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Magnesium in PDB 4kbn: Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE

Enzymatic activity of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE

All present enzymatic activity of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE:
1.5.1.3;

Protein crystallography data

The structure of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE, PDB code: 4kbn was solved by K.M.Lamb, A.C.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 1.84
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.669, 93.784, 95.991, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27.7

Other elements in 4kbn:

The structure of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE also contains other interesting chemical elements:

Strontium (Sr) 1 atom
Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE (pdb code 4kbn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE, PDB code: 4kbn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4kbn

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Magnesium binding site 1 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:45.6
occ:1.00
 O A:PRO160 2.4 56.1 1.0
O A:HOH425 2.7 35.3 1.0
O A:HOH377 3.3 36.3 1.0
C A:PRO160 3.4 41.9 1.0
O A:HOH352 3.4 35.2 1.0
OG A:SER167 3.6 30.4 1.0
CB A:SER167 3.7 22.9 1.0
OE2 A:GLU161 3.8 46.2 0.5
O A:HOH353 3.9 25.7 1.0
O A:HOH351 3.9 23.8 1.0
CA A:GLU161 4.0 43.0 0.5
CA A:GLU161 4.0 43.0 0.5
N A:GLU161 4.1 37.4 0.5
N A:GLU161 4.1 37.4 0.5
CA A:SER167 4.1 20.8 1.0
O A:LEU159 4.4 39.8 1.0
O A:SER167 4.4 26.4 1.0
CA A:PRO160 4.4 43.5 1.0
CD A:GLU161 4.8 51.3 0.5
C A:SER167 4.8 23.4 1.0
O A:PHE179 4.8 23.1 1.0
CG A:GLU161 4.9 51.3 0.5
CB A:GLU161 4.9 46.5 0.5
CB A:GLU161 5.0 46.5 0.5
C A:GLU161 5.0 51.4 0.5

Magnesium binding site 2 out of 9 in 4kbn

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Magnesium binding site 2 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:29.8
occ:1.00
 NE2 A:GLN170 2.8 18.9 1.0
CD A:GLN170 3.8 24.8 1.0
O A:HOH461 3.9 39.0 1.0
CB A:ASP168 3.9 19.8 1.0
CD1 A:LEU166 4.0 26.3 1.0
OE1 A:GLN170 4.0 31.3 1.0
OD2 A:ASP168 4.1 18.9 1.0
CD2 A:LEU166 4.2 24.2 1.0
CB A:LEU166 4.3 20.3 1.0
CG A:LEU166 4.4 23.2 1.0
CG A:ASP168 4.5 22.9 1.0
CL A:CL203 4.6 44.8 1.0
N A:ASP168 4.6 19.0 1.0
O A:ASP168 4.7 22.0 1.0
CA A:ASP168 4.7 21.0 1.0
C A:ASP168 4.9 22.6 1.0

Magnesium binding site 3 out of 9 in 4kbn

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Magnesium binding site 3 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:44.2
occ:1.00
 O A:HOH450 2.5 45.0 1.0
N A:VAL169 2.9 17.7 1.0
CG2 A:VAL169 3.5 20.0 1.0
O A:HOH464 3.5 30.3 1.0
CB A:VAL169 3.6 22.7 1.0
CA A:ASP168 3.6 21.0 1.0
CB A:ASP168 3.7 19.8 1.0
C A:ASP168 3.7 22.6 1.0
CA A:VAL169 3.8 20.0 1.0
OD1 A:ASP168 4.0 17.0 1.0
CG A:ASP168 4.2 22.9 1.0
O A:HOH449 4.3 46.6 1.0
O A:VAL169 4.6 20.3 1.0
C A:VAL169 4.7 18.4 1.0
O A:ASP168 4.9 22.0 1.0
N A:ASP168 5.0 19.0 1.0

Magnesium binding site 4 out of 9 in 4kbn

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Magnesium binding site 4 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:47.9
occ:1.00
 OD1 B:ASP21 2.8 38.6 1.0
OD2 B:ASP21 3.3 46.3 1.0
CG B:ASP21 3.4 39.4 1.0
N B:NH4211 3.7 46.2 1.0
O B:HOH463 4.0 43.1 1.0
CG B:PRO26 4.2 36.8 1.0
CG B:LEU22 4.2 34.5 1.0
CB B:LEU22 4.3 28.8 1.0
CD1 B:LEU22 4.4 33.1 1.0
O B:HOH358 4.4 49.3 1.0
N B:LEU22 4.4 22.1 1.0
O B:HOH326 4.6 37.9 1.0
CD B:PRO26 4.7 27.5 1.0
CB B:ASP21 4.7 31.9 1.0
O B:TRP24 4.7 26.0 1.0
CB B:PRO26 4.8 28.4 1.0
N B:PRO26 4.8 25.1 1.0
CA B:PRO26 4.9 28.6 1.0
CA B:LEU22 5.0 19.9 1.0

Magnesium binding site 5 out of 9 in 4kbn

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Magnesium binding site 5 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg209

b:54.7
occ:1.00
 OE1 B:GLU101 4.0 72.1 1.0
O B:HOH427 4.1 53.4 1.0

Magnesium binding site 6 out of 9 in 4kbn

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Magnesium binding site 6 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg210

b:45.9
occ:1.00
 OD1 B:ASP110 2.9 36.5 1.0
OE1 A:GLN140 3.0 40.5 1.0
OD2 B:ASP110 3.3 39.3 1.0
CG B:ASP110 3.5 28.6 1.0
CG2 B:VAL43 3.7 33.0 1.0
CD A:GLN140 3.8 38.2 1.0
CB A:GLN140 3.8 35.6 1.0
O A:HOH417 4.0 43.6 1.0
O A:HOH360 4.1 38.0 1.0
CG B:MET111 4.2 31.6 0.5
CG B:MET111 4.2 31.3 0.5
CG A:GLN140 4.4 26.6 1.0
SD B:MET111 4.5 40.6 0.5
OG B:SER42 4.5 40.6 1.0
SD B:MET111 4.6 30.1 0.5
NE2 A:GLN140 4.6 44.0 1.0
N B:SER42 4.8 35.1 1.0
CB B:VAL43 4.9 35.5 1.0
O A:MET139 4.9 32.5 0.3
OG B:SER41 5.0 33.0 1.0
CB B:ASP110 5.0 25.2 1.0

Magnesium binding site 7 out of 9 in 4kbn

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Magnesium binding site 7 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg212

b:34.7
occ:1.00
 O B:HOH413 2.5 40.8 1.0
OD1 B:ASP145 2.8 27.4 1.0
N B:GLY20 2.8 34.3 1.0
O3D B:NDP214 2.9 27.5 1.0
OG1 B:THR146 3.3 32.1 1.0
N B:ASN19 3.3 27.4 1.0
CA B:GLY20 3.5 33.8 1.0
N B:LYS18 3.6 28.3 1.0
C B:LYS18 3.6 27.2 1.0
CG B:ASP145 3.6 39.4 1.0
OD2 B:ASP145 3.7 28.4 1.0
C B:ASN19 3.8 35.6 1.0
CA B:LYS18 3.9 31.1 1.0
C3D B:NDP214 3.9 26.3 1.0
CA B:ASN19 3.9 35.4 1.0
C B:GLY17 4.0 27.1 1.0
C4D B:NDP214 4.0 22.9 1.0
O B:LYS18 4.3 31.9 1.0
CA B:GLY17 4.4 25.1 1.0
C B:GLY20 4.4 32.2 1.0
N B:ASP21 4.4 26.8 1.0
CB B:THR146 4.5 27.0 1.0
O B:GLY17 4.5 24.2 1.0
O B:ASP21 4.6 26.7 1.0
O4D B:NDP214 4.9 21.2 1.0
O B:ASN19 5.0 32.1 1.0

Magnesium binding site 8 out of 9 in 4kbn

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Magnesium binding site 8 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg213

b:42.4
occ:1.00
 O B:HOH445 2.4 30.7 1.0
O B:HOH336 2.8 35.4 1.0
O B:TYR156 3.0 30.6 1.0
O B:LEU153 3.1 29.7 1.0
O B:HOH426 3.4 52.4 1.0
CB B:LEU153 3.5 34.2 1.0
C B:LEU153 3.9 24.8 1.0
CA B:LYS157 3.9 28.5 1.0
CD2 B:LEU153 3.9 29.5 1.0
CA B:LEU153 4.0 27.8 1.0
O B:HOH441 4.0 45.2 1.0
C B:TYR156 4.1 33.3 1.0
CG B:LEU153 4.1 36.5 1.0
CD1 B:LEU153 4.3 44.6 1.0
N B:LYS157 4.4 25.3 1.0
CB B:LYS157 4.5 31.2 1.0
N B:LEU158 4.7 23.1 1.0
C B:LYS157 4.9 35.1 1.0

Magnesium binding site 9 out of 9 in 4kbn

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Magnesium binding site 9 out of 9 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3-(3,5- Pyrimidine)]-Phenyl-Prop-1-Yn-1-Yl}-6-Ethyl-Pyrimidine-2,4DIAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg215

b:53.2
occ:1.00
 O B:HOH423 3.5 43.7 1.0
CG2 B:THR40 3.7 26.7 1.0
CB B:SER42 4.0 33.5 1.0
OD2 A:ASP141 4.4 36.8 1.0
CA B:SER42 4.4 33.4 1.0
CB A:ASP141 4.5 32.7 1.0
N B:SER42 4.6 35.1 1.0
O A:HOH478 4.7 38.0 1.0
O B:SER41 4.8 32.8 1.0
C B:SER41 4.8 24.9 1.0
CG A:ASP141 4.8 40.7 1.0

Reference:

K.M.Lamb, N.G-Dayanandan, D.L.Wright, A.C.Anderson. Elucidating Features That Drive the Design of Selective Antifolates Using Crystal Structures of Human Dihydrofolate Reductase. Biochemistry V. 52 7318 2013.
ISSN: ISSN 0006-2960
PubMed: 24053334
DOI: 10.1021/BI400852H
Page generated: Sat Aug 17 03:32:44 2024

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