Atomistry » Magnesium » PDB 4k6e-4kft » 4kfj
Atomistry »
  Magnesium »
    PDB 4k6e-4kft »
      4kfj »

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

Go back to Magnesium Binding Sites List in 4kfj
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

Go back to Magnesium Binding Sites List in 4kfj
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

Go back to Magnesium Binding Sites List in 4kfj
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

Go back to Magnesium Binding Sites List in 4kfj
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: Sat Aug 17 03:34:23 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy