Magnesium in PDB 7w2i: Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis

Protein crystallography data

The structure of Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis, PDB code: 7w2i was solved by L.Shang, G.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.93 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.958, 75.976, 134.953, 90, 90, 90
R / Rfree (%) 16.5 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis (pdb code 7w2i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis, PDB code: 7w2i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7w2i

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Magnesium binding site 1 out of 4 in the Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis


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 Log (RV1205) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:35.8
occ:1.00
 OD2 A:ASP128 2.3 35.5 1.0
OD1 A:ASP124 2.3 24.0 1.0
O A:HOH401 2.8 30.8 1.0
O1 A:EDO204 2.9 34.5 1.0
C1 A:EDO204 2.9 29.2 1.0
O A:HOH427 3.1 30.2 1.0
O A:HOH409 3.2 19.2 1.0
CG A:ASP128 3.3 27.1 1.0
CG A:ASP124 3.4 17.7 1.0
O A:ASP124 3.4 10.2 1.0
CB A:ASP128 3.7 19.9 1.0
C A:ASP124 3.8 10.8 1.0
O B:HOH411 3.9 40.8 1.0
OD2 A:ASP124 4.0 23.6 1.0
O B:HOH356 4.1 19.2 1.0
C2 A:EDO204 4.1 30.3 1.0
O A:HOH455 4.3 38.9 1.0
N A:ALA125 4.4 9.2 1.0
CB A:ASP124 4.5 13.2 1.0
OD1 A:ASP128 4.5 26.3 1.0
CA A:ALA125 4.5 9.4 1.0
CA A:ASP124 4.6 11.7 1.0
O A:HOH419 4.7 22.3 1.0
CG A:GLU103 4.7 26.1 1.0
O A:HOH410 4.8 15.6 1.0
CA A:ASP128 5.0 18.1 1.0

Magnesium binding site 2 out of 4 in 7w2i

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Magnesium binding site 2 out of 4 in the Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis


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 Log (RV1205) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:32.6
occ:1.00
 OE1 B:GLU103 2.1 44.1 1.0
OE1 B:GLN100 2.3 37.6 1.0
O B:HOH379 2.4 33.4 1.0
O B:HOH360 2.4 35.8 1.0
O B:HOH318 2.4 33.3 1.0
OD2 B:ASP128 2.7 31.2 1.0
CD B:GLU103 3.2 37.2 1.0
CD B:GLN100 3.3 34.8 1.0
CG B:ASP128 3.6 32.0 1.0
NE2 B:GLN100 3.7 38.3 1.0
OE2 B:GLU103 3.8 41.4 1.0
OD1 B:ASP128 3.9 32.0 1.0
OD1 B:ASP124 4.0 28.2 1.0
O B:HOH345 4.0 31.6 1.0
O B:HOH355 4.2 28.3 1.0
O B:HOH428 4.2 44.0 1.0
CD1 A:TRP96 4.4 24.8 1.0
CG B:GLU103 4.4 32.0 1.0
CB B:GLU103 4.5 26.6 1.0
CA B:GLN100 4.5 22.4 1.0
O B:HOH388 4.6 24.3 1.0
CG B:GLN100 4.6 29.1 1.0
CB A:TRP96 4.7 22.2 1.0
CB B:ASP128 4.8 26.8 1.0
CB B:GLN100 4.9 26.4 1.0
CG A:TRP96 5.0 22.9 1.0
CG B:ASP124 5.0 20.8 1.0

Magnesium binding site 3 out of 4 in 7w2i

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Magnesium binding site 3 out of 4 in the Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis


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 Log (RV1205) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:24.6
occ:1.00
 OD1 C:ASP124 1.9 24.1 1.0
OD2 C:ASP128 2.1 28.0 1.0
O C:HOH319 2.1 23.1 1.0
O C:ASP124 2.2 17.2 1.0
O C:HOH367 2.2 28.4 1.0
C C:ASP124 3.0 17.2 1.0
CG C:ASP124 3.1 22.8 1.0
CG C:ASP128 3.3 28.0 1.0
CA C:ASP124 3.5 16.4 1.0
CB C:ASP124 3.8 18.3 1.0
CB C:ASP128 4.0 22.8 1.0
OD2 C:ASP124 4.0 24.1 1.0
O C:HOH335 4.1 41.9 1.0
N C:ALA125 4.2 15.0 1.0
OD1 C:ASP128 4.3 30.2 1.0
N C:ASP128 4.3 17.9 1.0
O C:HOH446 4.5 42.0 1.0
O C:HOH437 4.5 36.8 1.0
O C:HOH445 4.6 34.0 1.0
CA C:ASP128 4.7 21.7 1.0
CA C:ALA125 4.7 16.6 1.0
N C:ASP124 4.9 15.6 1.0
O C:HOH399 5.0 28.5 1.0

Magnesium binding site 4 out of 4 in 7w2i

Go back to Magnesium Binding Sites List in 7w2i
Magnesium binding site 4 out of 4 in the Crystal Structure of Log (RV1205) From Mycobacterium Tuberculosis


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 Log (RV1205) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:41.7
occ:1.00
 OD1 D:ASP124 2.1 25.4 1.0
OD2 D:ASP128 2.1 31.6 1.0
O D:ASP124 2.2 16.2 1.0
O D:HOH330 2.2 23.1 1.0
O D:HOH366 2.4 31.1 1.0
C D:ASP124 3.0 17.8 1.0
CG D:ASP124 3.1 25.1 1.0
CG D:ASP128 3.2 29.7 1.0
CA D:ASP124 3.4 18.8 1.0
CB D:ASP124 3.7 20.6 1.0
CB D:ASP128 3.7 26.2 1.0
O D:HOH379 4.0 33.6 1.0
N D:ALA125 4.1 15.7 1.0
OD2 D:ASP124 4.1 30.4 1.0
N D:ASP128 4.2 20.0 1.0
O D:HOH431 4.2 50.9 1.0
OD1 D:ASP128 4.3 34.8 1.0
O D:HOH453 4.5 40.3 1.0
CA D:ASP128 4.5 22.8 1.0
CA D:ALA125 4.6 16.4 1.0
O D:HOH412 4.6 33.0 1.0
N D:ASP124 4.8 16.7 1.0
CB D:THR127 5.0 21.9 1.0

Reference:

L.Shang, G.Li, Q.Lin, M.Ou, J.Liang, G.Xiao, Z.Wang, S.Cui, T.Zhang, L.Liu, G.Zhang. Crystal Structure of the Cytokinin-Producing Enzyme "Lonely Guy" (Log) From Mycobacterium Tuberculosis. Biochem.Biophys.Res.Commun. V. 598 113 2022.
ISSN: ESSN 1090-2104
PubMed: 35158209
DOI: 10.1016/J.BBRC.2022.01.103
Page generated: Fri Apr 7 01:29:04 2023

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