Magnesium in PDB 6f56: Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa
Enzymatic activity of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa
All present enzymatic activity of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa:
2.3.1.97;
Protein crystallography data
The structure of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa, PDB code: 6f56
was solved by
R.Brenk,
J.Kehrein,
C.Kersten,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
87.50 /
1.94
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.190,
159.130,
174.990,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20 /
23.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa
(pdb code 6f56). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa, PDB code: 6f56:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6f56
Go back to
Magnesium Binding Sites List in 6f56
Magnesium binding site 1 out
of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:42.7
occ:1.00
|
O
|
A:LEU254
|
2.6
|
32.0
|
1.0
|
N
|
A:LYS257
|
2.8
|
36.6
|
1.0
|
O4A
|
A:MYA501
|
3.0
|
32.0
|
1.0
|
O2A
|
A:MYA501
|
3.1
|
30.8
|
1.0
|
N
|
A:VAL259
|
3.2
|
31.0
|
1.0
|
N
|
A:ARG258
|
3.4
|
38.6
|
1.0
|
N
|
A:SER256
|
3.4
|
37.2
|
1.0
|
CA
|
A:LYS257
|
3.4
|
33.5
|
1.0
|
C
|
A:LYS257
|
3.4
|
37.0
|
1.0
|
CB
|
A:VAL259
|
3.5
|
30.3
|
1.0
|
CG2
|
A:VAL259
|
3.6
|
34.8
|
1.0
|
CB
|
A:LYS257
|
3.6
|
36.2
|
1.0
|
C
|
A:ARG255
|
3.6
|
38.6
|
1.0
|
C
|
A:LEU254
|
3.7
|
31.4
|
1.0
|
CA
|
A:ARG255
|
3.9
|
31.8
|
1.0
|
C
|
A:SER256
|
3.9
|
37.3
|
1.0
|
CA
|
A:VAL259
|
3.9
|
31.2
|
1.0
|
P1A
|
A:MYA501
|
4.0
|
33.4
|
1.0
|
CG1
|
A:VAL250
|
4.0
|
34.6
|
1.0
|
CA
|
A:SER256
|
4.1
|
32.8
|
1.0
|
O1A
|
A:MYA501
|
4.1
|
36.2
|
1.0
|
O
|
A:LYS257
|
4.2
|
34.3
|
1.0
|
C
|
A:ARG258
|
4.2
|
35.5
|
1.0
|
N
|
A:ARG255
|
4.3
|
33.1
|
1.0
|
CA
|
A:ARG258
|
4.3
|
35.4
|
1.0
|
O
|
A:ARG255
|
4.3
|
39.5
|
1.0
|
P2A
|
A:MYA501
|
4.3
|
36.1
|
1.0
|
CG
|
A:LYS257
|
4.4
|
37.7
|
1.0
|
N
|
A:ALA260
|
4.5
|
28.1
|
1.0
|
O3A
|
A:MYA501
|
4.6
|
32.2
|
1.0
|
C
|
A:VAL259
|
4.7
|
30.8
|
1.0
|
O6A
|
A:MYA501
|
4.8
|
37.6
|
1.0
|
CG1
|
A:VAL259
|
4.8
|
27.1
|
1.0
|
CB
|
A:VAL250
|
4.9
|
32.7
|
1.0
|
CA
|
A:LEU254
|
4.9
|
30.5
|
1.0
|
CG2
|
A:VAL250
|
5.0
|
28.8
|
1.0
|
CB
|
A:LEU254
|
5.0
|
30.1
|
1.0
|
O
|
A:SER256
|
5.0
|
35.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6f56
Go back to
Magnesium Binding Sites List in 6f56
Magnesium binding site 2 out
of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:40.8
occ:1.00
|
O2A
|
B:MYA501
|
2.7
|
28.5
|
1.0
|
N
|
B:VAL259
|
2.8
|
27.9
|
1.0
|
N
|
B:LYS257
|
2.9
|
42.0
|
1.0
|
O
|
B:LEU254
|
2.9
|
33.5
|
1.0
|
O4A
|
B:MYA501
|
3.0
|
35.2
|
1.0
|
N
|
B:ARG258
|
3.0
|
32.9
|
1.0
|
C
|
B:LYS257
|
3.3
|
40.6
|
1.0
|
CB
|
B:VAL259
|
3.3
|
28.8
|
1.0
|
CA
|
B:LYS257
|
3.4
|
36.8
|
1.0
|
CG2
|
B:VAL259
|
3.5
|
32.4
|
1.0
|
N
|
B:SER256
|
3.6
|
38.6
|
1.0
|
CA
|
B:VAL259
|
3.6
|
31.9
|
1.0
|
P1A
|
B:MYA501
|
3.7
|
29.2
|
1.0
|
C
|
B:ARG258
|
3.7
|
31.8
|
1.0
|
CB
|
B:LYS257
|
3.8
|
36.1
|
1.0
|
CA
|
B:ARG258
|
3.8
|
35.5
|
1.0
|
C
|
B:ARG255
|
3.9
|
38.5
|
1.0
|
O1A
|
B:MYA501
|
3.9
|
33.4
|
1.0
|
C
|
B:SER256
|
4.0
|
41.5
|
1.0
|
C
|
B:LEU254
|
4.1
|
34.7
|
1.0
|
O
|
B:LYS257
|
4.1
|
40.9
|
1.0
|
CA
|
B:ARG255
|
4.1
|
33.3
|
1.0
|
N
|
B:ALA260
|
4.2
|
22.3
|
1.0
|
CG1
|
B:VAL250
|
4.2
|
25.5
|
1.0
|
CA
|
B:SER256
|
4.2
|
35.4
|
1.0
|
P2A
|
B:MYA501
|
4.2
|
32.9
|
1.0
|
O3A
|
B:MYA501
|
4.4
|
27.4
|
1.0
|
C
|
B:VAL259
|
4.4
|
30.9
|
1.0
|
CG
|
B:LYS257
|
4.5
|
38.8
|
1.0
|
O
|
B:ARG255
|
4.6
|
38.9
|
1.0
|
N
|
B:ARG255
|
4.6
|
32.6
|
1.0
|
CG1
|
B:VAL259
|
4.7
|
27.0
|
1.0
|
O6A
|
B:MYA501
|
4.7
|
32.8
|
1.0
|
O
|
B:ARG258
|
4.9
|
34.5
|
1.0
|
CG2
|
B:VAL250
|
4.9
|
24.6
|
1.0
|
CB
|
B:VAL250
|
5.0
|
25.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6f56
Go back to
Magnesium Binding Sites List in 6f56
Magnesium binding site 3 out
of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:50.3
occ:1.00
|
N
|
C:LYS257
|
2.7
|
41.7
|
1.0
|
O
|
C:LEU254
|
2.8
|
40.6
|
1.0
|
O4A
|
C:MYA501
|
2.8
|
41.3
|
1.0
|
O2A
|
C:MYA501
|
2.9
|
45.7
|
1.0
|
N
|
C:ARG258
|
2.9
|
43.4
|
1.0
|
N
|
C:VAL259
|
3.0
|
41.5
|
1.0
|
C
|
C:LYS257
|
3.2
|
44.4
|
1.0
|
N
|
C:SER256
|
3.3
|
44.5
|
1.0
|
CA
|
C:LYS257
|
3.3
|
45.5
|
1.0
|
C
|
C:ARG255
|
3.6
|
46.5
|
1.0
|
CB
|
C:VAL259
|
3.7
|
40.7
|
1.0
|
C
|
C:SER256
|
3.7
|
46.3
|
1.0
|
CB
|
C:LYS257
|
3.8
|
41.7
|
1.0
|
P1A
|
C:MYA501
|
3.8
|
42.6
|
1.0
|
O1A
|
C:MYA501
|
3.8
|
47.1
|
1.0
|
CA
|
C:ARG258
|
3.8
|
43.4
|
1.0
|
CG2
|
C:VAL259
|
3.9
|
40.9
|
1.0
|
CA
|
C:VAL259
|
3.9
|
38.1
|
1.0
|
CA
|
C:ARG255
|
3.9
|
41.8
|
1.0
|
C
|
C:LEU254
|
3.9
|
35.2
|
1.0
|
CA
|
C:SER256
|
3.9
|
48.3
|
1.0
|
C
|
C:ARG258
|
3.9
|
42.6
|
1.0
|
O
|
C:LYS257
|
4.1
|
44.7
|
1.0
|
P2A
|
C:MYA501
|
4.1
|
43.1
|
1.0
|
O
|
C:ARG255
|
4.2
|
47.7
|
1.0
|
N
|
C:ALA260
|
4.3
|
40.1
|
1.0
|
CG1
|
C:VAL250
|
4.3
|
33.3
|
1.0
|
O3A
|
C:MYA501
|
4.4
|
31.0
|
1.0
|
N
|
C:ARG255
|
4.4
|
38.6
|
1.0
|
CG
|
C:LYS257
|
4.6
|
42.0
|
1.0
|
C
|
C:VAL259
|
4.7
|
40.9
|
1.0
|
O6A
|
C:MYA501
|
4.8
|
42.5
|
1.0
|
O
|
C:SER256
|
4.8
|
48.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6f56
Go back to
Magnesium Binding Sites List in 6f56
Magnesium binding site 4 out
of 4 in the Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Mutant of Human N-Myristoyltransferase with Bound Myristoyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:47.7
occ:1.00
|
O
|
D:LEU254
|
2.4
|
43.3
|
1.0
|
N
|
D:LYS257
|
2.9
|
43.1
|
1.0
|
CG2
|
D:VAL259
|
3.1
|
42.2
|
1.0
|
N
|
D:VAL259
|
3.1
|
34.8
|
1.0
|
O2A
|
D:MYA501
|
3.2
|
43.6
|
1.0
|
CB
|
D:VAL259
|
3.2
|
41.2
|
1.0
|
O4A
|
D:MYA501
|
3.3
|
39.5
|
1.0
|
C
|
D:LYS257
|
3.3
|
42.9
|
1.0
|
CA
|
D:LYS257
|
3.4
|
43.5
|
1.0
|
N
|
D:ARG258
|
3.4
|
42.8
|
1.0
|
CB
|
D:LYS257
|
3.6
|
40.1
|
1.0
|
C
|
D:LEU254
|
3.6
|
39.5
|
1.0
|
N
|
D:SER256
|
3.6
|
47.4
|
1.0
|
CA
|
D:VAL259
|
3.8
|
38.5
|
1.0
|
C
|
D:ARG255
|
3.8
|
45.4
|
1.0
|
O
|
D:LYS257
|
3.8
|
46.3
|
1.0
|
CA
|
D:ARG255
|
3.9
|
41.3
|
1.0
|
C
|
D:SER256
|
4.1
|
45.8
|
1.0
|
C
|
D:ARG258
|
4.1
|
39.1
|
1.0
|
P1A
|
D:MYA501
|
4.2
|
39.9
|
1.0
|
CG1
|
D:VAL250
|
4.2
|
37.2
|
1.0
|
O1A
|
D:MYA501
|
4.2
|
40.0
|
1.0
|
N
|
D:ARG255
|
4.2
|
42.0
|
1.0
|
CA
|
D:ARG258
|
4.3
|
40.8
|
1.0
|
CA
|
D:SER256
|
4.4
|
45.4
|
1.0
|
O
|
D:ARG255
|
4.4
|
39.1
|
1.0
|
N
|
D:ALA260
|
4.5
|
33.2
|
1.0
|
P2A
|
D:MYA501
|
4.5
|
41.8
|
1.0
|
CG1
|
D:VAL259
|
4.6
|
38.3
|
1.0
|
C
|
D:VAL259
|
4.7
|
33.2
|
1.0
|
CB
|
D:LEU254
|
4.8
|
40.1
|
1.0
|
CA
|
D:LEU254
|
4.8
|
41.9
|
1.0
|
O3A
|
D:MYA501
|
4.8
|
32.8
|
1.0
|
CE
|
D:LYS257
|
4.9
|
42.8
|
0.0
|
CG
|
D:LYS257
|
5.0
|
44.6
|
1.0
|
O6A
|
D:MYA501
|
5.0
|
39.0
|
1.0
|
|
Reference:
C.Kersten,
E.Fleischer,
J.Kehrein,
C.Borek,
E.Jaenicke,
C.Sotriffer,
R.Brenk.
How to Design Selective Ligands For Highly Conserved Binding Sites: A Case Study Usingn-Myristoyltransferases As A Model System. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31423787
DOI: 10.1021/ACS.JMEDCHEM.9B00586
Page generated: Tue Oct 1 00:06:35 2024
|