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Magnesium in PDB 3zkb: Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp

Enzymatic activity of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp

All present enzymatic activity of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp, PDB code: 3zkb was solved by A.Agrawal, M.Roue, C.Spitzfaden, S.Petrella, A.Aubry, C.Volker, D.Mossakowska, M.Hann, B.Bax, C.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.94 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 101.360, 138.200, 147.690, 105.28, 92.31, 107.23
R / Rfree (%) 18.16 / 23.97

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp (pdb code 3zkb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp, PDB code: 3zkb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in 3zkb

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Magnesium binding site 1 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:50.5
occ:1.00
 O2G A:ANP601 2.1 57.5 1.0
O1B A:ANP601 2.1 67.3 1.0
OD1 A:ASN52 2.3 57.5 1.0
O A:HOH2010 2.5 59.9 1.0
O2A A:ANP601 2.8 60.3 1.0
PG A:ANP601 3.3 58.4 1.0
CG A:ASN52 3.3 73.0 1.0
O A:HOH2011 3.3 55.5 1.0
PB A:ANP601 3.3 68.7 1.0
CA A:GLY119 3.5 57.5 1.0
N3B A:ANP601 3.5 63.3 1.0
NZ A:LYS108 3.6 84.4 1.0
ND2 A:ASN52 3.9 66.2 1.0
PA A:ANP601 4.0 65.0 1.0
O3A A:ANP601 4.0 70.0 1.0
O3G A:ANP601 4.1 56.5 1.0
OE1 A:GLU48 4.2 67.7 1.0
N A:GLY119 4.2 58.0 1.0
OD2 A:ASP55 4.3 75.7 1.0
O A:GLU48 4.4 56.8 1.0
N A:ASN52 4.5 58.5 1.0
CB A:ASN52 4.5 58.6 1.0
CA A:ASN52 4.5 60.0 1.0
O1G A:ANP601 4.6 57.2 1.0
O2B A:ANP601 4.6 69.7 1.0
C A:GLY119 4.7 62.6 1.0
O5' A:ANP601 4.7 66.4 1.0
CE A:LYS108 4.7 77.6 1.0
CD A:LYS108 4.7 69.5 1.0
CB A:ASP51 4.8 58.3 1.0
CA A:GLY124 4.8 50.8 1.0
NZ A:LYS372 4.9 52.7 1.0
C A:ASP51 5.0 61.8 1.0

Magnesium binding site 2 out of 20 in 3zkb

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Magnesium binding site 2 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:57.0
occ:1.00
 OD1 B:ASN52 2.2 67.2 1.0
O1G B:ANP601 2.4 63.4 1.0
O B:HOH2002 2.4 78.5 1.0
O2A B:ANP601 2.4 74.1 1.0
OE1 B:GLU48 2.9 87.9 1.0
CG B:ASN52 3.0 81.9 1.0
O B:GLU48 3.1 67.4 1.0
O1B B:ANP601 3.3 67.7 1.0
ND2 B:ASN52 3.4 83.7 1.0
CA B:GLY124 3.8 60.1 1.0
PA B:ANP601 3.9 77.9 1.0
C B:GLU48 3.9 66.2 1.0
PG B:ANP601 3.9 62.2 1.0
CA B:GLU48 4.1 60.5 1.0
CD B:GLU48 4.1 93.8 1.0
CB B:GLU48 4.2 61.9 1.0
PB B:ANP601 4.2 69.4 1.0
CB B:ASN52 4.3 67.5 1.0
N B:VAL125 4.3 65.1 1.0
O3A B:ANP601 4.3 73.8 1.0
N B:ASN52 4.4 65.1 1.0
C B:GLY124 4.5 65.7 1.0
N3B B:ANP601 4.5 66.6 1.0
N B:GLY124 4.5 61.3 1.0
CA B:ASN52 4.6 67.2 1.0
O5' B:ANP601 4.7 80.2 1.0
CB B:ASP51 4.7 60.3 1.0
O3G B:ANP601 4.7 64.6 1.0
CG B:GLU48 4.7 67.5 1.0
O2G B:ANP601 4.9 56.3 1.0
O1A B:ANP601 4.9 80.7 1.0

Magnesium binding site 3 out of 20 in 3zkb

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Magnesium binding site 3 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:83.2
occ:1.00
 OG1 B:THR167 2.7 0.7 1.0
O B:ASP80 2.8 0.8 1.0
O B:GLY81 2.8 0.9 1.0
O B:TYR61 3.1 0.3 1.0
C B:GLY81 3.5 0.2 1.0
O B:THR167 3.8 0.5 1.0
C B:ASP80 3.9 98.9 1.0
CA B:GLY81 3.9 93.0 1.0
C B:TYR61 4.0 0.8 1.0
CB B:THR167 4.1 0.6 1.0
CB B:TYR61 4.3 0.3 1.0
N B:GLY81 4.3 93.2 1.0
C B:THR167 4.4 0.7 1.0
N B:ARG82 4.4 97.8 1.0
CA B:TYR61 4.4 0.7 1.0
CA B:THR167 4.7 0.1 1.0
CA B:ARG82 4.8 0.9 1.0

Magnesium binding site 4 out of 20 in 3zkb

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Magnesium binding site 4 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:51.2
occ:1.00
 O2A C:ANP601 2.1 52.8 1.0
O2G C:ANP601 2.1 43.0 1.0
O1B C:ANP601 2.1 56.7 1.0
OD1 C:ASN52 2.1 69.9 1.0
O C:HOH2017 2.2 40.1 1.0
O C:HOH2012 2.2 43.8 1.0
PB C:ANP601 3.0 56.9 1.0
CG C:ASN52 3.2 80.4 1.0
PA C:ANP601 3.2 56.1 1.0
O3A C:ANP601 3.3 58.8 1.0
PG C:ANP601 3.3 47.2 1.0
N3B C:ANP601 3.4 53.0 1.0
ND2 C:ASN52 3.6 79.7 1.0
O5' C:ANP601 3.8 55.2 1.0
O C:HOH2013 3.9 60.5 1.0
NZ C:LYS108 4.1 75.2 1.0
O1G C:ANP601 4.1 46.2 1.0
CA C:GLY124 4.2 50.8 1.0
O C:GLU48 4.3 51.4 1.0
CA C:GLY119 4.3 53.3 1.0
O1A C:ANP601 4.4 53.2 1.0
O2B C:ANP601 4.4 54.9 1.0
CB C:ASN52 4.5 55.7 1.0
O3G C:ANP601 4.5 46.5 1.0
OE1 C:GLU48 4.6 45.3 1.0
N C:GLY124 4.6 51.6 1.0
N C:VAL125 4.6 52.2 1.0
N C:ASN52 4.8 53.2 1.0
CA C:ASN52 4.9 53.9 1.0
C C:GLY124 4.9 56.1 1.0

Magnesium binding site 5 out of 20 in 3zkb

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Magnesium binding site 5 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:85.7
occ:1.00
 O C:HOH2032 2.3 92.9 1.0
O C:ASP110 2.8 77.2 1.0
O C:TYR114 3.0 69.1 1.0
O C:HOH2033 3.0 56.6 1.0
OG C:SER117 3.2 57.8 1.0
OG C:SER111 3.6 88.2 1.0
O C:ALA115 3.7 69.0 1.0
C C:ASP110 3.9 80.5 1.0
O C:LYS108 4.0 65.7 1.0
O C:SER363 4.1 73.5 1.0
CA C:SER111 4.1 79.5 1.0
C C:TYR114 4.2 70.4 1.0
O C:HOH2031 4.2 58.3 1.0
C C:LYS108 4.4 66.8 1.0
N C:SER111 4.4 79.5 1.0
CA C:LYS108 4.4 61.1 1.0
C C:ALA115 4.5 68.5 1.0
CB C:SER111 4.5 82.8 1.0
CB C:SER117 4.5 57.2 1.0
CB C:LYS108 4.5 61.3 1.0
N C:SER117 4.6 58.5 1.0
CB C:TYR114 4.9 65.5 1.0
NH2 D:ARG29 4.9 66.7 1.0
CG C:LYS108 4.9 63.4 1.0
N C:ASP110 5.0 73.9 1.0
O C:GLY119 5.0 58.4 1.0

Magnesium binding site 6 out of 20 in 3zkb

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Magnesium binding site 6 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:58.8
occ:1.00
 O D:HOH2008 2.0 58.8 1.0
OD1 D:ASN52 2.2 72.5 1.0
O3G D:ANP601 2.2 61.4 1.0
O2A D:ANP601 2.5 62.9 1.0
O2B D:ANP601 3.1 60.1 1.0
CG D:ASN52 3.2 79.8 1.0
O D:GLU48 3.4 55.8 1.0
O D:HOH2004 3.4 76.0 1.0
OE1 D:GLU48 3.6 58.0 1.0
ND2 D:ASN52 3.7 73.1 1.0
PG D:ANP601 3.7 61.2 1.0
PA D:ANP601 3.9 65.8 1.0
PB D:ANP601 4.0 62.8 1.0
CA D:GLY124 4.1 54.1 1.0
N3B D:ANP601 4.1 61.6 1.0
C D:GLU48 4.3 54.9 1.0
O3A D:ANP601 4.3 65.2 1.0
N D:ASN52 4.4 57.8 1.0
CB D:ASN52 4.4 61.7 1.0
CA D:GLU48 4.4 50.3 1.0
CB D:ASP51 4.5 56.1 1.0
O2G D:ANP601 4.5 62.3 1.0
CA D:GLY119 4.6 52.2 1.0
O1G D:ANP601 4.6 59.0 1.0
CA D:ASN52 4.6 59.1 1.0
CD D:GLU48 4.7 74.3 1.0
N D:GLY124 4.7 54.0 1.0
N D:VAL125 4.7 56.9 1.0
CB D:GLU48 4.7 51.9 1.0
NZ D:LYS108 4.7 58.5 1.0
O1A D:ANP601 4.8 66.0 1.0
O5' D:ANP601 4.8 65.0 1.0
C D:GLY124 4.8 59.0 1.0

Magnesium binding site 7 out of 20 in 3zkb

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Magnesium binding site 7 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:78.5
occ:1.00
 O D:ASP80 2.1 77.6 1.0
O D:THR167 2.7 82.5 1.0
O D:GLY81 2.9 79.5 1.0
OG1 D:THR167 3.1 83.5 1.0
C D:ASP80 3.2 76.3 1.0
C D:THR167 3.7 84.2 1.0
O D:TYR61 3.8 83.2 1.0
C D:GLY81 3.9 76.3 1.0
CB D:THR167 4.0 85.3 1.0
N D:GLY81 4.1 71.5 1.0
CA D:ASP80 4.2 71.9 1.0
CA D:THR167 4.2 83.4 1.0
CB D:ASP80 4.2 75.1 1.0
CA D:GLY81 4.3 70.7 1.0
N D:THR167 4.3 86.6 1.0
OD2 D:ASP80 4.5 91.1 1.0
CG D:ASP80 4.6 84.5 1.0
N D:GLY168 4.8 79.2 1.0
C D:TYR61 4.9 81.9 1.0

Magnesium binding site 8 out of 20 in 3zkb

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Magnesium binding site 8 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:56.2
occ:1.00
 O E:HOH2010 1.9 66.6 1.0
O1B E:ANP601 2.0 62.1 1.0
OD1 E:ASN52 2.2 70.8 1.0
O1A E:ANP601 2.2 62.7 1.0
O3G E:ANP601 2.2 62.8 1.0
O E:HOH2014 2.4 38.4 1.0
PB E:ANP601 2.8 67.2 1.0
O3A E:ANP601 2.9 68.7 1.0
PA E:ANP601 3.0 67.0 1.0
N3B E:ANP601 3.3 66.9 1.0
PG E:ANP601 3.3 64.1 1.0
CG E:ASN52 3.3 81.2 1.0
O5' E:ANP601 3.8 66.6 1.0
ND2 E:ASN52 3.9 76.0 1.0
CA E:GLY124 4.0 59.0 1.0
O2G E:ANP601 4.1 63.8 1.0
O E:HOH2011 4.1 59.3 1.0
NZ E:LYS108 4.1 67.9 1.0
O2B E:ANP601 4.2 68.2 1.0
O E:GLU48 4.3 56.1 1.0
O2A E:ANP601 4.3 68.5 1.0
N E:GLY124 4.4 61.8 1.0
N E:VAL125 4.5 57.1 1.0
O1G E:ANP601 4.5 62.2 1.0
CA E:GLY119 4.5 57.4 1.0
CB E:ASN52 4.6 62.8 1.0
OE1 E:GLU48 4.7 89.2 1.0
C E:GLY124 4.8 59.8 1.0
CA E:ASN52 4.8 60.5 1.0
N E:ASN52 4.9 60.0 1.0
C5' E:ANP601 5.0 69.1 1.0

Magnesium binding site 9 out of 20 in 3zkb

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Magnesium binding site 9 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:53.9
occ:1.00
 OD1 F:ASN52 1.9 92.7 1.0
O F:HOH2003 2.3 61.5 1.0
O2B F:ANP601 2.5 81.8 1.0
O2G F:ANP601 2.5 76.0 1.0
O2A F:ANP601 2.6 77.1 1.0
CG F:ASN52 3.1 99.6 1.0
OE1 F:GLU48 3.4 97.5 1.0
O F:GLU48 3.5 81.3 1.0
PB F:ANP601 3.6 81.4 1.0
ND2 F:ASN52 3.6 94.0 1.0
PG F:ANP601 3.8 76.7 1.0
PA F:ANP601 3.9 80.1 1.0
N3B F:ANP601 4.0 79.3 1.0
O3A F:ANP601 4.0 81.1 1.0
CA F:GLY124 4.0 75.7 1.0
CA F:GLY119 4.3 77.9 1.0
CB F:ASN52 4.3 80.6 1.0
NZ F:LYS108 4.4 76.5 1.0
N F:ASN52 4.4 76.3 1.0
C F:GLU48 4.5 80.2 1.0
O5' F:ANP601 4.5 86.0 1.0
CA F:ASN52 4.6 78.1 1.0
CD F:GLU48 4.6 98.1 1.0
N F:VAL125 4.6 82.5 1.0
N F:GLY124 4.7 75.6 1.0
CA F:GLU48 4.8 73.4 1.0
C F:GLY124 4.8 82.8 1.0
O1G F:ANP601 4.8 72.2 1.0
O3G F:ANP601 4.8 79.2 1.0
CB F:ASP51 4.9 74.4 1.0
CB F:GLU48 4.9 74.6 1.0
OD2 F:ASP55 4.9 96.3 1.0
O1A F:ANP601 5.0 77.1 1.0

Magnesium binding site 10 out of 20 in 3zkb

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Magnesium binding site 10 out of 20 in the Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Atpase Region of Mycobacterium Tuberculosis Gyrb with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:63.6
occ:1.00
 O1G G:ANP601 1.9 68.0 1.0
O2B G:ANP601 2.1 75.2 1.0
O G:HOH2006 2.1 47.1 1.0
OD1 G:ASN52 2.2 85.8 1.0
O G:HOH2009 2.3 71.6 1.0
O2A G:ANP601 2.5 71.3 1.0
PB G:ANP601 3.0 74.7 1.0
PG G:ANP601 3.1 68.4 1.0
N3B G:ANP601 3.2 72.4 1.0
CG G:ASN52 3.3 0.9 1.0
O3A G:ANP601 3.5 74.8 1.0
PA G:ANP601 3.6 73.8 1.0
O G:HOH2007 3.6 47.8 1.0
ND2 G:ASN52 3.9 99.1 1.0
CA G:GLY119 4.0 73.7 1.0
NZ G:LYS108 4.0 0.6 1.0
O2G G:ANP601 4.2 67.5 1.0
O3G G:ANP601 4.2 63.6 1.0
O5' G:ANP601 4.2 76.5 1.0
O G:GLU48 4.3 75.7 1.0
CA G:GLY124 4.3 71.1 1.0
O1B G:ANP601 4.5 73.7 1.0
CB G:ASN52 4.5 81.9 1.0
CA G:ASN52 4.7 79.6 1.0
N G:GLY124 4.7 72.8 1.0
N G:ASN52 4.7 78.9 1.0
OD2 G:ASP55 4.7 98.1 1.0
O1A G:ANP601 4.8 73.9 1.0
N G:GLY119 4.8 74.5 1.0
OE1 G:GLU48 4.9 86.2 1.0
NZ G:LYS372 4.9 83.8 1.0

Reference:

A.Agrawal, M.Roue, C.Spitzfaden, S.Petrella, A.Aubry, M.M.Hann, B.Bax, C.Mayer. Mycobacterium Tuberculosis Dna Gyrase Atpase Domain Structures Suggest A Dissociative Mechanism That Explains How Atp Hydrolysis Is Coupled to Domain Motion. Biochem.J. V. 456 263 2013.
ISSN: ISSN 0264-6021
PubMed: 24015710
DOI: 10.1042/BJ20130538
Page generated: Thu Aug 15 13:56:58 2024

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