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Magnesium in PDB 3hy3: Structure of Human Mthfs with 10-Formyltetrahydrofolate

Enzymatic activity of Structure of Human Mthfs with 10-Formyltetrahydrofolate

All present enzymatic activity of Structure of Human Mthfs with 10-Formyltetrahydrofolate:
6.3.3.2;

Protein crystallography data

The structure of Structure of Human Mthfs with 10-Formyltetrahydrofolate, PDB code: 3hy3 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) 46.30 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.861, 144.974, 59.408, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.2

Other elements in 3hy3:

The structure of Structure of Human Mthfs with 10-Formyltetrahydrofolate also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Mthfs with 10-Formyltetrahydrofolate (pdb code 3hy3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Human Mthfs with 10-Formyltetrahydrofolate, PDB code: 3hy3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3hy3

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Magnesium binding site 1 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


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

b:11.3
occ:1.00
 OH A:TYR156 3.0 15.6 1.0
N A:MET92 3.3 12.7 1.0
O A:HOH218 3.3 24.6 1.0
N A:LEU124 3.4 19.7 1.0
N A:ALA123 3.4 15.3 1.0
O A:MET92 3.6 14.2 1.0
CE1 A:TYR156 3.6 14.4 1.0
CZ A:TYR156 3.8 16.2 1.0
CB A:GLU122 3.8 16.7 1.0
CG A:LEU124 3.8 21.3 1.0
CB A:LEU124 4.0 21.3 1.0
CA A:ASP91 4.1 14.5 1.0
CA A:MET92 4.1 14.6 1.0
CB A:ASP91 4.1 13.8 1.0
CB A:MET92 4.1 15.1 1.0
CA A:ALA123 4.1 16.5 1.0
CB A:ALA123 4.1 15.2 1.0
C A:GLU122 4.1 18.0 1.0
C A:ASP91 4.2 14.3 1.0
OD1 A:ASP91 4.2 18.8 1.0
C A:ALA123 4.2 17.6 1.0
C A:MET92 4.3 13.2 1.0
CD1 A:LEU124 4.3 18.7 1.0
CA A:LEU124 4.3 22.1 1.0
CA A:GLU122 4.3 17.2 1.0
NH2 A:ARG159 4.5 30.3 1.0
NH1 A:ARG159 4.6 27.1 1.0
CG A:GLU122 4.7 21.7 1.0
CG A:ASP91 4.7 16.4 1.0
CG A:MET92 4.8 14.1 1.0
OE1 A:GLU122 4.9 28.1 1.0
CZ A:ARG159 4.9 32.0 1.0
CD1 A:TYR156 4.9 16.8 1.0

Magnesium binding site 2 out of 9 in 3hy3

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Magnesium binding site 2 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


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 10-Formyltetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:38.4
occ:1.00
 N A:SER108 3.0 20.7 1.0
O A:HOH327 3.1 53.9 1.0
OG A:SER108 3.6 25.6 1.0
CA A:THR107 3.6 17.7 1.0
CB A:SER108 3.7 23.8 1.0
CB A:THR107 3.7 17.0 1.0
CE2 A:PHE85 3.7 31.5 1.0
C A:THR107 3.8 17.6 1.0
CZ A:PHE85 3.9 32.0 1.0
CA A:SER108 4.0 21.7 1.0
CD2 A:PHE85 4.1 34.4 1.0
CE1 A:PHE85 4.4 33.8 1.0
O A:HOH254 4.4 44.0 1.0
CG2 A:THR107 4.6 18.8 1.0
CG A:PHE85 4.6 31.1 1.0
CD1 A:PHE85 4.7 36.1 1.0
OG1 A:THR107 4.8 16.6 1.0
O A:THR107 4.9 17.9 1.0
N A:THR107 5.0 18.2 1.0

Magnesium binding site 3 out of 9 in 3hy3

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Magnesium binding site 3 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


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

b:98.1
occ:1.00
 OE1 A:GLU16 3.4 54.0 1.0
CD A:GLU16 4.1 47.8 1.0
CG A:GLU16 4.6 38.6 1.0
OE2 A:GLU16 4.8 53.0 1.0

Magnesium binding site 4 out of 9 in 3hy3

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Magnesium binding site 4 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


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 with 10-Formyltetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:52.2
occ:1.00
 OE1 A:GLN86 2.9 39.5 1.0
N A:PHE85 3.2 24.1 1.0
CD2 A:PHE85 3.5 34.4 1.0
CA A:ARG84 3.6 23.3 1.0
C A:ARG84 3.8 23.0 1.0
O A:TYR83 3.8 18.7 1.0
CD A:GLN86 3.8 44.8 1.0
CB A:PHE85 4.2 28.8 1.0
CG A:ARG84 4.2 26.4 1.0
CA A:PHE85 4.2 26.5 1.0
NE2 A:GLN86 4.2 45.9 1.0
CG A:PHE85 4.3 31.1 1.0
O A:HOH337 4.3 42.7 1.0
CB A:ARG84 4.4 24.8 1.0
CE2 A:PHE85 4.4 31.5 1.0
N A:GLN86 4.5 28.4 1.0
N A:ARG84 4.6 21.0 1.0
C A:TYR83 4.6 19.0 1.0
C A:PHE85 4.9 27.3 1.0

Magnesium binding site 5 out of 9 in 3hy3

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Magnesium binding site 5 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


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 with 10-Formyltetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:44.5
occ:1.00
 O A:HOH348 4.4 72.7 1.0
CG A:ARG31 4.9 32.2 1.0
CD A:ARG31 5.0 31.5 1.0

Magnesium binding site 6 out of 9 in 3hy3

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Magnesium binding site 6 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


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 with 10-Formyltetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:50.8
occ:1.00
 O A:GLY15 3.3 26.0 1.0
CA A:GLY15 4.0 22.2 1.0
C A:GLY15 4.0 23.7 1.0
N A:GLN19 4.0 26.0 1.0
CB A:LYS18 4.1 25.2 1.0
CB A:GLN19 4.3 28.6 1.0
CA A:GLN19 4.4 28.0 1.0
C A:LYS18 4.6 25.1 1.0
CA A:LYS18 4.9 24.1 1.0

Magnesium binding site 7 out of 9 in 3hy3

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Magnesium binding site 7 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


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 with 10-Formyltetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:66.6
occ:1.00
 O A:HOH311 2.4 50.6 1.0
OD2 A:ASP60 3.5 34.7 1.0
CG A:ASP60 3.7 32.5 1.0
OD1 A:ASP60 4.0 29.5 1.0
O A:HOH262 4.3 38.1 1.0
NZ A:LYS18 4.3 35.1 1.0
CB A:ASP60 4.3 29.3 1.0
NH1 A:ARG148 4.4 27.0 1.0
O A:HOH229 4.5 38.8 1.0
O A:HOH235 4.7 43.5 1.0
CZ3 A:TRP109 4.9 31.8 1.0

Magnesium binding site 8 out of 9 in 3hy3

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Magnesium binding site 8 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Human Mthfs with 10-Formyltetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:42.1
occ:1.00
 CD A:ARG159 2.7 29.6 1.0
O A:HOH289 3.0 18.9 1.0
NH1 A:ARG159 3.1 27.1 1.0
O A:MET90 3.2 17.7 1.0
O A:HOH293 3.3 50.0 1.0
ND1 A:HIS89 3.4 20.1 1.0
NE A:ARG159 3.6 29.8 1.0
CE1 A:HIS89 3.6 20.1 1.0
CZ A:ARG159 3.8 32.0 1.0
CG A:ARG159 3.9 32.0 1.0
CA A:TYR156 4.0 20.6 1.0
CD1 A:TYR156 4.1 16.8 1.0
N A:MET90 4.1 17.4 1.0
N A:TYR156 4.3 20.8 1.0
C A:MET90 4.3 16.0 1.0
O A:ALA155 4.3 21.8 1.0
C A:ALA155 4.5 24.0 1.0
CB A:TYR156 4.5 17.9 1.0
CG A:HIS89 4.6 21.3 1.0
CB A:ARG159 4.6 27.8 1.0
O A:HOH239 4.7 33.0 1.0
CB A:ALA155 4.7 23.2 1.0
CG A:TYR156 4.7 16.2 1.0
NE2 A:HIS89 4.8 24.5 1.0
CA A:MET90 4.8 16.0 1.0
CE1 A:TYR156 5.0 14.4 1.0
CA A:HIS89 5.0 22.4 1.0

Magnesium binding site 9 out of 9 in 3hy3

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Magnesium binding site 9 out of 9 in the Structure of Human Mthfs with 10-Formyltetrahydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Human Mthfs with 10-Formyltetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:52.2
occ:1.00
 O A:HOH227 3.7 26.2 1.0
O A:ARG74 4.3 23.7 1.0
O A:GLN47 4.6 19.9 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 15:28:42 2024

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