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Magnesium in PDB 7k72: Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad

Enzymatic activity of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad

All present enzymatic activity of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad:
6.5.1.2;

Protein crystallography data

The structure of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad, PDB code: 7k72 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.59 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.940, 63.810, 120.730, 96.22, 89.55, 111.97
R / Rfree (%) 16.8 / 20.6

Other elements in 7k72:

The structure of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad (pdb code 7k72). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad, PDB code: 7k72:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7k72

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Magnesium binding site 1 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:22.3
occ:1.00
 O1A A:NAD401 2.0 23.7 1.0
O A:HOH569 2.1 16.5 1.0
O A:HOH590 2.2 20.6 1.0
O A:HOH637 2.2 23.7 1.0
O A:HOH571 2.2 20.4 1.0
O A:HOH554 2.3 23.4 1.0
PA A:NAD401 3.5 25.9 1.0
NZ A:LYS123 3.6 31.5 1.0
O2N A:NAD401 3.9 25.7 1.0
O A:HOH623 4.0 18.5 1.0
OD1 A:ASP295 4.1 37.9 1.0
OH A:TYR31 4.1 18.6 1.0
OD1 A:ASP125 4.1 24.4 1.0
O A:HOH532 4.2 20.3 1.0
OE1 A:GLU184 4.2 24.1 1.0
C4B A:NAD401 4.3 19.0 1.0
O2A A:NAD401 4.3 28.9 1.0
O A:GLY126 4.3 19.0 1.0
O4B A:NAD401 4.3 21.1 1.0
O3 A:NAD401 4.4 25.6 1.0
C4D A:NAD401 4.4 25.6 1.0
O5B A:NAD401 4.5 24.0 1.0
O A:ILE124 4.5 22.1 1.0
O3D A:NAD401 4.5 32.2 1.0
C1B A:NAD401 4.6 21.2 1.0
PN A:NAD401 4.7 25.2 1.0
CE A:LYS123 4.8 32.5 1.0
CA A:ASP125 4.8 24.5 1.0
O4D A:NAD401 4.9 22.6 1.0
O A:HOH533 4.9 23.1 1.0
N A:GLY126 4.9 19.1 1.0
C5B A:NAD401 5.0 21.9 1.0

Magnesium binding site 2 out of 9 in 7k72

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Magnesium binding site 2 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.9
occ:1.00
 O A:HOH724 2.2 41.6 1.0
OE1 A:GLU26 2.5 37.0 1.0
O C:HOH644 2.6 41.0 1.0
OE2 A:GLU26 2.7 36.8 1.0
O A:HOH718 2.8 43.5 1.0
O A:HOH757 2.8 41.9 1.0
CD A:GLU26 3.0 38.5 1.0
OE1 A:GLU23 4.5 35.9 1.0
O A:HOH615 4.5 43.2 1.0
CG A:GLU26 4.5 30.4 1.0
OE2 A:GLU23 4.6 42.6 1.0
NH2 A:ARG30 4.6 29.9 1.0
CD1 A:ILE38 4.9 27.1 0.3
OE2 C:GLU22 4.9 55.3 1.0
OE1 C:GLU22 4.9 62.2 1.0
CD A:GLU23 4.9 37.3 1.0

Magnesium binding site 3 out of 9 in 7k72

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Magnesium binding site 3 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:27.1
occ:1.00
 O B:HOH664 2.1 30.8 1.0
O1A B:NAD401 2.1 27.3 1.0
O B:HOH541 2.1 20.6 1.0
O B:HOH596 2.2 22.5 1.0
O B:HOH548 2.2 22.8 1.0
O B:HOH601 2.4 27.1 1.0
PA B:NAD401 3.6 28.0 1.0
O2N B:NAD401 3.9 34.0 1.0
NZ B:LYS123 3.9 31.2 1.0
O B:HOH593 4.0 27.6 1.0
O B:GLY126 4.2 24.1 1.0
OH B:TYR31 4.2 29.1 1.0
OD2 B:ASP295 4.2 44.0 1.0
OD1 B:ASP125 4.2 34.9 1.0
OE1 B:GLU184 4.2 25.2 1.0
O B:HOH529 4.3 26.2 1.0
C4B B:NAD401 4.3 22.2 1.0
O4B B:NAD401 4.3 22.3 1.0
O2A B:NAD401 4.4 34.0 1.0
C4D B:NAD401 4.4 32.1 1.0
O3 B:NAD401 4.4 27.4 1.0
O B:ILE124 4.5 23.5 1.0
O5B B:NAD401 4.6 23.9 1.0
C1B B:NAD401 4.7 21.8 1.0
PN B:NAD401 4.7 32.0 1.0
O3D B:NAD401 4.7 42.4 1.0
O4D B:NAD401 4.8 26.2 1.0
O B:HOH530 4.9 30.3 1.0
CA B:ASP125 4.9 28.3 1.0
N B:GLY126 4.9 23.8 1.0

Magnesium binding site 4 out of 9 in 7k72

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Magnesium binding site 4 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:40.5
occ:1.00
 O B:HOH728 2.1 50.3 1.0
O B:HOH501 2.3 45.4 1.0
O B:ARG158 2.4 39.2 1.0
O B:HOH589 2.6 38.1 1.0
O B:HOH672 2.7 42.7 1.0
C B:ARG158 3.6 33.1 1.0
OE1 B:GLU165 4.0 46.8 1.0
CA B:ARG158 4.2 35.7 1.0
O B:VAL163 4.4 29.6 1.0
CB B:ARG158 4.5 36.8 1.0
O B:HOH619 4.5 40.9 1.0
N B:THR159 4.6 31.7 1.0
O B:ILE160 4.7 35.4 1.0
CA B:THR159 4.9 31.6 1.0
CB B:GLU165 4.9 36.9 1.0

Magnesium binding site 5 out of 9 in 7k72

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Magnesium binding site 5 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:29.8
occ:1.00
 O1A C:NAD401 1.9 31.6 1.0
O C:HOH585 2.0 35.8 1.0
O C:HOH545 2.1 28.6 1.0
O C:HOH526 2.2 28.5 1.0
O C:HOH530 2.2 31.8 1.0
O C:HOH574 2.3 32.0 1.0
PA C:NAD401 3.4 39.9 1.0
O2N C:NAD401 3.7 37.5 1.0
NZ C:LYS123 3.9 39.2 1.0
O C:HOH535 4.0 34.7 1.0
O2A C:NAD401 4.1 41.0 1.0
OD1 C:ASP125 4.2 37.0 1.0
OE2 C:GLU184 4.2 30.6 1.0
OH C:TYR31 4.2 33.4 1.0
O C:HOH553 4.2 28.9 1.0
O C:GLY126 4.2 28.7 1.0
O3 C:NAD401 4.3 37.5 1.0
C4B C:NAD401 4.3 31.1 1.0
O4B C:NAD401 4.4 34.1 1.0
OD2 C:ASP295 4.4 51.5 1.0
C4D C:NAD401 4.4 36.5 1.0
O5B C:NAD401 4.4 31.9 1.0
O C:ILE124 4.6 32.4 1.0
PN C:NAD401 4.6 37.6 1.0
C1B C:NAD401 4.7 31.5 1.0
O3D C:NAD401 4.8 42.3 1.0
O4D C:NAD401 4.8 31.4 1.0
CA C:ASP125 4.8 31.4 1.0
O C:HOH521 4.9 29.2 1.0
N C:GLY126 4.9 29.9 1.0
C5B C:NAD401 5.0 30.9 1.0
CE C:LYS123 5.0 41.4 1.0

Magnesium binding site 6 out of 9 in 7k72

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Magnesium binding site 6 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:27.9
occ:1.00
 OH C:TYR32 2.9 30.3 1.0
O C:HOH630 3.0 50.0 1.0
NE2 C:GLN28 3.3 26.6 1.0
O C:HOH540 3.3 37.6 1.0
CE2 C:TYR32 3.4 24.8 1.0
O5D C:NAD401 3.5 39.4 1.0
CZ C:TYR32 3.6 30.3 1.0
CE2 C:PHE44 3.7 32.4 1.0
C6N C:NAD401 3.7 27.9 1.0
CA C:GLY72 3.8 30.8 1.0
CZ C:PHE44 3.8 28.9 1.0
CG C:GLN28 4.0 28.1 1.0
C5N C:NAD401 4.0 31.8 1.0
C5D C:NAD401 4.0 37.1 1.0
CD C:GLN28 4.1 32.9 1.0
N C:GLY72 4.5 31.3 1.0
O1N C:NAD401 4.6 38.6 1.0
CD2 C:TYR32 4.6 27.4 1.0
O4D C:NAD401 4.7 31.4 1.0
C C:GLY72 4.9 34.4 1.0
PN C:NAD401 4.9 37.6 1.0
CD2 C:PHE44 4.9 32.7 1.0
N1N C:NAD401 4.9 32.6 1.0
O C:HOH550 4.9 33.5 1.0
CE1 C:TYR32 4.9 28.5 1.0
C4D C:NAD401 4.9 36.5 1.0

Magnesium binding site 7 out of 9 in 7k72

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Magnesium binding site 7 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:32.7
occ:1.00
 O1A D:NAD401 2.1 37.6 1.0
O D:HOH522 2.2 30.4 1.0
O D:HOH549 2.2 27.7 1.0
O D:HOH568 2.2 38.1 1.0
O D:HOH559 2.2 36.3 1.0
O D:HOH510 2.4 31.0 1.0
PA D:NAD401 3.6 40.1 1.0
NZ D:LYS123 3.9 50.4 1.0
O2N D:NAD401 3.9 40.9 1.0
O D:HOH550 4.1 30.0 1.0
OH D:TYR31 4.2 34.8 1.0
OD1 D:ASP125 4.2 35.8 1.0
O D:GLY126 4.2 30.4 1.0
O D:HOH524 4.2 31.3 1.0
OE1 D:GLU184 4.3 32.6 1.0
OD2 D:ASP295 4.3 51.5 1.0
O2A D:NAD401 4.4 47.8 1.0
C4B D:NAD401 4.4 29.0 1.0
O3 D:NAD401 4.4 33.4 1.0
C4D D:NAD401 4.5 38.7 1.0
O4B D:NAD401 4.5 34.6 1.0
O3D D:NAD401 4.6 41.4 1.0
O5B D:NAD401 4.6 36.1 1.0
O D:ILE124 4.7 37.2 1.0
O D:HOH539 4.7 39.2 1.0
C1B D:NAD401 4.7 33.1 1.0
PN D:NAD401 4.8 39.3 1.0
O4D D:NAD401 4.9 38.4 1.0
CA D:ASP125 4.9 36.1 1.0
N D:GLY126 5.0 32.2 1.0
CE D:LYS123 5.0 44.7 1.0

Magnesium binding site 8 out of 9 in 7k72

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Magnesium binding site 8 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:30.2
occ:1.00
 O D:HOH590 2.2 44.2 1.0
O D:HOH613 2.3 43.3 1.0
OE1 D:GLU26 2.5 40.7 1.0
O D:HOH513 2.5 39.7 1.0
OE2 D:GLU26 2.6 39.2 1.0
O D:HOH620 2.8 39.0 1.0
O D:HOH626 2.8 48.6 1.0
CD D:GLU26 2.9 41.1 1.0
CG D:GLU26 4.4 36.1 1.0
NH2 D:ARG30 4.4 38.4 1.0
OE1 D:GLU23 4.5 55.9 1.0
OE2 D:GLU23 4.6 50.3 1.0
CD D:GLU23 5.0 48.5 1.0

Magnesium binding site 9 out of 9 in 7k72

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Magnesium binding site 9 out of 9 in the Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:29.8
occ:1.00
 OH D:TYR32 2.8 34.9 1.0
NE2 D:GLN28 3.2 34.4 1.0
O D:HOH505 3.3 37.5 1.0
CE2 D:TYR32 3.4 31.6 1.0
O5D D:NAD401 3.5 41.6 1.0
CZ D:TYR32 3.5 34.1 1.0
C6N D:NAD401 3.7 34.0 1.0
CA D:GLY72 3.7 29.8 1.0
CE2 D:PHE44 3.8 31.7 1.0
CZ D:PHE44 3.8 35.1 1.0
C5N D:NAD401 3.9 31.6 1.0
C5D D:NAD401 3.9 35.8 1.0
CG D:GLN28 4.0 28.2 1.0
CD D:GLN28 4.1 39.1 1.0
N D:GLY72 4.4 34.0 1.0
O1N D:NAD401 4.6 33.2 1.0
O4D D:NAD401 4.6 38.4 1.0
CD2 D:TYR32 4.7 27.1 1.0
O D:HOH617 4.8 40.2 1.0
O D:HOH538 4.8 30.4 1.0
C D:GLY72 4.8 32.5 1.0
PN D:NAD401 4.8 39.3 1.0
N1N D:NAD401 4.9 36.8 1.0
CE1 D:TYR32 4.9 32.2 1.0
C4D D:NAD401 4.9 38.7 1.0
CD2 D:PHE44 4.9 31.2 1.0

Reference:

S.L.Delker, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Structure of Dna Ligase A From Mycobacterium Tuberculosis Bound to Nad To Be Published.
Page generated: Wed Oct 2 22:09:23 2024

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