Atomistry » Magnesium » PDB 1ye8-1yqw » 1yl7
Atomistry »
  Magnesium »
    PDB 1ye8-1yqw »
      1yl7 »

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

Go back to Magnesium Binding Sites List in 1yl7
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

Go back to Magnesium Binding Sites List in 1yl7
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

Go back to Magnesium Binding Sites List in 1yl7
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

Go back to Magnesium Binding Sites List in 1yl7
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

Go back to Magnesium Binding Sites List in 1yl7
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

Go back to Magnesium Binding Sites List in 1yl7
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: Sun Aug 10 08:20:28 2025

Last articles

Mg in 5QJZ
Mg in 5QJY
Mg in 5QJX
Mg in 5QJW
Mg in 5QJV
Mg in 5QJU
Mg in 5QJT
Mg in 5QJS
Mg in 5QJQ
Mg in 5QJR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy