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Magnesium in PDB 2xja: Structure of Mure From M.Tuberculosis with Dipeptide and Adp

Enzymatic activity of Structure of Mure From M.Tuberculosis with Dipeptide and Adp

All present enzymatic activity of Structure of Mure From M.Tuberculosis with Dipeptide and Adp:
6.3.2.13;

Protein crystallography data

The structure of Structure of Mure From M.Tuberculosis with Dipeptide and Adp, PDB code: 2xja was solved by C.Basavannacharya, P.R.Moody, S.Bhakta, N.Keep, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.30 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.040, 76.320, 81.990, 111.32, 91.42, 92.90
R / Rfree (%) 18.9 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp (pdb code 2xja). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp, PDB code: 2xja:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2xja

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Magnesium binding site 1 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1534

b:48.6
occ:1.00
 OE1 A:GLU220 1.9 38.6 1.0
O3B A:ADP1533 1.9 56.9 1.0
OG1 A:THR180 2.1 41.3 1.0
OG1 A:THR158 2.1 38.4 1.0
CD A:GLU220 2.9 34.3 1.0
O A:HOH2001 2.9 23.3 1.0
OE2 A:GLU220 3.2 33.0 1.0
PB A:ADP1533 3.3 57.8 1.0
CB A:THR180 3.3 40.3 1.0
CB A:THR158 3.5 37.1 1.0
O1B A:ADP1533 3.6 56.4 1.0
N A:THR158 3.9 31.4 1.0
CG2 A:THR180 3.9 40.6 1.0
NH2 A:ARG377 4.1 73.8 1.0
CA A:THR158 4.1 34.9 1.0
O2A A:ADP1533 4.2 78.4 1.0
CG A:GLU220 4.2 30.8 1.0
O3A A:ADP1533 4.3 64.9 1.0
CG2 A:THR195 4.3 39.5 1.0
CE A:LYS157 4.4 26.2 1.0
O20 A:UAG1536 4.4 47.1 1.0
O2B A:ADP1533 4.4 60.9 1.0
N A:THR180 4.4 40.0 1.0
CA A:THR180 4.5 40.2 1.0
CG2 A:THR158 4.5 39.4 1.0
CB A:LYS157 4.6 26.9 1.0
OG1 A:THR195 4.7 52.3 1.0
NZ A:LYS157 4.8 28.2 1.0
C A:LYS157 4.8 30.0 1.0
PA A:ADP1533 4.9 74.0 1.0

Magnesium binding site 2 out of 10 in 2xja

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Magnesium binding site 2 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1535

b:37.7
occ:1.00
 NE2 A:HIS248 2.1 44.1 1.0
O21 A:UAG1536 2.2 42.9 1.0
CD2 A:HIS248 2.9 44.5 1.0
OD2 A:ASP247 3.1 54.7 1.0
CE1 A:HIS248 3.2 42.2 1.0
C27 A:UAG1536 3.3 48.2 1.0
OQ2 A:KCX262 3.6 39.7 1.0
NZ A:LYS157 3.8 28.2 1.0
O A:HOH2001 3.8 23.3 1.0
OQ1 A:KCX262 3.8 39.0 1.0
O A:THR154 3.9 34.6 1.0
C26 A:UAG1536 4.1 45.8 1.0
CG A:HIS248 4.1 45.1 1.0
CG A:ASP247 4.2 56.2 1.0
CX A:KCX262 4.2 38.6 1.0
ND1 A:HIS248 4.2 43.6 1.0
O20 A:UAG1536 4.3 47.1 1.0
OH A:TYR258 4.4 57.3 1.0
CB A:ASP247 4.8 56.0 1.0
C A:THR154 4.8 34.5 1.0
CA A:THR154 5.0 33.7 1.0

Magnesium binding site 3 out of 10 in 2xja

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Magnesium binding site 3 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1533

b:30.3
occ:1.00
 O B:GLY140 2.2 52.5 1.0
OD1 D:ASP215 2.9 44.4 1.0
C B:GLY140 3.3 45.4 1.0
CG D:ASP215 3.5 47.5 1.0
CB D:ASP215 3.8 48.2 1.0
CA B:GLY140 4.0 46.4 1.0
CD B:ARG145 4.1 59.6 1.0
OD2 D:ASP215 4.3 56.2 1.0
NE B:ARG145 4.4 62.1 1.0
N B:HIS141 4.4 40.9 1.0
CB B:HIS141 4.4 41.0 1.0
O B:HIS141 4.4 43.5 1.0
NE D:ARG173 4.6 49.5 1.0
C B:HIS141 4.7 42.5 1.0
CG B:ARG145 4.7 53.3 1.0
CA B:HIS141 4.7 40.0 1.0
NH2 D:ARG173 4.9 46.6 1.0
CZ D:ARG173 5.0 47.4 1.0

Magnesium binding site 4 out of 10 in 2xja

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Magnesium binding site 4 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1535

b:46.5
occ:1.00
 O3B B:ADP1534 1.9 46.8 1.0
OG1 B:THR180 2.1 40.0 1.0
O B:HOH2001 2.4 20.4 1.0
O1B B:ADP1534 2.5 51.2 1.0
PB B:ADP1534 2.5 44.7 1.0
OE1 B:GLU220 2.6 38.3 1.0
OG1 B:THR158 2.6 31.0 1.0
CB B:THR180 3.3 42.2 1.0
O2A B:ADP1534 3.4 54.5 1.0
CD B:GLU220 3.7 40.3 1.0
O3A B:ADP1534 3.7 51.3 1.0
CG2 B:THR180 3.8 46.0 1.0
O2B B:ADP1534 3.8 41.8 1.0
NH2 B:ARG377 3.9 47.3 1.0
CB B:THR158 4.0 31.2 1.0
OE2 B:GLU220 4.2 46.2 1.0
PA B:ADP1534 4.3 56.7 1.0
O20 B:UAG1536 4.4 40.0 1.0
N B:THR158 4.4 26.9 1.0
CG2 B:THR195 4.5 44.3 1.0
OG1 B:THR195 4.6 50.2 1.0
CE B:LYS157 4.6 25.7 1.0
CA B:THR180 4.6 39.3 1.0
CA B:THR158 4.7 27.9 1.0
NZ B:LYS157 4.7 26.7 1.0
N B:THR180 4.8 37.2 1.0
CG B:GLU220 5.0 36.2 1.0
CE2 B:TYR393 5.0 67.1 1.0
CG2 B:THR158 5.0 33.2 1.0

Magnesium binding site 5 out of 10 in 2xja

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Magnesium binding site 5 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1537

b:39.8
occ:1.00
 NE2 B:HIS248 2.1 45.8 1.0
O21 B:UAG1536 2.2 41.5 1.0
CD2 B:HIS248 2.9 45.7 1.0
CE1 B:HIS248 3.1 45.6 1.0
C27 B:UAG1536 3.1 40.8 1.0
OQ1 B:KCX262 3.4 36.9 1.0
NZ B:LYS157 3.5 26.7 1.0
OQ2 B:KCX262 3.5 41.5 1.0
O20 B:UAG1536 3.6 40.0 1.0
O B:HOH2001 3.8 20.4 1.0
OD2 B:ASP247 3.9 48.0 1.0
CX B:KCX262 3.9 37.2 1.0
CG B:HIS248 4.1 45.3 1.0
ND1 B:HIS248 4.1 44.6 1.0
C26 B:UAG1536 4.2 41.8 1.0
O B:THR154 4.4 32.4 1.0
OH B:TYR258 4.6 55.6 1.0
CE B:LYS157 4.7 25.7 1.0
CG B:ASP247 4.9 49.6 1.0
C25 B:UAG1536 4.9 40.8 1.0

Magnesium binding site 6 out of 10 in 2xja

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Magnesium binding site 6 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1534

b:60.6
occ:1.00
 O3B C:ADP1533 1.9 53.1 1.0
OG1 C:THR180 2.1 42.5 1.0
OE1 C:GLU220 2.5 46.1 1.0
O C:HOH2001 2.5 27.0 1.0
OG1 C:THR158 2.8 33.5 1.0
PB C:ADP1533 3.0 53.2 1.0
CB C:THR180 3.3 37.5 1.0
O20 C:UAG1535 3.4 47.4 1.0
O1B C:ADP1533 3.4 55.1 1.0
CD C:GLU220 3.5 43.2 1.0
CG2 C:THR180 3.6 39.8 1.0
O2B C:ADP1533 3.7 56.5 1.0
OE2 C:GLU220 3.9 47.0 1.0
OG1 C:THR195 4.1 44.8 1.0
NH2 C:ARG377 4.2 64.4 1.0
CG2 C:THR195 4.2 36.2 1.0
CB C:THR158 4.2 34.7 1.0
CE C:LYS157 4.4 31.5 1.0
C27 C:UAG1535 4.4 51.3 1.0
O3A C:ADP1533 4.5 57.2 1.0
CA C:THR180 4.5 35.4 1.0
O2A C:ADP1533 4.5 53.4 1.0
NZ C:LYS157 4.6 35.1 1.0
N C:THR158 4.6 31.9 1.0
N C:THR180 4.7 32.3 1.0
CB C:THR195 4.8 39.3 1.0
CG C:GLU220 4.9 37.2 1.0
CA C:THR158 4.9 33.7 1.0
O21 C:UAG1535 5.0 47.8 1.0

Magnesium binding site 7 out of 10 in 2xja

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Magnesium binding site 7 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1536

b:43.8
occ:1.00
 NE2 C:HIS248 2.1 47.4 1.0
O21 C:UAG1535 2.3 47.8 1.0
CD2 C:HIS248 3.0 45.0 1.0
CE1 C:HIS248 3.1 45.6 1.0
OD2 C:ASP247 3.3 60.1 1.0
C27 C:UAG1535 3.5 51.3 1.0
O C:HOH2001 3.5 27.0 1.0
OQ2 C:KCX262 3.7 45.0 1.0
NZ C:LYS157 3.8 35.1 1.0
OQ1 C:KCX262 3.9 41.9 1.0
O C:THR154 4.0 36.5 1.0
O20 C:UAG1535 4.2 47.4 1.0
CG C:HIS248 4.2 46.3 1.0
ND1 C:HIS248 4.2 46.2 1.0
CX C:KCX262 4.3 43.9 1.0
CG C:ASP247 4.4 59.9 1.0
OH C:TYR258 4.7 45.7 1.0
C26 C:UAG1535 4.7 49.9 1.0
C25 C:UAG1535 4.8 52.4 1.0
C C:THR154 5.0 37.6 1.0
O C:GLY153 5.0 39.1 1.0

Magnesium binding site 8 out of 10 in 2xja

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Magnesium binding site 8 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1533

b:50.0
occ:1.00
 O D:GLY502 2.2 81.9 1.0
OD1 D:ASP448 2.8 85.5 1.0
CB D:HIS395 3.2 0.5 1.0
C D:GLY502 3.2 71.7 1.0
CA D:GLY502 3.7 70.0 1.0
CG D:ASP448 3.8 84.5 1.0
CG D:HIS395 4.1 0.2 1.0
CD2 D:HIS395 4.2 0.7 1.0
OD2 D:ASP448 4.3 82.2 1.0
N D:LYS503 4.3 67.5 1.0
CA D:HIS395 4.4 0.8 1.0
CA D:LYS503 4.7 67.1 1.0
O D:TYR393 4.9 0.6 1.0
O D:GLY419 5.0 73.5 1.0

Magnesium binding site 9 out of 10 in 2xja

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Magnesium binding site 9 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1535

b:51.9
occ:1.00
 O3B D:ADP1534 1.9 60.5 1.0
OE1 D:GLU220 1.9 48.2 1.0
OG1 D:THR180 2.1 44.0 1.0
PB D:ADP1534 2.5 57.2 1.0
O D:HOH2001 2.5 27.5 1.0
OG1 D:THR158 2.7 30.4 1.0
CD D:GLU220 3.1 47.5 1.0
O1B D:ADP1534 3.1 63.9 1.0
O2B D:ADP1534 3.2 52.8 1.0
CB D:THR180 3.5 42.1 1.0
OE2 D:GLU220 3.6 49.5 1.0
CB D:THR158 3.9 31.9 1.0
O3A D:ADP1534 4.0 54.5 1.0
O2A D:ADP1534 4.0 52.8 1.0
CG2 D:THR180 4.1 44.7 1.0
CG2 D:THR195 4.1 47.2 1.0
CE D:LYS157 4.1 33.3 1.0
N D:THR158 4.2 30.2 1.0
O20 D:UAG1536 4.3 48.7 1.0
OG1 D:THR195 4.3 60.3 1.0
CG D:GLU220 4.3 40.5 1.0
NZ D:LYS157 4.3 35.9 1.0
CB D:LYS157 4.5 29.6 1.0
NH2 D:ARG377 4.5 71.3 1.0
CA D:THR158 4.5 30.1 1.0
PA D:ADP1534 4.6 55.5 1.0
CA D:THR180 4.6 41.6 1.0
N D:THR180 4.7 38.8 1.0
CB D:THR195 4.9 49.6 1.0
O21 D:UAG1536 4.9 54.5 1.0

Magnesium binding site 10 out of 10 in 2xja

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Magnesium binding site 10 out of 10 in the Structure of Mure From M.Tuberculosis with Dipeptide and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Mure From M.Tuberculosis with Dipeptide and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1537

b:53.6
occ:1.00
 NE2 D:HIS248 2.0 57.9 1.0
O21 D:UAG1536 2.2 54.5 1.0
CD2 D:HIS248 2.9 56.6 1.0
CE1 D:HIS248 3.1 58.4 1.0
C27 D:UAG1536 3.2 51.7 1.0
OQ2 D:KCX262 3.4 42.7 1.0
OQ1 D:KCX262 3.5 43.5 1.0
OD2 D:ASP247 3.5 59.5 1.0
NZ D:LYS157 3.6 35.9 1.0
C26 D:UAG1536 3.7 49.5 1.0
O D:HOH2001 3.7 27.5 1.0
CX D:KCX262 3.9 40.8 1.0
CG D:HIS248 4.1 56.2 1.0
O20 D:UAG1536 4.1 48.7 1.0
O D:THR154 4.1 45.8 1.0
ND1 D:HIS248 4.2 57.0 1.0
OH D:TYR258 4.5 48.5 1.0
CG D:ASP247 4.6 62.0 1.0
O1B D:ADP1534 4.8 63.9 1.0
CE D:LYS157 4.8 33.3 1.0
O D:GLY153 5.0 42.1 1.0

Reference:

C.Basavannacharya, P.R.Moody, T.Munshi, N.Cronin, N.H.Keep, S.Bhakta. Essential Residues For the Enzyme Activity of Atp-Dependent Mure Ligase From Mycobacterium Tuberculosis. Protein Cell V. 1 1011 2010.
ISSN: ISSN 1674-800X
PubMed: 21153518
DOI: 10.1007/S13238-010-0132-9
Page generated: Wed Aug 14 07:10:27 2024

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