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Magnesium in PDB 3hy6: Structure of Human Mthfs with Adp

Enzymatic activity of Structure of Human Mthfs with Adp

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

Protein crystallography data

The structure of Structure of Human Mthfs with Adp, PDB code: 3hy6 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) 46.09 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.511, 145.221, 59.655, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.5

Other elements in 3hy6:

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

Nickel (Ni) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of Human Mthfs with Adp (pdb code 3hy6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of Human Mthfs with Adp, PDB code: 3hy6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3hy6

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Magnesium binding site 1 out of 12 in the Structure of Human Mthfs with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:77.0
occ:1.00
 N A:PHE85 3.0 45.0 1.0
OE1 A:GLN86 3.3 54.2 1.0
CD2 A:PHE85 3.4 50.5 1.0
CB A:PHE85 3.7 47.1 1.0
O A:TYR83 3.8 35.2 1.0
CA A:ARG84 3.8 41.9 1.0
C A:ARG84 3.8 43.3 1.0
CA A:PHE85 3.9 46.8 1.0
CG A:PHE85 4.0 48.8 1.0
CD A:GLN86 4.4 53.8 1.0
CE2 A:PHE85 4.4 50.7 1.0
C A:TYR83 4.6 35.8 1.0
O A:HOH348 4.7 46.4 1.0
N A:ARG84 4.7 38.5 1.0
N A:GLN86 4.7 47.9 1.0
C A:PHE85 4.8 47.5 1.0
CB A:ARG84 4.9 42.7 1.0
NE2 A:GLN86 4.9 53.4 1.0
OE2 A:GLU116 4.9 49.9 1.0
O A:ARG84 5.0 43.8 1.0

Magnesium binding site 2 out of 12 in 3hy6

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Magnesium binding site 2 out of 12 in the Structure of Human Mthfs with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:66.4
occ:1.00
 O A:GLU61 3.2 31.3 1.0
O A:GLN59 3.4 39.4 1.0
CD A:ARG29 3.4 49.9 1.0
CB A:ARG29 3.7 43.1 1.0
C A:GLN59 4.0 38.8 1.0
CG A:ARG29 4.0 45.6 1.0
O A:MET58 4.2 38.1 1.0
C A:GLU61 4.3 31.9 1.0
CA A:GLN59 4.4 39.7 1.0
N A:GLU61 4.5 33.9 1.0
CZ A:PHE175 4.5 29.6 1.0
NE A:ARG29 4.6 53.8 1.0
N A:GLU63 4.7 30.6 1.0
CB A:GLU63 4.7 31.5 1.0
O A:HOH342 4.8 61.4 1.0
OE1 A:GLN59 4.9 52.7 1.0
CA A:ARG29 4.9 43.0 1.0
N A:ASP60 4.9 37.9 1.0

Magnesium binding site 3 out of 12 in 3hy6

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Magnesium binding site 3 out of 12 in the Structure of Human Mthfs with Adp


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

b:51.5
occ:1.00
 O A:HOH264 2.7 29.8 1.0
NH1 A:ARG159 3.0 35.5 1.0
CD A:ARG159 3.3 35.4 1.0
O A:MET90 3.5 29.0 1.0
ND1 A:HIS89 3.5 33.2 1.0
N A:MET90 3.8 32.4 1.0
CZ A:ARG159 4.0 35.1 1.0
CA A:TYR156 4.0 30.0 1.0
N A:TYR156 4.0 30.3 1.0
NE A:ARG159 4.1 34.4 1.0
CE1 A:HIS89 4.1 32.2 1.0
C A:ALA155 4.2 30.5 1.0
CA A:HIS89 4.2 36.2 1.0
O A:ASN88 4.3 42.4 1.0
CB A:ALA155 4.3 30.1 1.0
O A:ALA155 4.4 31.0 1.0
CD1 A:TYR156 4.4 25.7 1.0
CB A:TYR156 4.4 29.5 1.0
CG A:ARG159 4.4 37.0 1.0
CG A:HIS89 4.4 33.9 1.0
C A:MET90 4.5 29.8 1.0
C A:HIS89 4.6 34.2 1.0
CA A:MET90 4.7 31.1 1.0
CB A:HIS89 4.8 35.8 1.0
O A:TYR152 4.9 28.4 1.0
CG A:MET90 4.9 32.8 1.0
CG A:TYR156 4.9 27.3 1.0
CA A:ALA155 5.0 30.9 1.0
CB A:ARG159 5.0 37.0 1.0

Magnesium binding site 4 out of 12 in 3hy6

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Magnesium binding site 4 out of 12 in the Structure of Human Mthfs with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:51.8
occ:0.84
 O A:LEU104 2.7 25.6 1.0
CG A:LYS106 3.3 31.8 1.0
CD A:LYS106 3.3 37.5 1.0
O A:HOH221 3.5 27.1 1.0
O A:HOH318 3.7 62.9 1.0
N A:LYS106 3.7 28.5 1.0
CA A:PRO105 3.7 27.1 1.0
C A:LEU104 3.8 26.6 1.0
C A:PRO105 3.8 28.1 1.0
CB A:LYS106 4.1 30.7 1.0
N A:PRO105 4.2 26.4 1.0
CA A:LYS106 4.5 29.9 1.0
O A:PRO105 4.6 26.9 1.0
CE A:LYS106 4.7 41.1 1.0

Magnesium binding site 5 out of 12 in 3hy6

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Magnesium binding site 5 out of 12 in the Structure of Human Mthfs with Adp


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

b:51.7
occ:1.00
 O A:HOH313 2.4 57.0 1.0
O A:HOH255 2.5 41.7 1.0
N A:LEU181 3.1 38.9 1.0
CA A:CYS180 3.5 37.4 1.0
CB A:CYS180 3.6 37.4 1.0
C A:CYS180 3.8 37.9 1.0
CB A:LEU181 3.9 39.4 1.0
CA A:LEU181 4.1 39.3 1.0
SG A:CYS180 4.5 40.9 1.0
NH2 A:ARG20 4.5 53.5 1.0
N A:GLN182 4.7 39.8 1.0
OE2 A:GLU16 4.8 48.8 1.0
O A:ILE179 4.8 35.6 1.0
N A:CYS180 4.8 35.9 1.0
O A:CYS180 5.0 38.5 1.0

Magnesium binding site 6 out of 12 in 3hy6

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Magnesium binding site 6 out of 12 in the Structure of Human Mthfs with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:16.8
occ:1.00
 O A:HOH220 3.2 29.6 1.0
OH A:TYR156 3.2 27.2 1.0
N A:MET92 3.3 25.4 1.0
N A:LEU124 3.4 30.1 1.0
N A:ALA123 3.6 28.4 1.0
NH2 A:ARG159 3.7 35.2 1.0
O A:MET92 3.7 26.0 1.0
CE1 A:TYR156 3.7 25.2 1.0
CB A:GLU122 3.8 28.7 1.0
CB A:LEU124 3.8 31.4 1.0
CG A:LEU124 3.9 31.8 1.0
CB A:ASP91 3.9 27.8 1.0
CZ A:TYR156 4.0 25.9 1.0
CA A:ASP91 4.0 27.5 1.0
C A:GLU122 4.1 28.4 1.0
CB A:ALA123 4.2 28.2 1.0
CD1 A:LEU124 4.2 31.6 1.0
CA A:ALA123 4.2 28.9 1.0
C A:ASP91 4.2 26.8 1.0
CA A:MET92 4.2 25.0 1.0
CA A:LEU124 4.2 32.1 1.0
CB A:MET92 4.3 24.9 1.0
OD1 A:ASP91 4.3 31.4 1.0
CA A:GLU122 4.3 28.9 1.0
C A:ALA123 4.3 29.6 1.0
C A:MET92 4.4 24.6 1.0
CG A:ASP91 4.6 30.2 1.0
CZ A:ARG159 4.6 35.1 1.0
CG A:GLU122 4.7 29.6 1.0
OE1 A:GLU122 4.8 33.8 1.0
O A:GLU122 4.8 28.8 1.0
CG A:MET92 4.9 24.1 1.0
CD1 A:TYR156 5.0 25.7 1.0
NH1 A:ARG159 5.0 35.5 1.0

Magnesium binding site 7 out of 12 in 3hy6

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Magnesium binding site 7 out of 12 in the Structure of Human Mthfs with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:51.3
occ:1.00
 O3B A:ADP302 2.8 43.2 1.0
OD1 A:ASP189 2.8 39.9 1.0
O A:HOH307 2.8 35.2 1.0
OD2 A:ASP154 2.9 37.5 1.0
OD1 A:ASP154 3.0 33.6 1.0
O A:ARG145 3.2 29.6 1.0
CG A:ASP154 3.3 33.5 1.0
CG A:ASP189 3.4 40.3 1.0
O1A A:ADP302 3.5 51.7 1.0
CB A:ASP189 3.7 40.6 1.0
O A:HOH273 3.8 33.7 1.0
O A:HOH306 4.0 38.6 1.0
PB A:ADP302 4.1 44.2 1.0
O A:HOH298 4.2 36.6 1.0
C A:ARG145 4.2 30.1 1.0
NH2 A:ARG145 4.2 37.6 1.0
CA A:ASP189 4.2 40.8 1.0
O1B A:ADP302 4.3 43.5 1.0
O A:HOH328 4.4 42.5 1.0
OD2 A:ASP189 4.4 39.2 1.0
N A:GLY147 4.5 29.2 1.0
N A:MET190 4.6 38.9 1.0
CZ A:ARG145 4.8 34.9 1.0
NE A:ARG145 4.8 37.4 1.0
CB A:ASP154 4.9 30.6 1.0
CB A:ARG145 4.9 31.1 1.0
CA A:LEU146 4.9 28.8 1.0
PA A:ADP302 4.9 50.2 1.0
C A:ASP189 4.9 40.1 1.0
N A:LEU146 4.9 28.7 1.0

Magnesium binding site 8 out of 12 in 3hy6

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Magnesium binding site 8 out of 12 in the Structure of Human Mthfs with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:52.0
occ:1.00
 ND2 A:ASN144 2.7 35.4 1.0
O A:HOH298 3.0 36.6 1.0
CG A:LYS191 3.4 39.0 1.0
O A:ASP189 3.6 40.3 1.0
CG1 A:VAL185 3.6 39.5 1.0
N A:LYS191 3.8 36.0 1.0
CG A:ASN144 3.8 36.7 1.0
C A:ASP189 3.9 40.1 1.0
CB A:VAL185 3.9 40.1 1.0
CB A:ASP189 4.0 40.6 1.0
CG2 A:VAL185 4.1 40.0 1.0
C A:MET190 4.1 37.0 1.0
CA A:LYS191 4.2 35.8 1.0
CB A:ASN144 4.2 34.5 1.0
CE A:LYS191 4.2 48.4 1.0
CA A:ASN144 4.2 34.5 1.0
N A:MET190 4.3 38.9 1.0
CB A:LYS191 4.3 36.4 1.0
CD A:LYS191 4.5 44.8 1.0
CA A:MET190 4.6 38.0 1.0
CA A:ASP189 4.6 40.8 1.0
O A:MET190 4.6 37.2 1.0
OD1 A:ASN144 4.9 37.3 1.0
O A:HOH355 4.9 47.9 1.0
N A:ARG145 5.0 32.3 1.0

Magnesium binding site 9 out of 12 in 3hy6

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Magnesium binding site 9 out of 12 in the Structure of Human Mthfs with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg215

b:62.3
occ:1.00
 OE1 A:GLU45 3.7 44.9 1.0
CB A:ASP130 3.8 25.8 1.0
CA A:SER49 3.9 31.5 1.0
CB A:SER49 4.0 31.6 1.0
N A:SER49 4.1 30.3 1.0
O A:GLU45 4.2 27.5 1.0
O A:ASP130 4.2 25.4 1.0
O A:HOH259 4.3 41.1 1.0
C A:LYS48 4.4 29.9 1.0
CG A:ASP130 4.4 27.3 1.0
O A:LYS48 4.5 29.7 1.0
CA A:ASP130 4.5 26.2 1.0
C A:ASP130 4.5 25.8 1.0
OD1 A:ASP130 4.6 30.6 1.0
CD A:GLU45 4.6 43.5 1.0
CB A:LYS48 4.6 29.8 1.0

Magnesium binding site 10 out of 12 in 3hy6

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Magnesium binding site 10 out of 12 in the Structure of Human Mthfs with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Human Mthfs with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg216

b:63.3
occ:1.00
 OE2 A:GLU100 2.8 39.1 1.0
OE1 A:GLU100 3.3 36.6 1.0
CD A:GLU100 3.3 36.3 1.0
O A:HOH291 3.6 43.3 1.0
NH1 A:ARG120 3.7 25.5 1.0
CG A:GLU96 3.7 37.1 1.0
CZ A:ARG120 3.9 26.2 1.0
NH2 A:ARG120 3.9 23.3 1.0
CB A:GLU96 4.6 32.2 1.0
NE A:ARG120 4.7 27.4 1.0
CG A:GLU100 4.7 32.1 1.0
OE2 A:GLU96 4.7 46.0 1.0
CD A:GLU96 4.7 41.9 1.0
N A:GLU96 4.8 30.2 1.0
O A:ARG94 5.0 27.1 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: Sun Aug 10 22:10:24 2025

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