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:
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 Sites List in 4kbn
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 Sites List in 4kbn
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 Sites List in 4kbn
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 Sites List in 4kbn
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 Sites List in 4kbn
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 Sites List in 4kbn
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 Sites List in 4kbn
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 Sites List in 4kbn
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 Sites List in 4kbn
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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