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Magnesium in PDB 6nmm: Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate

Protein crystallography data

The structure of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate, PDB code: 6nmm was solved by M.J.Cuneo, B.Selvaraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.58 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.510, 59.250, 102.040, 90.00, 94.80, 90.00
R / Rfree (%) 17.4 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate (pdb code 6nmm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate, PDB code: 6nmm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6nmm

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Magnesium binding site 1 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:15.7
occ:1.00
 O A:HOH941 2.1 29.2 1.0
OD2 A:ASP50 2.2 28.6 1.0
OE2 D:GLU145 2.2 50.4 1.0
OE1 A:GLU52 2.3 33.0 1.0
OP2 A:A801 2.5 26.4 1.0
O A:HOH901 2.7 34.1 1.0
OE1 D:GLU145 2.7 36.6 1.0
CD D:GLU145 2.8 40.7 1.0
CG A:ASP50 3.1 26.2 1.0
P A:A801 3.3 42.0 1.0
O A:HOH908 3.3 20.0 1.0
OD1 A:ASP50 3.3 27.1 1.0
CD A:GLU52 3.3 19.4 1.0
O4 A:NMY800 3.4 31.3 1.0
CG A:GLU52 3.8 20.0 1.0
NZ A:LYS74 3.9 47.8 1.0
MG A:MG804 3.9 11.9 1.0
CG D:GLU145 4.2 35.9 1.0
OE2 A:GLU52 4.4 24.0 1.0
OP1 A:A801 4.5 45.7 1.0
O5' A:A801 4.5 36.8 1.0
CB A:ASP50 4.5 20.0 1.0
C5' A:A801 4.6 27.4 1.0
O D:HOH936 4.6 27.1 1.0
C4 A:NMY800 4.7 28.7 1.0
OE2 A:GLU76 4.8 30.4 1.0

Magnesium binding site 2 out of 8 in 6nmm

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Magnesium binding site 2 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:11.9
occ:1.00
 O32 A:PPV802 2.2 24.7 1.0
OD1 A:ASP50 2.2 27.1 1.0
O A:HOH904 2.3 31.3 1.0
O21 A:PPV802 2.4 33.5 1.0
OE1 A:GLU52 2.4 33.0 1.0
O A:HOH901 2.4 34.1 1.0
OE2 A:GLU52 2.6 24.0 1.0
CD A:GLU52 2.8 19.4 1.0
CG A:ASP50 3.4 26.2 1.0
P1 A:PPV802 3.5 27.8 1.0
P2 A:PPV802 3.6 40.1 1.0
OP2 A:A801 3.7 26.4 1.0
OG A:SER39 3.8 29.1 1.0
O11 A:PPV802 3.8 27.6 1.0
MG A:MG803 3.9 15.7 1.0
OD2 A:ASP50 3.9 28.6 1.0
OPP A:PPV802 3.9 41.5 1.0
O A:ASP50 4.0 27.1 1.0
N A:SER39 4.2 20.4 1.0
C A:ASP50 4.2 25.8 1.0
N A:ASP50 4.2 20.2 1.0
CG A:GLU52 4.3 20.0 1.0
C5' A:A801 4.4 27.4 1.0
O22 A:PPV802 4.5 25.0 1.0
O12 A:PPV802 4.5 41.4 1.0
CB A:ASP50 4.6 20.0 1.0
CA A:ASP50 4.6 21.8 1.0
CB A:SER39 4.6 16.3 1.0
OE2 D:GLU145 4.7 50.4 1.0
N A:ILE51 4.7 14.5 1.0
O31 A:PPV802 4.8 25.6 1.0
CA A:GLY38 4.8 16.4 1.0
O D:HOH936 4.9 27.1 1.0
P A:A801 4.9 42.0 1.0

Magnesium binding site 3 out of 8 in 6nmm

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Magnesium binding site 3 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:10.9
occ:1.00
 OE1 B:GLU52 2.1 35.4 1.0
O C:HOH923 2.1 33.0 1.0
OE2 C:GLU145 2.2 34.5 1.0
OD2 B:ASP50 2.3 34.2 1.0
OP2 B:A801 2.6 30.2 1.0
OE1 C:GLU145 2.8 28.1 1.0
CD C:GLU145 2.8 26.7 1.0
O4 B:NMY800 3.1 34.5 1.0
P B:A801 3.1 34.8 1.0
CG B:ASP50 3.1 23.7 1.0
CD B:GLU52 3.2 24.9 1.0
OD1 B:ASP50 3.3 27.3 1.0
MG B:MG804 3.6 13.7 1.0
CG B:GLU52 3.8 28.1 1.0
NZ B:LYS74 4.1 43.5 1.0
OP1 B:A801 4.3 38.3 1.0
OE2 B:GLU52 4.3 31.8 1.0
CG C:GLU145 4.3 25.5 1.0
C4 B:NMY800 4.3 28.3 1.0
O5' B:A801 4.4 32.5 1.0
O3 B:NMY800 4.5 32.3 1.0
C3 B:NMY800 4.6 31.0 1.0
CB B:ASP50 4.6 20.8 1.0
C5' B:A801 4.6 26.1 1.0
OE2 B:GLU76 4.8 40.0 1.0
C5 B:NMY800 4.9 33.7 1.0
NZ C:LYS149 4.9 38.4 1.0
O21 B:PPV802 4.9 25.6 1.0

Magnesium binding site 4 out of 8 in 6nmm

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Magnesium binding site 4 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:13.7
occ:1.00
 O21 B:PPV802 2.2 25.6 1.0
OD1 B:ASP50 2.2 27.3 1.0
OE1 B:GLU52 2.4 35.4 1.0
O B:HOH924 2.6 31.5 1.0
OE2 B:GLU52 2.7 31.8 1.0
O12 B:PPV802 2.7 38.3 1.0
CD B:GLU52 2.8 24.9 1.0
OP2 B:A801 3.1 30.2 1.0
CG B:ASP50 3.3 23.7 1.0
P1 B:PPV802 3.6 31.9 1.0
MG B:MG803 3.6 10.9 1.0
OD2 B:ASP50 3.9 34.2 1.0
P2 B:PPV802 4.0 47.0 1.0
O B:ASP50 4.0 19.0 1.0
OPP B:PPV802 4.2 39.8 1.0
C B:ASP50 4.2 19.3 1.0
N B:ASP50 4.2 22.0 1.0
C5' B:A801 4.2 26.1 1.0
O31 B:PPV802 4.3 39.9 1.0
O B:HOH913 4.3 16.9 1.0
OG B:SER39 4.3 33.9 1.0
CG B:GLU52 4.3 28.1 1.0
P B:A801 4.4 34.8 1.0
CB B:ASP50 4.5 20.8 1.0
OE2 C:GLU145 4.6 34.5 1.0
CA B:ASP50 4.6 24.5 1.0
N B:SER39 4.6 21.9 1.0
O11 B:PPV802 4.6 28.6 1.0
N B:ILE51 4.7 23.2 1.0
O5' B:A801 4.7 32.5 1.0
O32 B:PPV802 4.8 60.0 1.0

Magnesium binding site 5 out of 8 in 6nmm

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Magnesium binding site 5 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:7.7
occ:1.00
 O C:HOH902 2.2 19.2 1.0
OD1 C:ASP50 2.3 20.1 1.0
O21 C:PPV802 2.4 16.8 1.0
OE1 C:GLU52 2.4 24.4 1.0
O12 C:PPV802 2.5 15.6 1.0
O C:HOH904 2.5 19.2 1.0
OE2 C:GLU52 2.6 16.2 1.0
CD C:GLU52 2.8 11.2 1.0
CG C:ASP50 3.4 14.7 1.0
P1 C:PPV802 3.5 26.4 1.0
O31 C:PPV802 3.7 29.3 1.0
P2 C:PPV802 3.8 28.0 1.0
MG C:MG804 3.8 13.8 1.0
OG C:SER39 3.9 21.3 1.0
OP1 C:A801 3.9 22.9 1.0
O C:ASP50 3.9 13.8 1.0
OD2 C:ASP50 4.0 13.3 1.0
OPP C:PPV802 4.0 21.7 1.0
C C:ASP50 4.2 15.1 1.0
N C:ASP50 4.2 16.1 1.0
O C:HOH917 4.3 9.3 1.0
CG C:GLU52 4.3 16.8 1.0
N C:SER39 4.3 17.5 1.0
C5' C:A801 4.5 18.1 1.0
O32 C:PPV802 4.5 32.4 1.0
CA C:ASP50 4.6 13.7 1.0
CB C:ASP50 4.6 14.1 1.0
OE1 B:GLU145 4.6 35.4 1.0
N C:ILE51 4.7 10.7 1.0
O11 C:PPV802 4.7 18.3 1.0
CB C:SER39 4.7 10.1 1.0
O22 C:PPV802 4.9 34.1 1.0
CA C:GLY38 4.9 12.6 1.0

Magnesium binding site 6 out of 8 in 6nmm

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Magnesium binding site 6 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg804

b:13.8
occ:1.00
 O C:HOH945 2.0 26.0 1.0
OE1 B:GLU145 2.2 35.4 1.0
OE1 C:GLU52 2.3 24.4 1.0
OD2 C:ASP50 2.4 13.3 1.0
OP1 C:A801 2.4 22.9 1.0
OE2 B:GLU145 2.7 20.3 1.0
CD B:GLU145 2.8 34.4 1.0
O C:HOH902 3.0 19.2 1.0
CG C:ASP50 3.2 14.7 1.0
CD C:GLU52 3.3 11.2 1.0
O C:HOH940 3.4 26.2 1.0
OD1 C:ASP50 3.4 20.1 1.0
P C:A801 3.4 26.1 1.0
O4 C:NMY800 3.4 17.6 1.0
NZ C:LYS74 3.8 31.0 1.0
CG C:GLU52 3.8 16.8 1.0
MG C:MG803 3.8 7.7 1.0
CG B:GLU145 4.2 27.6 1.0
OE2 C:GLU52 4.4 16.2 1.0
O5' C:A801 4.4 22.6 1.0
C5' C:A801 4.4 18.1 1.0
OP2 C:A801 4.6 27.7 1.0
CB C:ASP50 4.6 14.1 1.0
O C:HOH901 4.7 30.9 1.0
O B:HOH937 4.7 18.7 1.0
C4 C:NMY800 4.7 20.7 1.0
OE2 C:GLU76 4.8 29.1 1.0
O3 C:NMY800 5.0 24.2 1.0

Magnesium binding site 7 out of 8 in 6nmm

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Magnesium binding site 7 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:24.8
occ:1.00
 OD2 D:ASP50 2.2 30.6 1.0
OE2 A:GLU145 2.4 42.7 1.0
O D:HOH907 2.4 38.3 1.0
OE1 D:GLU52 2.5 47.7 1.0
OE1 A:GLU145 2.5 33.9 1.0
OP1 D:A801 2.5 33.0 1.0
CD A:GLU145 2.8 34.7 1.0
O4 D:NMY800 3.1 38.2 1.0
CG D:ASP50 3.2 30.5 1.0
P D:A801 3.2 59.2 1.0
O D:HOH902 3.4 37.0 1.0
OD1 D:ASP50 3.4 38.2 1.0
CD D:GLU52 3.5 34.4 1.0
CG D:GLU52 3.8 30.3 1.0
NZ D:LYS74 3.9 43.9 1.0
MG D:MG804 4.0 25.0 1.0
CG A:GLU145 4.2 31.6 1.0
OP2 D:A801 4.3 45.9 1.0
C4 D:NMY800 4.4 37.9 1.0
OE2 D:GLU76 4.5 44.3 1.0
O5' D:A801 4.5 49.9 1.0
CB D:ASP50 4.6 26.0 1.0
OE2 D:GLU52 4.6 39.2 1.0
O3 D:NMY800 4.6 50.2 1.0
O A:HOH931 4.6 35.8 1.0
C3 D:NMY800 4.7 43.4 1.0
C5' D:A801 4.7 41.9 1.0
O A:HOH909 4.7 41.3 1.0
C5 D:NMY800 5.0 47.8 1.0

Magnesium binding site 8 out of 8 in 6nmm

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Magnesium binding site 8 out of 8 in the Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ternary Complex Structure of the T130K Mutant of Ant-4 with Neomycin, Ampcpp and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:25.0
occ:1.00
 OD1 D:ASP50 2.2 38.2 1.0
O D:HOH902 2.2 37.0 1.0
OE1 D:GLU52 2.3 47.7 1.0
O31 D:PPV802 2.6 39.1 1.0
OE2 D:GLU52 2.6 39.2 1.0
O22 D:PPV802 2.6 31.8 1.0
O D:HOH920 2.7 26.6 1.0
CD D:GLU52 2.7 34.4 1.0
CG D:ASP50 3.3 30.5 1.0
OP1 D:A801 3.6 33.0 1.0
P1 D:PPV802 3.7 35.3 1.0
OD2 D:ASP50 3.9 30.6 1.0
O D:ASP50 3.9 26.8 1.0
P2 D:PPV802 4.0 42.0 1.0
MG D:MG803 4.0 24.8 1.0
O11 D:PPV802 4.0 39.4 1.0
OG D:SER39 4.0 30.9 1.0
C D:ASP50 4.1 34.8 1.0
O D:HOH914 4.1 29.6 1.0
N D:ASP50 4.2 24.3 1.0
CG D:GLU52 4.2 30.3 1.0
OPP D:PPV802 4.2 63.9 1.0
C5' D:A801 4.3 41.9 1.0
N D:SER39 4.4 27.9 1.0
CA D:ASP50 4.5 25.3 1.0
CB D:ASP50 4.5 26.0 1.0
N D:ILE51 4.6 28.8 1.0
O A:HOH931 4.6 35.8 1.0
OE2 A:GLU145 4.6 42.7 1.0
O32 D:PPV802 4.8 35.9 1.0
P D:A801 4.8 59.2 1.0
CA D:GLY38 4.9 23.7 1.0
CB D:SER39 4.9 23.8 1.0
O21 D:PPV802 5.0 36.4 1.0
O5' D:A801 5.0 49.9 1.0
O12 D:PPV802 5.0 51.5 1.0

Reference:

P.Kumar, E.H.Serpersu, M.J.Cuneo. Catch and Release: A Novel Variation of the Archetypal Nucleotidyl Transfer Reaction To Be Published.
Page generated: Tue Oct 1 12:47:50 2024

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