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Magnesium in PDB 1xxx: Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis:
4.2.1.52;

Protein crystallography data

The structure of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis, PDB code: 1xxx was solved by G.Kefala, S.Panjikar, R.Janowski, M.S.Weiss, Tb Structural Genomicsconsortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.790, 87.370, 139.850, 90.00, 107.78, 90.00
R / Rfree (%) 14.8 / 21.5

Other elements in 1xxx:

The structure of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis (pdb code 1xxx). 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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis, PDB code: 1xxx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1xxx

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Magnesium binding site 1 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) 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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:31.8
occ:1.00
 O A:HOH3026 2.2 21.9 1.0
O A:ALA162 2.3 28.4 1.0
O A:ILE167 2.5 24.7 1.0
O A:HIS164 2.7 27.4 1.0
O A:HOH3233 2.8 30.2 1.0
O A:HOH3080 2.9 33.9 1.0
C A:ALA162 3.4 27.4 1.0
C A:ILE167 3.7 26.1 1.0
C A:HIS164 3.8 26.7 1.0
O A:HOH3215 3.9 40.7 1.0
CA A:ALA162 3.9 26.6 1.0
CD2 A:LEU189 4.4 28.3 1.0
N A:HIS164 4.4 26.1 1.0
N A:SER163 4.5 26.1 1.0
N A:ILE167 4.5 28.9 1.0
CA A:ILE167 4.5 26.7 1.0
CA A:PRO165 4.6 26.8 1.0
C A:PRO165 4.6 26.6 1.0
N A:VAL168 4.6 26.1 1.0
O A:LEU161 4.6 27.6 1.0
N A:PRO165 4.6 27.8 1.0
O A:PRO165 4.7 28.1 1.0
CA A:VAL168 4.7 26.9 1.0
C A:SER163 4.7 25.5 1.0
CB A:ALA162 4.7 25.2 1.0
CA A:HIS164 4.7 27.4 1.0
CB A:ILE167 4.7 26.7 1.0
CA A:SER163 4.8 25.6 1.0
O A:HOH3230 5.0 36.8 1.0

Magnesium binding site 2 out of 8 in 1xxx

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Magnesium binding site 2 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) 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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:34.8
occ:1.00
 O B:ALA162 2.3 28.2 1.0
O B:ILE167 2.4 26.4 1.0
O B:HIS164 2.4 28.2 1.0
O B:HOH3072 2.5 31.7 1.0
O B:HOH3232 2.6 31.4 1.0
C B:ALA162 3.4 28.5 1.0
C B:ILE167 3.5 26.7 1.0
C B:HIS164 3.5 28.3 1.0
N B:ILE167 4.1 28.0 1.0
N B:HIS164 4.2 29.6 1.0
CA B:ILE167 4.2 27.2 1.0
CA B:ALA162 4.2 28.2 1.0
C B:SER163 4.2 29.8 1.0
O B:PRO165 4.2 28.9 1.0
C B:PRO165 4.3 28.4 1.0
CA B:PRO165 4.3 28.1 1.0
N B:SER163 4.3 28.5 1.0
N B:PRO165 4.4 28.4 1.0
CA B:SER163 4.4 29.8 1.0
O B:HOH3178 4.4 30.4 1.0
CA B:HIS164 4.5 28.4 1.0
N B:VAL168 4.5 26.9 1.0
CB B:ILE167 4.5 26.8 1.0
CD2 B:LEU189 4.5 30.2 1.0
CA B:VAL168 4.5 26.2 1.0
O B:SER163 4.7 29.7 1.0
O B:LEU161 4.7 28.7 1.0
N B:ASN166 4.9 27.7 1.0

Magnesium binding site 3 out of 8 in 1xxx

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Magnesium binding site 3 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) 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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:28.2
occ:1.00
 O C:HIS164 2.2 25.9 1.0
O C:ALA162 2.3 26.9 1.0
O C:ILE167 2.3 24.7 1.0
O C:HOH3160 2.5 24.4 1.0
C C:ALA162 3.3 27.6 1.0
C C:HIS164 3.3 26.7 1.0
C C:ILE167 3.4 26.1 1.0
N C:HIS164 4.0 27.1 1.0
N C:ILE167 4.1 26.1 1.0
CA C:ALA162 4.1 27.2 1.0
C C:SER163 4.2 25.5 1.0
CA C:ILE167 4.2 25.9 1.0
C C:PRO165 4.2 26.8 1.0
O C:PRO165 4.2 26.2 1.0
N C:PRO165 4.2 27.8 1.0
CA C:PRO165 4.2 27.8 1.0
CA C:HIS164 4.3 27.0 1.0
N C:SER163 4.3 26.1 1.0
CB C:ILE167 4.4 26.5 1.0
CA C:SER163 4.4 25.9 1.0
O C:HOH3098 4.5 23.1 1.0
N C:VAL168 4.5 25.6 1.0
O C:LEU161 4.5 29.9 1.0
CD2 C:LEU189 4.6 28.9 1.0
CA C:VAL168 4.6 26.9 1.0
O C:SER163 4.6 25.2 1.0
N C:ASN166 4.8 25.9 1.0
O C:HOH3151 4.9 33.1 1.0
CB C:HIS164 5.0 26.8 1.0
CB C:ALA162 5.0 26.0 1.0

Magnesium binding site 4 out of 8 in 1xxx

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Magnesium binding site 4 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) 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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:38.4
occ:1.00
 O D:ILE167 2.3 25.6 1.0
O D:ALA162 2.4 28.6 1.0
O D:HIS164 2.4 28.7 1.0
O D:HOH3090 2.6 29.0 1.0
C D:ALA162 3.4 28.4 1.0
C D:ILE167 3.5 26.8 1.0
C D:HIS164 3.5 28.1 1.0
N D:ILE167 4.1 28.2 1.0
N D:HIS164 4.2 27.7 1.0
CA D:ALA162 4.2 27.2 1.0
CA D:ILE167 4.2 27.2 1.0
C D:SER163 4.2 28.6 1.0
O D:PRO165 4.2 27.7 1.0
CA D:PRO165 4.3 28.1 1.0
C D:PRO165 4.3 28.1 1.0
N D:PRO165 4.3 27.9 1.0
N D:SER163 4.4 29.6 1.0
CA D:HIS164 4.4 27.4 1.0
N D:VAL168 4.5 25.8 1.0
CB D:ILE167 4.5 27.4 1.0
O D:SER163 4.5 27.8 1.0
CA D:SER163 4.5 30.6 1.0
CA D:VAL168 4.5 25.6 1.0
CD2 D:LEU189 4.6 31.1 1.0
O D:LEU161 4.7 27.7 1.0
N D:ASN166 4.9 28.7 1.0

Magnesium binding site 5 out of 8 in 1xxx

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Magnesium binding site 5 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2005

b:41.2
occ:1.00
 O E:HIS164 2.2 28.2 1.0
O E:ALA162 2.2 29.8 1.0
O E:ILE167 2.2 26.1 1.0
O E:HOH3038 3.0 36.5 1.0
C E:ALA162 3.3 29.1 1.0
C E:HIS164 3.3 28.5 1.0
C E:ILE167 3.4 26.9 1.0
N E:HIS164 3.9 29.7 1.0
N E:ILE167 4.0 28.1 1.0
C E:SER163 4.0 30.7 1.0
CA E:ALA162 4.0 27.6 1.0
CA E:ILE167 4.1 26.9 1.0
CA E:HIS164 4.1 28.6 1.0
N E:PRO165 4.2 28.3 1.0
N E:SER163 4.2 30.1 1.0
CB E:ILE167 4.3 26.3 1.0
C E:PRO165 4.3 28.6 1.0
CA E:PRO165 4.3 28.3 1.0
O E:LEU161 4.3 28.0 1.0
O E:PRO165 4.3 28.1 1.0
O E:SER163 4.4 31.1 1.0
N E:VAL168 4.4 27.1 1.0
CA E:SER163 4.5 30.9 1.0
CA E:VAL168 4.6 27.1 1.0
CD2 E:LEU189 4.6 30.6 1.0
N E:ASN166 4.8 28.6 1.0
CB E:HIS164 4.8 28.1 1.0
CB E:ALA162 4.9 27.0 1.0
C E:ASN166 4.9 28.8 1.0
CG2 E:ILE167 5.0 28.0 1.0

Magnesium binding site 6 out of 8 in 1xxx

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Magnesium binding site 6 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2006

b:52.7
occ:1.00
 O F:ILE167 2.0 25.5 1.0
O F:HIS164 2.3 27.5 1.0
O F:ALA162 2.5 26.9 1.0
C F:ILE167 3.1 26.7 1.0
C F:HIS164 3.4 28.3 1.0
C F:ALA162 3.6 27.8 1.0
N F:ILE167 3.8 27.1 1.0
CA F:ILE167 3.9 26.7 1.0
C F:PRO165 4.1 28.4 1.0
O F:PRO165 4.1 29.5 1.0
CA F:PRO165 4.2 28.4 1.0
N F:VAL168 4.2 26.9 1.0
CB F:ILE167 4.2 26.2 1.0
N F:PRO165 4.2 28.6 1.0
N F:HIS164 4.2 29.3 1.0
CA F:ALA162 4.3 26.7 1.0
CA F:VAL168 4.3 27.0 1.0
CA F:HIS164 4.4 28.5 1.0
C F:SER163 4.4 30.1 1.0
N F:ASN166 4.5 27.8 1.0
N F:SER163 4.6 29.1 1.0
CD2 F:LEU189 4.6 30.4 1.0
O F:LEU161 4.6 28.4 1.0
CA F:SER163 4.7 30.1 1.0
C F:ASN166 4.7 28.7 1.0
O F:SER163 4.9 30.3 1.0
CG1 F:VAL168 4.9 27.4 1.0
CG2 F:ILE167 5.0 24.6 1.0

Magnesium binding site 7 out of 8 in 1xxx

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Magnesium binding site 7 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg2007

b:32.7
occ:1.00
 O G:HOH3147 2.2 33.2 1.0
O G:HIS164 2.4 27.1 1.0
O G:ALA162 2.4 28.3 1.0
O G:ILE167 2.5 25.7 1.0
O G:HOH3226 2.6 30.5 1.0
C G:HIS164 3.4 27.3 1.0
C G:ALA162 3.5 28.0 1.0
C G:ILE167 3.6 26.0 1.0
C G:SER163 4.1 28.7 1.0
N G:HIS164 4.1 28.4 1.0
CA G:PRO165 4.2 28.3 1.0
C G:PRO165 4.2 27.8 1.0
N G:ILE167 4.2 26.8 1.0
O G:PRO165 4.2 25.7 1.0
N G:PRO165 4.2 27.8 1.0
N G:SER163 4.3 28.0 1.0
CA G:ILE167 4.3 26.4 1.0
CA G:SER163 4.3 29.4 1.0
CA G:ALA162 4.4 27.5 1.0
CA G:HIS164 4.4 27.5 1.0
O G:SER163 4.5 29.6 1.0
N G:VAL168 4.6 26.1 1.0
CA G:VAL168 4.6 26.1 1.0
CB G:ILE167 4.6 25.1 1.0
N G:ASN166 4.7 27.3 1.0
CD2 G:LEU189 4.8 31.7 1.0
O G:LEU161 4.8 28.6 1.0

Magnesium binding site 8 out of 8 in 1xxx

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Magnesium binding site 8 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg2008

b:34.6
occ:1.00
 O H:ALA162 2.3 29.1 1.0
O H:ILE167 2.3 25.1 1.0
O H:HOH3095 2.3 32.4 1.0
O H:HIS164 2.5 27.9 1.0
O H:HOH3184 3.0 38.7 1.0
C H:ALA162 3.4 28.3 1.0
C H:ILE167 3.5 26.4 1.0
C H:HIS164 3.6 29.0 1.0
CA H:ALA162 4.1 27.7 1.0
N H:HIS164 4.2 32.2 1.0
N H:ILE167 4.3 26.1 1.0
CA H:ILE167 4.3 26.1 1.0
N H:SER163 4.4 29.4 1.0
C H:SER163 4.4 33.6 1.0
N H:PRO165 4.4 29.1 1.0
CA H:PRO165 4.4 28.5 1.0
O H:PRO165 4.4 29.0 1.0
C H:PRO165 4.4 28.1 1.0
CA H:HIS164 4.4 29.8 1.0
N H:VAL168 4.5 26.0 1.0
CB H:ILE167 4.5 25.4 1.0
CD2 H:LEU189 4.5 30.4 1.0
CA H:VAL168 4.6 26.5 1.0
CA H:SER163 4.6 31.9 1.0
O H:LEU161 4.7 28.2 1.0
CB H:ALA162 4.9 26.2 1.0
O H:SER163 5.0 36.9 1.0

Reference:

G.Kefala, G.L.Evans, M.D.Griffin, S.R.Devenish, F.G.Pearce, M.A.Perugini, J.A.Gerrard, M.S.Weiss, R.C.Dobson. Crystal Structure and Kinetic Study of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis. Biochem.J. V. 411 351 2008.
ISSN: ISSN 0264-6021
PubMed: 18062777
DOI: 10.1042/BJ20071360
Page generated: Tue Aug 13 18:25:23 2024

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