:GLY151 4.9 21.9 1.0 CE1 A:TYR153 4.9 12.9 1.0 C A:LYS150 4.9 31.1 1.0 N A:ASP154 5.0 21.9 1.0

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