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Magnesium in PDB 1yl7: The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)

Enzymatic activity of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)

All present enzymatic activity of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C):
1.3.1.26;

Protein crystallography data

The structure of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C), PDB code: 1yl7 was solved by R.Janowski, G.Kefala, M.S.Weiss, Tb Structural Genomics Consortium(Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.34
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 238.600, 67.520, 154.490, 90.00, 117.08, 90.00
R / Rfree (%) 18.1 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C) (pdb code 1yl7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C), PDB code: 1yl7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1yl7

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Magnesium binding site 1 out of 6 in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:52.7
occ:1.00
 O A:ALA23 2.1 46.6 1.0
O A:LEU26 2.2 42.8 1.0
O A:VAL20 2.5 41.8 1.0
O A:ALA21 2.9 42.1 1.0
C A:ALA23 3.2 45.9 1.0
C A:ALA21 3.4 42.1 1.0
C A:LEU26 3.4 43.3 1.0
C A:VAL20 3.5 41.1 1.0
CA A:ALA21 3.6 41.7 1.0
N A:ALA23 3.9 44.0 1.0
CA A:ASP24 4.0 46.2 1.0
N A:ALA21 4.0 41.2 1.0
N A:ASP24 4.1 46.0 1.0
CA A:ALA23 4.2 45.2 1.0
N A:LEU26 4.2 43.6 1.0
CA A:LEU26 4.3 43.1 1.0
N A:ALA22 4.3 42.4 1.0
N A:THR27 4.4 43.3 1.0
C A:ALA22 4.4 43.4 1.0
CB A:LEU26 4.5 42.7 1.0
CA A:THR27 4.5 43.6 1.0
CB A:ALA23 4.8 45.1 1.0
C A:ASP24 4.8 45.8 1.0
CA A:VAL20 4.8 40.2 1.0
N A:LEU28 4.8 44.1 1.0
CG1 A:VAL20 4.8 40.2 1.0
N A:ASP25 4.9 45.1 1.0
CA A:ALA22 4.9 42.8 1.0
CB A:ASP24 5.0 46.8 1.0
O A:ALA22 5.0 43.2 1.0

Magnesium binding site 2 out of 6 in 1yl7

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Magnesium binding site 2 out of 6 in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:40.1
occ:1.00
 O B:LEU26 2.1 36.7 1.0
O B:ALA23 2.2 35.7 1.0
O B:VAL20 2.4 36.5 1.0
O B:HOH555 2.6 43.3 1.0
O B:ALA21 2.9 34.9 1.0
C B:LEU26 3.3 36.1 1.0
C B:ALA23 3.3 35.4 1.0
C B:ALA21 3.4 33.1 1.0
C B:VAL20 3.5 34.4 1.0
CA B:ALA21 3.8 33.4 1.0
N B:ALA23 3.9 34.3 1.0
CA B:ALA23 4.0 35.0 1.0
N B:ALA21 4.1 34.1 1.0
CA B:LEU26 4.2 35.3 1.0
N B:LEU26 4.2 34.1 1.0
CB B:ALA23 4.3 34.8 1.0
N B:THR27 4.3 36.3 1.0
N B:ALA22 4.4 32.8 1.0
N B:ASP24 4.4 35.3 1.0
CA B:THR27 4.5 37.1 1.0
C B:ALA22 4.5 33.3 1.0
CB B:LEU26 4.5 34.7 1.0
N B:LEU28 4.7 38.4 1.0
CA B:ASP24 4.7 36.3 1.0
CA B:VAL20 4.7 33.9 1.0
C B:ASP24 4.8 35.9 1.0
CG1 B:VAL20 4.8 33.4 1.0
CA B:ALA22 4.9 32.8 1.0
O B:HOH551 5.0 42.3 1.0
O B:ASP24 5.0 36.3 1.0

Magnesium binding site 3 out of 6 in 1yl7

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Magnesium binding site 3 out of 6 in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:26.2
occ:1.00
 O D:LEU26 2.2 24.0 1.0
O D:ALA23 2.4 27.0 1.0
O D:HOH505 2.4 20.5 1.0
O D:HOH585 2.5 40.0 1.0
O D:VAL20 2.5 25.0 1.0
O D:ALA21 2.7 25.2 1.0
C D:ALA21 3.3 24.9 1.0
C D:LEU26 3.4 23.8 1.0
C D:ALA23 3.5 26.3 1.0
C D:VAL20 3.6 24.8 1.0
CA D:ALA21 3.6 24.6 1.0
O D:HOH584 3.8 30.0 1.0
N D:ALA23 4.0 25.5 1.0
N D:ALA21 4.1 24.3 1.0
CA D:ALA23 4.2 25.9 1.0
N D:THR27 4.2 23.9 1.0
CA D:THR27 4.3 24.8 1.0
CA D:LEU26 4.3 23.3 1.0
N D:ALA22 4.3 25.4 1.0
N D:LEU26 4.4 23.6 1.0
N D:LEU28 4.4 25.4 1.0
C D:ALA22 4.5 25.0 1.0
N D:ASP24 4.5 26.6 1.0
CB D:LEU26 4.5 22.2 1.0
CB D:ALA23 4.6 24.8 1.0
CA D:ASP24 4.7 27.5 1.0
C D:THR27 4.8 24.7 1.0
CA D:VAL20 4.9 23.6 1.0
CA D:ALA22 4.9 24.3 1.0
C D:ASP24 4.9 27.0 1.0
CG1 D:VAL20 5.0 21.8 1.0

Magnesium binding site 4 out of 6 in 1yl7

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Magnesium binding site 4 out of 6 in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:35.7
occ:1.00
 O E:ALA23 2.0 33.9 1.0
O E:LEU26 2.1 33.9 1.0
O E:VAL20 2.2 33.1 1.0
O E:ALA21 3.0 30.2 1.0
C E:ALA23 3.1 34.2 1.0
C E:LEU26 3.2 34.0 1.0
C E:VAL20 3.3 32.2 1.0
C E:ALA21 3.3 31.4 1.0
CA E:ALA21 3.6 31.2 1.0
N E:ALA23 3.7 33.3 1.0
CA E:ALA23 3.8 33.6 1.0
N E:ALA21 3.9 32.4 1.0
CA E:LEU26 4.0 33.9 1.0
CB E:ALA23 4.0 32.3 1.0
N E:LEU26 4.0 33.6 1.0
CB E:LEU26 4.0 33.1 1.0
N E:ALA22 4.2 31.2 1.0
N E:ASP24 4.2 35.2 1.0
N E:THR27 4.3 33.9 1.0
C E:ALA22 4.3 32.3 1.0
CA E:THR27 4.4 34.3 1.0
CA E:VAL20 4.5 31.9 1.0
N E:LEU28 4.5 34.8 1.0
CA E:ASP24 4.6 36.2 1.0
CG1 E:VAL20 4.6 32.8 1.0
C E:ASP24 4.7 35.4 1.0
CA E:ALA22 4.8 31.4 1.0
O E:ALA22 4.9 32.5 1.0
C E:THR27 5.0 34.7 1.0

Magnesium binding site 5 out of 6 in 1yl7

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Magnesium binding site 5 out of 6 in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg406

b:80.5
occ:1.00
 O F:ALA23 2.1 55.7 1.0
O F:VAL20 2.2 53.1 1.0
O F:LEU26 2.6 55.1 1.0
O F:ALA21 3.3 54.2 1.0
C F:VAL20 3.3 52.9 1.0
C F:ALA23 3.3 56.0 1.0
C F:ALA21 3.4 54.1 1.0
CA F:ALA21 3.5 53.6 1.0
C F:LEU26 3.5 55.5 1.0
N F:ALA21 3.8 53.1 1.0
N F:ALA23 4.0 55.5 1.0
N F:ALA22 4.1 54.5 1.0
CA F:ALA23 4.1 55.8 1.0
N F:THR27 4.2 55.8 1.0
CA F:THR27 4.3 56.1 1.0
N F:ASP24 4.4 56.3 1.0
CB F:ALA23 4.4 56.1 1.0
CA F:LEU26 4.4 55.3 1.0
C F:ALA22 4.5 55.3 1.0
CA F:ASP24 4.6 56.7 1.0
CA F:VAL20 4.6 52.5 1.0
N F:LEU28 4.6 56.5 1.0
CB F:LEU26 4.6 55.0 1.0
N F:LEU26 4.6 55.5 1.0
CG1 F:VAL20 4.8 50.8 1.0
CA F:ALA22 4.8 55.0 1.0
CB F:ALA21 4.8 53.3 1.0
C F:THR27 4.9 56.4 1.0

Magnesium binding site 6 out of 6 in 1yl7

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Magnesium binding site 6 out of 6 in the The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of Mycobacterium Tuberculosis Dihydrodipicolinate Reductase (RV2773C) in Complex with Nadh (Crystal Form C) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg402

b:42.1
occ:1.00
 O G:LEU26 2.2 32.3 1.0
O G:ALA23 2.3 37.3 1.0
O G:VAL20 2.4 33.3 1.0
O G:HOH511 2.7 26.2 1.0
O G:ALA21 2.8 34.2 1.0
C G:ALA21 3.3 34.6 1.0
C G:LEU26 3.4 32.8 1.0
C G:VAL20 3.4 33.1 1.0
C G:ALA23 3.5 36.8 1.0
CA G:ALA21 3.5 34.1 1.0
N G:ALA23 3.9 36.6 1.0
N G:ALA21 3.9 33.4 1.0
CA G:ALA23 4.1 36.7 1.0
CA G:LEU26 4.3 32.5 1.0
N G:THR27 4.3 33.5 1.0
N G:ALA22 4.3 35.2 1.0
CA G:THR27 4.3 34.0 1.0
N G:LEU26 4.4 32.8 1.0
CB G:LEU26 4.5 32.3 1.0
CB G:ALA23 4.5 36.0 1.0
N G:ASP24 4.5 36.3 1.0
C G:ALA22 4.5 36.7 1.0
N G:LEU28 4.6 33.5 1.0
CA G:VAL20 4.7 32.0 1.0
CA G:ASP24 4.7 37.1 1.0
CG1 G:VAL20 4.8 29.5 1.0
C G:THR27 4.9 33.7 1.0
CA G:ALA22 5.0 35.9 1.0
CB G:ALA21 5.0 34.2 1.0

Reference:

R.Janowski, G.Kefala, M.S.Weiss. The Structure of Dihydrodipicolinate Reductase (Dapb) From Mycobacterium Tuberculosis in Three Crystal Forms. Acta Crystallogr.,Sect.D V. 66 61 2010.
ISSN: ISSN 0907-4449
PubMed: 20057050
DOI: 10.1107/S0907444909043960
Page generated: Mon Dec 14 07:09:56 2020

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