Atomistry » Magnesium » PDB 6el4-6f5d » 6f56
Atomistry »
  Magnesium »
    PDB 6el4-6f5d »
      6f56 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy