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Magnesium in PDB 5irp: Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis

Enzymatic activity of Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis:
5.1.1.1;

Protein crystallography data

The structure of Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis, PDB code: 5irp was solved by N.Bernardo-Garcia, F.Gago, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 2.10
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 72.888, 72.888, 332.833, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19.9

Other elements in 5irp:

The structure of Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis (pdb code 5irp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis, PDB code: 5irp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in 5irp

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Magnesium binding site 1 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:35.0
occ:1.00
 O A:HOH753 2.3 30.3 1.0
O A:ASN301 2.4 26.6 1.0
O A:HOH661 3.2 51.0 1.0
C A:ASN301 3.4 31.2 1.0
O A:HOH625 3.7 31.5 1.0
N A:ARG302 4.2 29.9 1.0
CA A:ASN301 4.3 28.3 1.0
CA A:ARG302 4.4 28.5 1.0
O A:HOH529 4.4 31.8 1.0
CB A:ASN301 4.5 25.4 1.0

Magnesium binding site 2 out of 20 in 5irp

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Magnesium binding site 2 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:56.4
occ:1.00
 O A:HOH624 2.2 50.0 1.0
O A:HOH526 2.6 30.3 1.0
O A:HOH519 2.8 62.0 1.0
O A:HOH802 3.8 48.3 1.0
O A:LEU202 4.2 25.2 1.0
OD2 A:ASP222 4.4 25.6 1.0
OD1 A:ASP222 4.4 27.3 1.0
O A:HOH786 4.7 54.0 1.0
CG A:ASP222 4.8 24.6 1.0
O A:PRO203 4.8 24.5 1.0

Magnesium binding site 3 out of 20 in 5irp

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Magnesium binding site 3 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:64.6
occ:1.00
 O A:HOH760 2.5 49.2 1.0
O B:HOH585 2.6 38.3 1.0
O A:HOH834 2.7 49.6 1.0
OE1 A:GLN107 2.7 51.1 1.0
O A:HOH750 2.8 56.3 1.0
CD A:GLN107 3.5 47.8 1.0
NE2 A:GLN107 3.6 45.7 1.0
OH B:TYR259 3.8 30.6 1.0
O A:HOH582 4.6 39.6 1.0
CE1 B:TYR259 4.6 24.6 1.0
CZ B:TYR259 4.7 30.7 1.0
O A:HOH539 4.7 31.7 1.0
O B:HOH682 4.7 29.9 1.0
CG A:GLN107 5.0 36.2 1.0

Magnesium binding site 4 out of 20 in 5irp

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Magnesium binding site 4 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg412

b:32.5
occ:1.00
 O A:HOH645 2.2 38.6 1.0
O A:LEU161 2.5 30.1 1.0
O A:SER158 2.6 27.5 1.0
O A:LEU155 2.6 28.6 1.0
O A:HOH755 2.7 16.0 1.0
O A:LYS156 3.5 35.1 1.0
C A:LEU161 3.5 28.6 1.0
C A:SER158 3.5 30.1 1.0
C A:LEU155 3.6 24.2 1.0
CA A:LYS156 3.7 32.6 1.0
NH2 A:ARG126 3.7 61.6 1.0
C A:LYS156 3.8 35.7 1.0
N A:LYS156 4.1 26.1 1.0
N A:SER158 4.2 30.5 1.0
CA A:SER158 4.3 28.1 1.0
CA A:LEU161 4.3 26.8 1.0
N A:ARG162 4.3 24.2 1.0
N A:LEU161 4.4 26.7 1.0
N A:LYS159 4.4 26.3 1.0
CB A:LEU161 4.4 25.2 1.0
CA A:ARG162 4.5 24.8 1.0
CA A:LYS159 4.5 35.7 1.0
CB A:SER158 4.6 24.5 1.0
N A:ALA157 4.7 31.4 1.0
CD1 A:LEU155 4.7 25.0 1.0
CZ A:ARG126 4.7 64.0 1.0
C A:LYS159 4.8 29.9 1.0
NE A:ARG126 4.8 57.7 1.0
CA A:LEU155 4.9 22.6 1.0
C A:ALA157 4.9 36.2 1.0
CG A:LEU155 5.0 26.8 1.0
CB A:LYS156 5.0 39.9 1.0
O A:LYS159 5.0 28.5 1.0

Magnesium binding site 5 out of 20 in 5irp

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Magnesium binding site 5 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg413

b:59.2
occ:0.50
 O A:HOH528 2.4 29.2 1.0
O A:HOH663 3.7 24.5 1.0
O A:GLN241 3.9 32.8 1.0
O A:HOH585 4.0 33.5 1.0
O A:HOH501 4.7 41.4 0.5
C A:GLN241 4.7 30.2 1.0

Magnesium binding site 6 out of 20 in 5irp

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Magnesium binding site 6 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg414

b:54.4
occ:1.00
 O A:HOH811 2.7 73.1 1.0
O A:HOH546 2.9 50.1 1.0
O A:HOH792 3.0 45.7 1.0
OE2 A:GLU282 3.1 34.6 1.0
O A:ILE277 3.3 34.3 1.0
OH A:TYR276 3.5 34.2 1.0
CZ A:TYR276 3.9 36.2 1.0
CD A:GLU282 3.9 37.5 1.0
CG A:GLU279 4.0 44.5 1.0
OE1 A:GLU282 4.1 34.9 1.0
N A:GLU279 4.2 35.5 1.0
CE1 A:TYR276 4.2 30.4 1.0
OE1 A:GLU279 4.2 63.0 1.0
CA A:ALA278 4.3 29.7 1.0
C A:ILE277 4.4 34.2 1.0
C A:ALA278 4.5 34.1 1.0
CD A:GLU279 4.6 56.5 1.0
CE2 A:TYR276 4.6 36.7 1.0
N A:ALA278 4.8 32.1 1.0
CB A:GLU279 5.0 41.0 1.0

Magnesium binding site 7 out of 20 in 5irp

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Magnesium binding site 7 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg415

b:63.2
occ:1.00
 O B:HOH754 2.1 44.4 1.0
O A:HOH732 2.2 51.9 1.0
O A:HOH816 2.3 41.9 1.0
O A:HOH515 2.5 33.8 1.0
OE2 A:GLU175 4.6 45.8 1.0
OE1 A:GLU175 4.8 33.8 1.0
O B:GLY273 4.8 32.7 1.0
NH2 B:ARG317 5.0 52.2 1.0

Magnesium binding site 8 out of 20 in 5irp

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Magnesium binding site 8 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


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 the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg417

b:65.5
occ:1.00
 O A:HOH698 2.0 63.4 1.0
CE A:MET1 2.6 58.5 1.0
O A:HOH831 2.7 49.6 1.0
SD A:MET1 3.5 71.0 1.0
OE2 A:GLU11 3.7 27.4 1.0
OE1 A:GLU338 4.0 34.5 1.0
O A:HOH717 4.3 48.1 1.0
CD1 A:ILE2 4.3 36.9 1.0
CD1 A:ILE384 4.3 60.1 1.0
CD A:GLU11 4.8 29.5 1.0
CZ2 A:TRP9 4.8 22.9 1.0
CD A:GLU338 4.8 31.1 1.0
NZ A:LYS254 4.8 35.0 1.0
OE2 A:GLU338 4.9 34.2 1.0
CG1 A:ILE2 4.9 42.6 1.0

Magnesium binding site 9 out of 20 in 5irp

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Magnesium binding site 9 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg418

b:55.9
occ:1.00
 O A:HOH720 2.3 41.6 1.0
O A:HOH630 2.8 33.0 1.0
O A:HOH713 2.9 44.7 1.0
CD A:PRO249 3.9 23.0 1.0
NZ A:LYS344 4.1 50.5 1.0
CG A:PRO249 4.2 26.1 1.0
O A:HOH787 4.2 47.3 1.0
OE2 A:GLU349 4.5 40.0 1.0
OE1 A:GLU349 4.7 38.5 1.0
CE A:LYS344 4.7 51.1 1.0
O A:LEU247 4.9 28.8 1.0
O A:HOH589 4.9 28.4 1.0

Magnesium binding site 10 out of 20 in 5irp

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Magnesium binding site 10 out of 20 in the Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Alanine Racemase BSU17640 From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg409

b:43.1
occ:1.00
 O A:HOH799 2.2 27.9 1.0
O B:HOH781 2.2 32.9 1.0
O B:HOH536 2.2 38.0 1.0
O B:HOH811 2.2 26.3 1.0
O A:HOH806 2.2 26.7 1.0
O B:HOH623 2.2 42.1 1.0
O B:HOH510 3.3 43.0 1.0
O A:HOH593 3.7 43.9 1.0
O A:HOH556 3.9 41.4 1.0
O A:HOH595 3.9 15.2 1.0
O B:HOH784 4.1 19.8 1.0
O B:HOH553 4.3 19.1 1.0
OG1 B:THR369 4.4 18.9 1.0
OE2 B:GLU365 4.5 19.8 1.0
O B:HOH820 4.5 22.2 1.0
CG2 B:THR369 4.5 23.5 1.0
CB B:THR369 4.6 21.2 1.0
O A:HOH554 4.7 27.1 1.0
O B:HOH562 4.8 23.5 1.0
O A:HOH778 4.8 16.6 1.0
CD B:GLU365 4.9 22.5 1.0

Reference:

N.Bernardo-Garcia, P.A.Sanchez-Murcia, A.Espaillat, S.Martinez-Caballero, F.Cava, J.A.Hermoso, F.Gago. Cold-Induced Aldimine Bond Cleavage By Tris in Bacillus Subtilis Alanine Racemase. Org.Biomol.Chem. V. 17 4350 2019.
ISSN: ESSN 1477-0539
PubMed: 30977502
DOI: 10.1039/C9OB00223E
Page generated: Sun Sep 29 16:54:19 2024

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