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Magnesium in PDB 6bwh: Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep

Enzymatic activity of Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep

All present enzymatic activity of Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep:
2.7.7.68;

Protein crystallography data

The structure of Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep, PDB code: 6bwh was solved by E.N.M.Jirgis, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.89 / 2.18
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 66.170, 110.441, 165.906, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 28.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep (pdb code 6bwh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep, PDB code: 6bwh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6bwh

Go back to Magnesium Binding Sites List in 6bwh
Magnesium binding site 1 out of 6 in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep


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 Mycoibacterium Tuberculosis RV2983 in Complex with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:45.8
occ:1.00
 O A:HOH421 2.1 48.5 1.0
O A:HOH428 2.1 29.7 1.0
O A:HOH422 2.1 46.7 1.0
O1P A:PEP301 2.2 50.9 1.0
OD2 A:ASP190 2.2 51.2 1.0
OD2 A:ASP188 2.2 43.8 1.0
MG A:MG303 3.1 49.1 1.0
CG A:ASP188 3.2 37.7 1.0
CG A:ASP190 3.2 43.3 1.0
P A:PEP301 3.3 65.0 1.0
O2 A:PEP301 3.5 59.1 1.0
OD2 A:ASP142 3.6 51.7 1.0
OD1 A:ASP190 3.6 49.4 1.0
OD1 A:ASP188 3.6 39.4 1.0
O A:HOH405 4.0 44.6 1.0
O A:HOH446 4.0 44.5 1.0
O2P A:PEP301 4.0 72.8 1.0
O A:HOH408 4.1 47.0 1.0
O A:HOH417 4.4 32.9 1.0
CB A:ASP188 4.5 36.5 1.0
CB A:ASP190 4.5 38.0 1.0
O3P A:PEP301 4.6 63.4 1.0
CG A:ASP142 4.6 36.2 1.0
O1 A:PEP301 4.7 39.4 1.0
O A:HOH403 4.8 34.8 1.0
C2 A:PEP301 4.9 46.6 1.0
CB A:ASP142 5.0 35.4 1.0

Magnesium binding site 2 out of 6 in 6bwh

Go back to Magnesium Binding Sites List in 6bwh
Magnesium binding site 2 out of 6 in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep


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 Mycoibacterium Tuberculosis RV2983 in Complex with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:49.1
occ:1.00
 O A:HOH403 2.1 34.8 1.0
O A:HOH417 2.2 32.9 1.0
O1P A:PEP301 2.2 50.9 1.0
OD2 A:ASP188 2.2 43.8 1.0
OD1 A:ASP190 2.2 49.4 1.0
OD2 A:ASP116 2.2 41.1 1.0
MG A:MG302 3.1 45.8 1.0
CG A:ASP190 3.1 43.3 1.0
CG A:ASP116 3.2 37.0 1.0
CG A:ASP188 3.2 37.7 1.0
OD2 A:ASP190 3.3 51.2 1.0
P A:PEP301 3.3 65.0 1.0
OD1 A:ASP116 3.5 37.0 1.0
CB A:ASP188 3.5 36.5 1.0
O3P A:PEP301 3.5 63.4 1.0
O A:HOH446 3.8 44.5 1.0
NZ A:LYS23 3.9 45.2 1.0
O2 A:PEP301 3.9 59.1 1.0
O A:HOH422 4.0 46.7 1.0
N A:VAL189 4.3 36.8 1.0
OD1 A:ASP188 4.4 39.4 1.0
CB A:ASP190 4.5 38.0 1.0
CB A:ASP116 4.6 32.5 1.0
O A:HOH421 4.6 48.5 1.0
NE2 A:GLN114 4.6 41.0 1.0
O2P A:PEP301 4.6 72.8 1.0
O A:VAL189 4.7 38.4 1.0
C A:ASP188 4.7 34.4 1.0
O A:HOH428 4.7 29.7 1.0
CA A:ASP188 4.7 33.2 1.0
C A:VAL189 4.7 34.9 1.0
O A:HOH440 4.8 51.2 1.0
N A:ASP190 4.8 41.7 1.0

Magnesium binding site 3 out of 6 in 6bwh

Go back to Magnesium Binding Sites List in 6bwh
Magnesium binding site 3 out of 6 in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep


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 Mycoibacterium Tuberculosis RV2983 in Complex with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:35.2
occ:1.00
 O B:HOH431 2.1 39.2 1.0
OD2 B:ASP188 2.1 35.6 1.0
OD2 B:ASP190 2.1 40.6 1.0
O B:HOH417 2.2 35.2 1.0
O B:HOH401 2.2 35.5 1.0
O1P B:PEP301 2.2 39.7 1.0
CG B:ASP188 3.0 32.8 1.0
CG B:ASP190 3.1 47.7 1.0
MG B:MG303 3.2 36.8 1.0
OD1 B:ASP188 3.2 38.8 1.0
OD1 B:ASP190 3.4 42.0 1.0
P B:PEP301 3.5 42.4 1.0
OD2 B:ASP142 3.7 38.3 1.0
O B:HOH424 3.8 39.5 1.0
O2 B:PEP301 3.8 43.0 1.0
O2P B:PEP301 3.9 47.5 1.0
O B:HOH421 4.0 43.8 1.0
O B:HOH415 4.3 33.8 1.0
CB B:ASP188 4.4 34.4 1.0
CB B:ASP190 4.5 41.3 1.0
O1 B:PEP301 4.6 31.8 1.0
CG B:ASP142 4.7 41.4 1.0
O B:HOH410 4.8 28.6 1.0
O3P B:PEP301 4.8 50.0 1.0

Magnesium binding site 4 out of 6 in 6bwh

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Magnesium binding site 4 out of 6 in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep


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 Mycoibacterium Tuberculosis RV2983 in Complex with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:36.8
occ:1.00
 OD2 B:ASP188 2.1 35.6 1.0
O B:HOH410 2.1 28.6 1.0
O1P B:PEP301 2.2 39.7 1.0
OD1 B:ASP190 2.2 42.0 1.0
OD2 B:ASP116 2.2 35.8 1.0
O B:HOH415 2.2 33.8 1.0
CG B:ASP116 3.1 38.0 1.0
CG B:ASP188 3.1 32.8 1.0
MG B:MG302 3.2 35.2 1.0
CG B:ASP190 3.2 47.7 1.0
P B:PEP301 3.3 42.4 1.0
OD1 B:ASP116 3.3 33.9 1.0
CB B:ASP188 3.5 34.4 1.0
OD2 B:ASP190 3.5 40.6 1.0
O3P B:PEP301 3.6 50.0 1.0
O B:HOH417 4.0 35.2 1.0
O2 B:PEP301 4.1 43.0 1.0
O B:HOH421 4.1 43.8 1.0
OD1 B:ASP188 4.2 38.8 1.0
O B:HOH402 4.2 43.1 1.0
O B:HOH401 4.3 35.5 1.0
O2P B:PEP301 4.4 47.5 1.0
NE2 B:GLN114 4.5 60.0 1.0
CB B:ASP116 4.5 38.6 1.0
CB B:ASP190 4.5 41.3 1.0
N B:VAL189 4.6 27.7 1.0
O B:VAL189 4.6 30.7 1.0
CA B:ASP188 4.7 32.8 1.0
C B:ASP188 4.7 32.0 1.0
C B:VAL189 4.7 32.3 1.0
N B:ASP190 4.8 34.0 1.0
CA B:ASP190 4.9 38.5 1.0
O B:HOH431 4.9 39.2 1.0

Magnesium binding site 5 out of 6 in 6bwh

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Magnesium binding site 5 out of 6 in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep


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 Mycoibacterium Tuberculosis RV2983 in Complex with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:56.1
occ:1.00
 OD2 C:ASP190 2.1 59.7 1.0
OD2 C:ASP188 2.2 67.3 1.0
O C:HOH412 2.2 49.6 1.0
O C:HOH408 2.2 61.5 1.0
O C:HOH401 2.2 50.4 1.0
O3P C:PEP301 2.2 52.5 1.0
MG C:MG303 2.7 52.2 1.0
CG C:ASP190 2.9 60.9 1.0
CG C:ASP188 3.0 63.0 1.0
OD1 C:ASP190 3.1 70.3 1.0
OD1 C:ASP188 3.4 60.5 1.0
P C:PEP301 3.5 59.2 1.0
O2 C:PEP301 3.8 61.6 1.0
O C:HOH403 3.9 45.6 1.0
OD2 C:ASP142 4.3 59.2 1.0
O C:HOH404 4.3 55.0 1.0
CB C:ASP190 4.3 55.1 1.0
CB C:ASP188 4.3 54.6 1.0
O1P C:PEP301 4.4 61.5 1.0
O C:HOH402 4.5 44.0 1.0
O C:HOH423 4.5 43.2 1.0
O2P C:PEP301 4.6 64.0 1.0
O2' C:PEP301 4.6 48.3 1.0
OD2 C:ASP116 4.7 48.7 1.0

Magnesium binding site 6 out of 6 in 6bwh

Go back to Magnesium Binding Sites List in 6bwh
Magnesium binding site 6 out of 6 in the Crystal Structure of Mycoibacterium Tuberculosis RV2983 in Complex with Pep


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 Mycoibacterium Tuberculosis RV2983 in Complex with Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:52.2
occ:1.00
 OD2 C:ASP116 2.1 48.7 1.0
O3P C:PEP301 2.2 52.5 1.0
O C:HOH402 2.2 44.0 1.0
OD1 C:ASP190 2.2 70.3 1.0
O C:HOH404 2.2 55.0 1.0
OD2 C:ASP188 2.2 67.3 1.0
MG C:MG302 2.7 56.1 1.0
CG C:ASP190 3.0 60.9 1.0
OD2 C:ASP190 3.2 59.7 1.0
CG C:ASP188 3.2 63.0 1.0
P C:PEP301 3.2 59.2 1.0
CG C:ASP116 3.2 42.8 1.0
O2P C:PEP301 3.3 64.0 1.0
CB C:ASP188 3.6 54.6 1.0
OD1 C:ASP116 3.7 42.1 1.0
O2 C:PEP301 3.8 61.6 1.0
O C:HOH422 3.9 33.4 1.0
O C:HOH412 3.9 49.6 1.0
O C:HOH401 4.1 50.4 1.0
OD1 C:ASP188 4.3 60.5 1.0
O C:VAL189 4.4 62.1 1.0
CB C:ASP190 4.4 55.1 1.0
NE2 C:GLN114 4.5 81.6 1.0
CB C:ASP116 4.5 38.8 1.0
O1P C:PEP301 4.6 61.5 1.0
C C:VAL189 4.7 49.8 1.0
C C:ASP188 4.7 58.6 1.0
N C:VAL189 4.7 43.1 1.0
O C:HOH408 4.7 61.5 1.0
CA C:ASP188 4.7 57.5 1.0
N C:ASP190 4.8 55.4 1.0
CA C:ASP190 4.9 56.3 1.0

Reference:

G.Bashiri, E.N.M.Jirgis. Crystal Structure of Mycobacterium Tuberculosis RV2983 in Complex with Pep To Be Published.
Page generated: Mon Sep 30 20:02:24 2024

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