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Magnesium in PDB 3hxt: Structure of Human Mthfs

Enzymatic activity of Structure of Human Mthfs

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

Protein crystallography data

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

Other elements in 3hxt:

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

Nickel (Ni) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Mthfs (pdb code 3hxt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of Human Mthfs, PDB code: 3hxt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3hxt

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Magnesium binding site 1 out of 7 in the Structure of Human Mthfs


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:63.8
occ:1.00
 CD2 A:PHE85 3.4 39.0 1.0
N A:PHE85 3.5 26.8 1.0
O A:TYR83 3.6 11.9 1.0
OE1 A:GLN86 3.8 39.9 1.0
CA A:ARG84 3.9 21.0 1.0
O A:HOH260 4.1 29.3 1.0
CE2 A:PHE85 4.2 40.8 1.0
C A:ARG84 4.2 23.3 1.0
CG A:PHE85 4.3 35.5 1.0
CB A:PHE85 4.3 31.6 1.0
C A:TYR83 4.5 13.1 1.0
CA A:PHE85 4.5 30.4 1.0
CD A:GLN86 4.6 39.3 1.0
NE2 A:GLN113 4.7 9.6 1.0
N A:ARG84 4.7 16.4 1.0
NE2 A:GLN86 4.7 41.1 1.0
O A:HOH251 4.9 25.5 1.0
CB A:ARG84 4.9 21.7 1.0

Magnesium binding site 2 out of 7 in 3hxt

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Magnesium binding site 2 out of 7 in the Structure of Human Mthfs


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:41.9
occ:1.00
 CB A:MET24 2.7 31.3 1.0
CG A:ARG29 3.8 33.9 1.0
CG A:PHE175 3.9 18.6 1.0
CD2 A:PHE175 3.9 18.2 1.0
OE1 A:GLU177 4.1 26.4 1.0
CD1 A:PHE175 4.1 17.5 1.0
CD A:GLU177 4.2 26.6 1.0
CE2 A:PHE175 4.2 18.0 1.0
CA A:MET24 4.2 31.5 1.0
CE1 A:PHE175 4.3 17.8 1.0
OE2 A:GLU177 4.3 27.2 1.0
CZ A:PHE175 4.3 18.3 1.0
CB A:PHE175 4.4 19.2 1.0
NE A:ARG29 4.5 47.4 1.0
NE2 A:GLN32 4.7 22.9 1.0
CG A:GLU28 4.7 29.8 1.0
O A:LEU21 4.7 37.1 1.0
CD A:ARG29 4.7 40.9 1.0
CA A:ARG29 4.8 27.7 1.0
CG A:GLU177 4.8 25.2 1.0
N A:ARG29 4.9 27.5 1.0
O A:HOH325 4.9 38.9 1.0
CB A:ARG29 4.9 28.7 1.0
N A:MET24 5.0 31.5 1.0
CB A:GLU177 5.0 24.4 1.0

Magnesium binding site 3 out of 7 in 3hxt

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Magnesium binding site 3 out of 7 in the Structure of Human Mthfs


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:47.8
occ:1.00
 O A:GLU61 2.9 14.6 1.0
O A:GLN59 3.7 23.4 1.0
O A:MET58 3.7 17.6 1.0
CD A:ARG29 3.9 40.9 1.0
C A:GLN59 4.1 23.2 1.0
C A:GLU61 4.1 15.7 1.0
CA A:GLN59 4.1 23.4 1.0
CB A:ARG29 4.2 28.7 1.0
OE1 A:GLN59 4.2 38.3 1.0
CB A:GLU63 4.3 16.3 1.0
N A:GLU63 4.3 15.0 1.0
N A:GLU61 4.5 19.2 1.0
CG A:ARG29 4.6 33.9 1.0
OE1 A:GLU63 4.6 18.8 1.0
CD A:GLN59 4.6 36.6 1.0
CA A:GLU63 4.6 15.8 1.0
CZ A:PHE175 4.7 18.3 1.0
C A:MET58 4.7 18.2 1.0
C A:ILE62 4.7 14.9 1.0
NE2 A:GLN59 4.8 38.5 1.0
N A:GLN59 4.9 20.6 1.0
CA A:GLU61 4.9 17.2 1.0
N A:ASP60 5.0 23.0 1.0

Magnesium binding site 4 out of 7 in 3hxt

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Magnesium binding site 4 out of 7 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Mthfs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:43.9
occ:1.00
 O A:HOH277 2.9 21.4 1.0
CD A:ARG159 3.0 19.9 1.0
ND1 A:HIS89 3.0 13.8 1.0
O A:MET90 3.2 12.3 1.0
NH1 A:ARG159 3.2 16.6 1.0
CE1 A:HIS89 3.6 12.8 1.0
N A:MET90 3.7 14.2 1.0
NE A:ARG159 3.9 17.9 1.0
CZ A:ARG159 3.9 15.8 1.0
CG A:HIS89 4.1 15.0 1.0
CA A:HIS89 4.2 18.0 1.0
C A:MET90 4.2 12.5 1.0
CG A:ARG159 4.2 20.7 1.0
CA A:TYR156 4.3 15.1 1.0
CD1 A:TYR156 4.3 9.9 1.0
N A:TYR156 4.4 16.8 1.0
C A:HIS89 4.5 15.9 1.0
O A:ALA155 4.5 18.0 1.0
C A:ALA155 4.6 18.6 1.0
CA A:MET90 4.6 13.1 1.0
CB A:HIS89 4.6 17.2 1.0
O A:ASN88 4.7 26.8 1.0
CB A:TYR156 4.7 13.7 1.0
CB A:ALA155 4.8 20.4 1.0
NE2 A:HIS89 4.8 12.0 1.0
CG A:MET90 4.8 14.0 1.0

Magnesium binding site 5 out of 7 in 3hxt

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Magnesium binding site 5 out of 7 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Human Mthfs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:46.9
occ:0.50
 O A:LEU104 2.7 8.9 1.0
O A:HOH218 3.6 17.2 1.0
C A:LEU104 3.8 8.6 1.0
CD A:LYS106 3.8 21.9 1.0
CG A:LYS106 4.1 15.4 1.0
CA A:PRO105 4.2 9.4 1.0
O A:SER102 4.3 14.9 1.0
N A:PRO105 4.4 8.6 1.0
O A:LEU103 4.5 11.4 1.0
C A:LEU103 4.6 11.4 1.0
C A:PRO105 4.6 9.9 1.0
N A:LYS106 4.7 10.6 1.0
N A:LEU104 4.7 9.6 1.0
CA A:LEU104 4.9 8.6 1.0

Magnesium binding site 6 out of 7 in 3hxt

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Magnesium binding site 6 out of 7 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Human Mthfs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:48.1
occ:1.00
 O A:HOH237 3.3 17.3 1.0
NH2 A:ARG82 3.4 9.7 1.0
O A:HOH339 3.4 12.1 1.0
CZ A:ARG82 3.6 9.8 1.0
NH1 A:ARG82 3.9 8.2 1.0
NE A:ARG82 4.1 10.0 1.0
O A:HOH255 4.2 33.0 1.0
O A:HOH228 4.5 23.1 1.0
NI A:NI205 4.6 20.1 1.0
O A:HOH260 4.7 29.3 1.0
O A:HOH231 4.7 23.6 1.0
OE2 A:GLU122 4.8 11.7 1.0
OD2 A:ASP91 4.8 13.7 1.0

Magnesium binding site 7 out of 7 in 3hxt

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Magnesium binding site 7 out of 7 in the Structure of Human Mthfs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Human Mthfs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:39.1
occ:1.00
 O A:HOH263 2.6 36.8 1.0
N A:LEU181 3.1 29.3 1.0
CA A:CYS180 3.7 26.1 1.0
CB A:LEU181 3.8 31.5 1.0
CB A:CYS180 3.9 25.6 1.0
C A:CYS180 3.9 27.4 1.0
CA A:LEU181 4.0 31.0 1.0
OE2 A:GLU16 4.6 50.7 1.0
SG A:CYS180 4.7 26.2 1.0
N A:GLN182 4.7 30.8 1.0
NH2 A:ARG20 4.7 43.2 1.0
C A:LEU181 4.9 31.1 1.0
CD1 A:LEU13 5.0 22.6 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: Wed Aug 14 15:28:12 2024

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