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Magnesium in PDB 3na8: Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa

Enzymatic activity of Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa:
4.2.1.52;

Protein crystallography data

The structure of Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa, PDB code: 3na8 was solved by W.Qiu, R.Lam, V.Romanov, K.Jones, E.F.Pai, N.Y.Chirgadze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.06 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.370, 156.210, 76.580, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa (pdb code 3na8). 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 A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa, PDB code: 3na8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3na8

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Magnesium binding site 1 out of 4 in the Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa


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 A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg316

b:22.1
occ:1.00
 O A:VAL175 2.2 25.1 1.0
O A:VAL181 2.2 22.3 1.0
O A:VAL178 2.3 24.8 1.0
O A:HOH324 2.4 30.0 1.0
O A:HOH399 2.4 29.2 1.0
O A:ASP179 2.9 24.4 1.0
C A:VAL181 3.3 22.3 1.0
C A:VAL175 3.3 25.2 1.0
C A:VAL178 3.3 24.9 1.0
C A:ASP179 3.4 24.3 1.0
CA A:ASP179 3.7 24.6 1.0
N A:VAL181 3.8 22.9 1.0
O A:HOH396 3.9 33.7 1.0
N A:ASP179 3.9 24.7 1.0
CA A:VAL175 3.9 25.1 1.0
CA A:VAL181 4.0 22.5 1.0
CG1 A:VAL175 4.2 24.9 1.0
N A:THR182 4.3 22.0 1.0
CB A:VAL181 4.3 22.5 1.0
N A:ASN180 4.3 23.9 1.0
N A:ARG176 4.4 25.4 1.0
CA A:VAL178 4.5 25.0 1.0
CA A:THR182 4.5 21.8 1.0
CG2 A:THR182 4.5 21.7 1.0
N A:VAL178 4.5 25.2 1.0
O A:ILE174 4.5 24.8 1.0
C A:ASN180 4.6 23.3 1.0
O A:HOH1028 4.6 41.5 1.0
CB A:VAL175 4.7 25.1 1.0
C A:ARG176 4.7 25.7 1.0
CA A:ARG176 4.7 25.7 1.0
O A:ARG176 4.8 25.8 1.0
O A:HOH635 4.9 29.9 1.0
CA A:ASN180 4.9 23.6 1.0

Magnesium binding site 2 out of 4 in 3na8

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Magnesium binding site 2 out of 4 in the Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa


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 A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg316

b:23.1
occ:1.00
 O B:VAL175 2.2 24.3 1.0
O B:VAL178 2.4 24.2 1.0
O B:VAL181 2.4 22.2 1.0
O B:HOH602 2.5 24.3 1.0
O B:HOH361 2.5 24.1 1.0
O B:ASP179 2.7 24.0 1.0
C B:ASP179 3.3 23.9 1.0
C B:VAL175 3.3 24.4 1.0
C B:VAL178 3.4 24.2 1.0
C B:VAL181 3.4 22.3 1.0
CA B:ASP179 3.6 24.2 1.0
N B:ASP179 3.9 24.1 1.0
O B:HOH382 3.9 32.1 1.0
N B:VAL181 3.9 22.8 1.0
CA B:VAL175 4.0 24.1 1.0
CA B:VAL181 4.1 22.5 1.0
CG1 B:VAL175 4.2 24.0 1.0
N B:ASN180 4.3 23.6 1.0
N B:THR182 4.3 22.2 1.0
CG2 B:THR182 4.4 22.1 1.0
CA B:THR182 4.4 22.1 1.0
N B:ARG176 4.4 24.5 1.0
CB B:VAL181 4.5 22.5 1.0
C B:ASN180 4.6 23.1 1.0
CA B:VAL178 4.6 24.2 1.0
O B:ILE174 4.6 24.1 1.0
N B:VAL178 4.6 24.4 1.0
CA B:ARG176 4.7 24.6 0.5
CB B:VAL175 4.7 24.2 1.0
CA B:ARG176 4.8 24.6 0.5
C B:ARG176 4.8 24.6 1.0
O B:ARG176 4.9 24.6 1.0
O B:HOH709 4.9 56.8 1.0
CA B:ASN180 4.9 23.4 1.0
O B:HOH420 5.0 33.8 1.0

Magnesium binding site 3 out of 4 in 3na8

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Magnesium binding site 3 out of 4 in the Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa


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 A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg316

b:28.4
occ:1.00
 O C:VAL175 2.2 28.5 1.0
O C:HOH829 2.4 44.3 1.0
O C:VAL178 2.4 28.4 1.0
O C:HOH334 2.5 33.3 1.0
O C:VAL181 2.5 27.6 1.0
O C:ASP179 2.8 28.2 1.0
C C:VAL178 3.3 28.4 1.0
C C:VAL175 3.3 28.4 1.0
C C:ASP179 3.3 28.3 1.0
C C:VAL181 3.5 27.7 1.0
CA C:ASP179 3.6 28.5 1.0
N C:ASP179 3.8 28.4 1.0
N C:VAL181 3.9 27.9 1.0
CA C:VAL175 4.0 28.3 1.0
CA C:VAL181 4.1 27.7 1.0
CG1 C:VAL175 4.2 28.3 1.0
N C:ASN180 4.3 28.2 1.0
N C:ARG176 4.4 28.6 1.0
CA C:VAL178 4.4 28.5 1.0
N C:THR182 4.4 27.7 1.0
CB C:VAL181 4.5 27.7 1.0
N C:VAL178 4.5 28.6 1.0
O C:ILE174 4.5 27.9 1.0
CG2 C:THR182 4.5 27.6 1.0
O C:ARG176 4.6 28.9 1.0
CA C:THR182 4.6 27.7 1.0
C C:ARG176 4.6 28.9 1.0
C C:ASN180 4.7 28.0 1.0
CA C:ARG176 4.7 28.9 1.0
CB C:VAL175 4.8 28.2 1.0
CA C:ASN180 5.0 28.1 1.0

Magnesium binding site 4 out of 4 in 3na8

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Magnesium binding site 4 out of 4 in the Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa


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 A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg316

b:36.0
occ:1.00
 O D:VAL181 2.2 29.2 1.0
O D:VAL175 2.2 31.2 1.0
O D:HOH332 2.4 32.5 1.0
O D:VAL178 2.4 31.3 1.0
O D:HOH1029 2.5 35.4 1.0
O D:ASP179 2.8 30.9 1.0
C D:VAL181 3.2 29.2 1.0
C D:VAL178 3.4 31.3 1.0
C D:VAL175 3.4 31.2 1.0
C D:ASP179 3.4 30.9 1.0
N D:VAL181 3.7 29.8 1.0
CA D:ASP179 3.7 31.2 1.0
O D:HOH451 3.8 39.1 1.0
CA D:VAL181 3.9 29.4 1.0
N D:ASP179 4.0 31.2 1.0
CA D:VAL175 4.0 31.0 1.0
N D:THR182 4.1 29.1 1.0
CG1 D:VAL175 4.2 30.8 1.0
CB D:VAL181 4.2 29.4 1.0
CG2 D:THR182 4.3 28.9 1.0
N D:ASN180 4.3 30.6 1.0
CA D:THR182 4.3 28.9 1.0
C D:ASN180 4.5 30.1 1.0
CA D:VAL178 4.5 31.4 1.0
N D:ARG176 4.5 31.4 1.0
N D:VAL178 4.5 31.6 1.0
O D:ILE174 4.6 30.7 1.0
CB D:VAL175 4.7 30.9 1.0
O D:HOH808 4.7 47.3 1.0
CA D:ARG176 4.8 31.8 1.0
O D:HOH347 4.9 28.1 1.0
CA D:ASN180 4.9 30.4 1.0
C D:ARG176 5.0 31.8 1.0
CG1 D:VAL181 5.0 29.3 1.0
CB D:THR182 5.0 28.9 1.0

Reference:

W.Qiu, R.Lam, V.Romanov, K.Jones, E.F.Pai, N.Y.Chirgadze. Crystal Structure of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa To Be Published.
Page generated: Thu Aug 15 07:55:38 2024

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