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Magnesium in PDB 4kfj: Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine

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

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

Protein crystallography data

The structure of Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine, PDB code: 4kfj 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) 19.89 / 1.76
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.811, 94.075, 96.294, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.5

Other elements in 4kfj:

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

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 4kfj

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


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- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:30.8
occ:1.00
 O A:ASN64 2.9 27.2 1.0
N A:LYS68 3.0 14.7 1.0
O A:PRO66 3.6 19.7 1.0
CB A:LYS68 3.6 20.3 1.0
CA A:LEU67 3.6 14.2 1.0
C A:ASN64 3.7 30.5 1.0
CG A:LYS68 3.7 23.5 1.0
C A:LEU67 3.8 15.9 1.0
CAL A:1R0202 3.8 57.8 1.0
CA A:ASN64 3.9 30.8 1.0
CA A:LYS68 3.9 15.2 1.0
CD A:LYS68 4.0 22.3 1.0
CB A:ASN64 4.0 28.9 1.0
NAR A:1R0202 4.1 73.0 1.0
CE A:LYS68 4.2 32.2 1.0
C A:PRO66 4.4 19.5 1.0
OD1 A:ASN64 4.4 34.7 0.8
N A:LEU67 4.4 17.7 1.0
NH2 A:ARG70 4.5 13.1 1.0
CG A:ASN64 4.5 36.6 1.0
CD2 A:LEU67 4.6 21.6 1.0
O A:HOH447 4.6 35.9 1.0
CBD A:1R0202 4.6 61.8 1.0
CB A:LEU67 4.7 14.5 1.0
N A:ARG65 4.9 23.2 1.0
CAJ A:1R0202 4.9 38.2 1.0
O A:LEU67 5.0 14.1 1.0

Magnesium binding site 2 out of 5 in 4kfj

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


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- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:26.0
occ:1.00
 O A:GLU143 2.7 14.1 1.0
O A:PRO23 2.9 13.4 1.0
O A:HOH411 3.2 33.8 1.0
OE1 A:GLU143 3.3 41.7 1.0
CB A:GLU143 3.5 16.9 1.0
N A:GLU143 3.5 12.5 1.0
C A:GLU143 3.6 11.0 1.0
CD A:GLU143 3.7 60.1 1.0
C A:PRO23 3.8 16.2 1.0
CA A:GLU143 3.8 14.3 1.0
CA A:PRO23 3.8 8.3 1.0
CB A:PRO23 4.0 9.3 1.0
CB B:PRO163 4.0 23.1 1.0
CG A:LYS18 4.1 21.5 1.0
CG A:GLU143 4.2 31.9 1.0
OE2 A:GLU143 4.3 58.0 1.0
CB A:PHE142 4.3 15.8 1.0
C A:PHE142 4.3 16.1 1.0
CB A:LYS18 4.4 16.6 1.0
CD1 A:PHE142 4.6 8.9 1.0
CA A:PHE142 4.7 9.1 1.0
CD A:LYS18 4.8 21.8 1.0
N A:SER144 4.9 15.2 1.0
CG A:PHE142 5.0 9.2 1.0

Magnesium binding site 3 out of 5 in 4kfj

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


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- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:35.8
occ:1.00
 O B:HOH412 2.6 15.2 1.0
OD1 B:ASP21 2.9 18.8 1.0
O B:SER59 3.0 15.2 1.0
O B:HOH345 3.2 24.2 1.0
C13 B:FOL202 3.5 22.2 1.0
CG B:ASP21 3.9 26.4 1.0
C B:SER59 3.9 17.3 1.0
OG B:SER59 4.0 10.7 1.0
O B:HOH433 4.1 27.4 1.0
CB B:SER59 4.2 14.2 1.0
CG B:LEU22 4.3 15.2 1.0
C12 B:FOL202 4.3 20.6 1.0
CA B:ASP21 4.3 13.5 1.0
N10 B:FOL202 4.4 14.7 1.0
O2D B:NDP201 4.4 8.5 1.0
N B:LEU22 4.4 9.8 1.0
C14 B:FOL202 4.4 17.6 1.0
CA B:SER59 4.6 12.5 1.0
OD2 B:ASP21 4.6 28.4 1.0
CD2 B:LEU22 4.7 12.7 1.0
CB B:ASP21 4.7 15.9 1.0
C B:ASP21 4.7 9.0 1.0
N B:ILE60 4.8 11.0 1.0
CD1 B:LEU22 4.9 17.5 1.0
O B:GLY20 4.9 15.4 1.0
CD B:PRO61 4.9 20.1 1.0

Magnesium binding site 4 out of 5 in 4kfj

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


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- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:35.6
occ:1.00
 N B:SER41 2.9 13.3 1.0
O B:SER41 3.0 14.9 1.0
C B:SER41 3.7 15.1 1.0
CA B:THR40 3.7 17.6 1.0
CA B:SER41 3.8 15.0 1.0
C B:THR40 3.8 12.8 1.0
O B:THR39 3.8 12.3 1.0
CB B:SER41 4.2 18.1 1.0
CG2 B:THR40 4.4 14.9 1.0
C B:THR39 4.5 12.7 1.0
N B:THR40 4.6 15.1 1.0
CB B:THR40 4.6 8.6 1.0
O B:HOH466 4.6 31.8 1.0
O B:HOH314 4.6 12.9 1.0
N B:SER42 4.9 20.5 1.0
OG1 B:THR40 5.0 14.2 1.0
O B:THR40 5.0 14.7 1.0
CG2 B:THR39 5.0 11.3 1.0

Magnesium binding site 5 out of 5 in 4kfj

Go back to Magnesium Binding Sites List in 4kfj
Magnesium binding site 5 out of 5 in the Human Dihydrofolate Reductase Complexed with Nadph and 5-{3-[3- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine


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- Methoxy-5-(Isoquin-5-Yl)Phenyl]Prop-1-Yn-1-Yl}6-Ethylprimidine-2,4- Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:31.5
occ:1.00
 O B:HOH383 2.8 20.7 1.0
O B:TYR156 3.0 16.0 1.0
O B:LEU153 3.1 19.2 1.0
CB B:LEU153 3.4 19.7 1.0
C B:LEU153 3.9 13.7 1.0
CA B:LEU153 3.9 9.6 1.0
CA B:LYS157 3.9 14.9 1.0
CD2 B:LEU153 4.0 20.6 1.0
C B:TYR156 4.0 14.8 1.0
CG B:LEU153 4.1 18.7 1.0
CD1 B:LEU153 4.2 21.4 1.0
N B:LYS157 4.4 11.5 1.0
CG B:LYS157 4.6 34.8 1.0
CB B:LYS157 4.7 17.1 1.0
N B:LEU158 4.7 10.2 1.0
C B:LYS157 4.9 16.0 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: Mon Dec 14 19:02:32 2020

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