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Magnesium in PDB 3zkd: 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: 3zkd 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) 24.81 / 2.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.953, 97.851, 138.075, 108.21, 105.18, 91.04
R / Rfree (%) 18.17 / 25.7

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 3zkd

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Magnesium binding site 1 out of 8 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:38.5
occ:1.00
 O2A A:ANP601 1.9 50.0 1.0
O2B A:ANP601 2.2 56.9 1.0
O2G A:ANP601 2.3 53.6 1.0
OD1 A:ASN52 2.3 53.8 1.0
O A:HOH2006 2.8 37.2 1.0
PA A:ANP601 3.0 52.7 1.0
O3A A:ANP601 3.0 57.6 1.0
PB A:ANP601 3.0 59.4 1.0
CG A:ASN52 3.1 70.5 1.0
O A:HOH2004 3.2 65.7 1.0
ND2 A:ASN52 3.3 67.9 1.0
PG A:ANP601 3.3 55.0 1.0
N3B A:ANP601 3.5 58.2 1.0
CA A:GLY124 3.8 50.4 1.0
O1G A:ANP601 3.9 53.9 1.0
O1A A:ANP601 4.0 54.4 1.0
O5' A:ANP601 4.1 51.7 1.0
O A:GLU48 4.1 54.2 1.0
C5' A:ANP601 4.2 53.1 1.0
N A:GLY124 4.2 51.1 1.0
N A:VAL125 4.3 51.5 1.0
NZ A:LYS108 4.4 59.2 1.0
O1B A:ANP601 4.5 57.7 1.0
CB A:ASN52 4.5 54.9 1.0
C A:GLY124 4.5 54.8 1.0
CA A:GLY119 4.7 48.1 1.0
O3G A:ANP601 4.7 55.3 1.0
OE1 A:GLU48 4.8 75.1 1.0
CA A:ASN52 4.9 53.3 1.0
C A:GLU48 5.0 54.8 1.0

Magnesium binding site 2 out of 8 in 3zkd

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Magnesium binding site 2 out of 8 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:37.5
occ:1.00
 O B:HOH2005 2.3 53.7 1.0
OE1 B:GLU48 2.4 78.8 1.0
O3G B:ANP601 2.7 54.6 1.0
O B:GLU48 2.7 56.1 1.0
ND2 B:ASN52 2.8 66.7 1.0
O2A B:ANP601 2.9 67.0 1.0
OD1 B:ASN52 2.9 71.6 1.0
O2B B:ANP601 2.9 52.5 1.0
CG B:ASN52 2.9 78.3 1.0
CD B:GLU48 3.5 86.9 1.0
C B:GLU48 3.6 57.5 1.0
O B:HOH2003 3.7 51.6 1.0
CA B:GLU48 3.7 54.5 1.0
CB B:GLU48 3.9 56.3 1.0
PG B:ANP601 4.0 55.7 1.0
CB B:ASN52 4.1 62.7 1.0
PB B:ANP601 4.1 60.8 1.0
CG B:GLU48 4.2 67.3 1.0
PA B:ANP601 4.2 65.4 1.0
N B:ASN52 4.3 59.5 1.0
CA B:GLY124 4.3 55.0 1.0
N B:VAL125 4.4 60.0 1.0
O2G B:ANP601 4.5 56.0 1.0
N3B B:ANP601 4.5 59.4 1.0
OE2 B:GLU48 4.5 80.7 1.0
CA B:ASN52 4.5 60.9 1.0
CB B:ASP51 4.6 56.8 1.0
O3A B:ANP601 4.6 64.9 1.0
C B:GLY124 4.7 61.6 1.0
N B:VAL49 4.8 55.1 1.0
O5' B:ANP601 4.9 63.7 1.0
N B:GLY124 4.9 55.3 1.0

Magnesium binding site 3 out of 8 in 3zkd

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Magnesium binding site 3 out of 8 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
C:Mg602

b:35.5
occ:1.00
 OD1 C:ASN52 2.1 53.6 1.0
O C:HOH2004 2.2 18.1 1.0
O2B C:ANP601 2.3 60.4 1.0
O C:HOH2008 2.5 43.6 1.0
O2G C:ANP601 2.6 57.2 1.0
O2A C:ANP601 2.6 48.1 1.0
N3B C:ANP601 2.8 57.3 1.0
PB C:ANP601 2.9 61.3 1.0
PG C:ANP601 3.2 54.7 1.0
CG C:ASN52 3.3 60.3 1.0
O3A C:ANP601 3.4 59.0 1.0
PA C:ANP601 3.6 52.8 1.0
CA C:GLY119 3.7 50.8 1.0
NZ C:LYS108 3.7 49.2 1.0
ND2 C:ASN52 4.0 50.7 1.0
O1G C:ANP601 4.2 50.0 1.0
OE1 C:GLU48 4.2 48.5 1.0
O5' C:ANP601 4.2 54.5 1.0
O C:GLU48 4.2 48.0 1.0
OD2 C:ASP55 4.3 62.1 1.0
N C:GLY119 4.4 50.5 1.0
O1B C:ANP601 4.4 62.5 1.0
O3G C:ANP601 4.5 57.4 1.0
CB C:ASN52 4.5 50.0 1.0
N C:ASN52 4.6 51.8 1.0
CA C:ASN52 4.6 51.3 1.0
CA C:GLY124 4.6 48.0 1.0
CD C:LYS108 4.7 60.0 1.0
O1A C:ANP601 4.8 53.2 1.0
CE C:LYS108 4.8 55.5 1.0
C C:GLY119 4.8 57.5 1.0
NZ C:LYS372 4.9 46.6 1.0
CB C:ASP51 4.9 57.7 1.0

Magnesium binding site 4 out of 8 in 3zkd

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Magnesium binding site 4 out of 8 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
D:Mg602

b:60.4
occ:1.00
 O1G D:ANP601 1.9 60.5 1.0
OD1 D:ASN52 1.9 78.4 1.0
CG D:ASN52 2.9 81.7 1.0
O2A D:ANP601 2.9 63.3 1.0
O2B D:ANP601 2.9 65.0 1.0
PG D:ANP601 3.4 57.6 1.0
ND2 D:ASN52 3.5 75.7 1.0
O D:GLU48 3.7 62.3 1.0
OE1 D:GLU48 3.8 74.2 1.0
CA D:GLY119 3.9 58.4 1.0
PB D:ANP601 3.9 64.4 1.0
N3B D:ANP601 3.9 61.9 1.0
NZ D:LYS108 3.9 95.5 1.0
CB D:ASN52 4.0 58.5 1.0
CA D:ASN52 4.1 57.6 1.0
PA D:ANP601 4.1 67.5 1.0
N D:ASN52 4.1 56.2 1.0
O3G D:ANP601 4.2 59.5 1.0
OD2 D:ASP55 4.3 76.1 1.0
O3A D:ANP601 4.3 64.9 1.0
N D:GLY119 4.5 58.7 1.0
O2G D:ANP601 4.5 49.7 1.0
C D:ASP51 4.7 59.8 1.0
O5' D:ANP601 4.7 68.8 1.0
C D:GLU48 4.7 63.1 1.0
CB D:ASP51 4.9 58.1 1.0

Magnesium binding site 5 out of 8 in 3zkd

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Magnesium binding site 5 out of 8 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
E:Mg602

b:51.8
occ:1.00
 O E:HOH2006 2.0 37.0 1.0
O1G E:ANP601 2.1 47.6 1.0
O2A E:ANP601 2.4 57.5 1.0
O2B E:ANP601 2.5 49.6 1.0
OD1 E:ASN52 2.7 64.8 1.0
OE1 E:GLU48 3.0 74.0 1.0
PG E:ANP601 3.3 49.6 1.0
PB E:ANP601 3.4 54.0 1.0
CG E:ASN52 3.5 70.7 1.0
O E:GLU48 3.5 52.7 1.0
PA E:ANP601 3.6 56.4 1.0
N3B E:ANP601 3.6 53.0 1.0
O3A E:ANP601 3.7 55.6 1.0
ND2 E:ASN52 3.7 61.2 1.0
O3G E:ANP601 3.9 49.0 1.0
CA E:GLY124 3.9 50.7 1.0
O E:HOH2004 4.1 49.5 1.0
CD E:GLU48 4.3 84.1 1.0
CA E:GLY119 4.4 49.2 1.0
N E:GLY124 4.5 50.6 1.0
C E:GLU48 4.5 52.3 1.0
O5' E:ANP601 4.5 55.3 1.0
O2G E:ANP601 4.6 49.5 1.0
O1A E:ANP601 4.6 58.3 1.0
N E:VAL125 4.6 54.9 1.0
C E:GLY124 4.7 57.2 1.0
CA E:GLU48 4.7 48.2 1.0
N E:ASN52 4.7 54.7 1.0
CB E:ASN52 4.7 54.8 1.0
CB E:ASP51 4.8 54.3 1.0
CB E:GLU48 4.8 49.5 1.0
NZ E:LYS108 4.9 54.9 1.0
O1B E:ANP601 4.9 53.3 1.0
CA E:ASN52 4.9 53.6 1.0

Magnesium binding site 6 out of 8 in 3zkd

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Magnesium binding site 6 out of 8 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
F:Mg602

b:48.3
occ:1.00
 O2G F:ANP601 2.1 43.5 1.0
OD1 F:ASN52 2.1 72.1 1.0
O2A F:ANP601 2.5 50.5 1.0
O2B F:ANP601 2.5 50.3 1.0
CG F:ASN52 3.0 81.1 1.0
PG F:ANP601 3.4 42.3 1.0
OE1 F:GLU48 3.4 85.6 1.0
ND2 F:ASN52 3.5 78.5 1.0
PB F:ANP601 3.5 49.4 1.0
N3B F:ANP601 3.6 45.0 1.0
PA F:ANP601 3.8 52.5 1.0
O F:GLU48 3.8 46.6 1.0
O3A F:ANP601 4.0 51.2 1.0
CA F:GLY119 4.1 50.1 1.0
O3G F:ANP601 4.2 38.7 1.0
CA F:GLY124 4.2 42.8 1.0
CB F:ASN52 4.2 49.0 1.0
N F:VAL125 4.6 44.1 1.0
O1G F:ANP601 4.6 42.3 1.0
N F:GLY124 4.6 44.0 1.0
CA F:ASN52 4.6 50.2 1.0
O5' F:ANP601 4.6 55.5 1.0
N F:ASN52 4.7 49.5 1.0
CD F:GLU48 4.7 88.0 1.0
O1A F:ANP601 4.7 51.7 1.0
C F:GLU48 4.7 48.2 1.0
C F:GLY124 4.8 45.6 1.0
N F:GLY119 4.9 49.9 1.0
O1B F:ANP601 4.9 49.8 1.0

Magnesium binding site 7 out of 8 in 3zkd

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Magnesium binding site 7 out of 8 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
G:Mg602

b:35.0
occ:1.00
 O1G G:ANP601 2.2 50.0 1.0
O2A G:ANP601 2.2 53.0 1.0
OD1 G:ASN52 2.3 35.9 1.0
O G:HOH2005 2.5 38.8 1.0
O2B G:ANP601 2.9 50.4 1.0
CG G:ASN52 3.3 46.4 1.0
OE1 G:GLU48 3.3 95.2 1.0
PA G:ANP601 3.4 56.3 1.0
O G:GLU48 3.5 44.9 1.0
CA G:GLY124 3.5 43.0 1.0
O3A G:ANP601 3.5 56.0 1.0
PG G:ANP601 3.6 48.5 1.0
ND2 G:ASN52 3.6 34.3 1.0
PB G:ANP601 3.6 52.1 1.0
N3B G:ANP601 3.9 51.1 1.0
N G:GLY124 4.2 45.0 1.0
O3G G:ANP601 4.3 45.1 1.0
N G:VAL125 4.3 40.1 1.0
C G:GLY124 4.3 44.5 1.0
C G:GLU48 4.3 45.7 1.0
O5' G:ANP601 4.3 55.8 1.0
CD G:GLU48 4.4 93.7 1.0
O1A G:ANP601 4.4 58.0 1.0
CA G:GLU48 4.5 47.8 1.0
CB G:GLU48 4.5 50.0 1.0
CB G:ASN52 4.6 36.8 1.0
O2G G:ANP601 4.7 49.4 1.0
N G:ASN52 4.7 43.7 1.0
CB G:ASP51 4.8 47.8 1.0
CA G:GLY119 4.9 49.1 1.0
CA G:ASN52 4.9 43.1 1.0
NZ G:LYS108 5.0 65.5 1.0

Magnesium binding site 8 out of 8 in 3zkd

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Magnesium binding site 8 out of 8 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
H:Mg602

b:37.7
occ:1.00
 O1G H:ANP601 2.1 55.8 1.0
OD1 H:ASN52 2.4 60.7 1.0
O2B H:ANP601 2.4 63.3 1.0
O2A H:ANP601 3.0 60.8 1.0
OE1 H:GLU48 3.2 75.5 1.0
CG H:ASN52 3.3 73.4 1.0
PG H:ANP601 3.5 53.3 1.0
PB H:ANP601 3.5 62.0 1.0
N3B H:ANP601 3.7 57.6 1.0
O H:GLU48 3.8 63.2 1.0
ND2 H:ASN52 3.8 68.2 1.0
CB H:ASP51 4.0 60.4 1.0
CA H:GLY119 4.0 63.3 1.0
N H:ASN52 4.1 62.5 1.0
PA H:ANP601 4.1 65.3 1.0
O3A H:ANP601 4.2 64.4 1.0
NZ H:LYS108 4.2 76.5 1.0
O3G H:ANP601 4.2 51.1 1.0
OD2 H:ASP55 4.3 89.2 1.0
CB H:ASN52 4.4 61.9 1.0
CA H:ASN52 4.4 63.9 1.0
CD H:GLU48 4.5 89.9 1.0
NZ H:LYS372 4.5 84.1 1.0
N H:GLY119 4.6 63.8 1.0
C H:ASP51 4.6 65.2 1.0
O2G H:ANP601 4.7 51.8 1.0
C H:GLU48 4.8 62.0 1.0
CA H:GLY124 4.8 52.0 1.0
OD2 H:ASP51 4.9 91.9 1.0
O5' H:ANP601 4.9 72.1 1.0
CA H:ASP51 4.9 58.6 1.0
O1B H:ANP601 4.9 62.6 1.0
CG H:ASP51 5.0 84.2 1.0
CA H:GLU48 5.0 55.7 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 13:57:31 2024

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