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Magnesium in PDB 1tkk: The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis

Protein crystallography data

The structure of The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis, PDB code: 1tkk was solved by V.A.Klenchin, D.M.Schmidt, J.A.Gerlt, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.400, 134.600, 194.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 28.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis (pdb code 1tkk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis, PDB code: 1tkk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1tkk

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Magnesium binding site 1 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:30.8
occ:1.00
 OD2 A:ASP244 2.2 21.9 1.0
OE1 A:GLU219 2.3 24.1 1.0
O A:HOH2472 2.4 29.8 1.0
OD2 A:ASP191 2.5 25.0 1.0
O A:GLU2471 2.6 23.8 1.0
C A:GLU2471 3.2 29.3 1.0
CG A:ASP191 3.2 24.3 1.0
CD A:GLU219 3.2 22.3 1.0
CG A:ASP244 3.3 20.7 1.0
OD1 A:ASP191 3.3 20.9 1.0
NZ A:LYS160 3.6 20.7 1.0
CB A:ASP244 3.7 20.5 1.0
OE2 A:GLU219 3.8 27.2 1.0
CB A:GLU219 4.0 19.8 1.0
NZ A:LYS268 4.0 26.2 1.0
OD1 A:ASN193 4.1 27.7 1.0
ND2 A:ASN266 4.1 22.6 1.0
CG A:GLU219 4.2 20.7 1.0
OD1 A:ASP244 4.3 21.3 1.0
NZ A:LYS162 4.4 25.7 1.0
CB A:ASP191 4.5 25.1 1.0
CA A:GLU2471 4.7 28.2 1.0
O A:HOH2545 4.8 25.6 1.0
CE A:LYS160 4.8 19.1 1.0
OE1 A:GLU245 4.8 12.0 1.0
O A:HOH2577 4.8 29.4 1.0
CG A:ASN266 4.8 23.4 1.0
O A:HOH2537 4.9 25.2 1.0
CE A:LYS268 4.9 23.6 1.0
OE2 A:GLU245 4.9 20.1 1.0
CG A:ASN193 5.0 22.7 1.0

Magnesium binding site 2 out of 8 in 1tkk

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Magnesium binding site 2 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1602

b:25.7
occ:1.00
 OD2 B:ASP191 2.1 16.1 1.0
OD2 B:ASP244 2.3 15.1 1.0
O B:GLU2473 2.4 21.1 1.0
O B:HOH2474 2.4 25.9 1.0
OE1 B:GLU219 2.5 22.6 1.0
C B:GLU2473 2.8 25.5 1.0
CG B:ASP191 3.1 14.7 1.0
CD B:GLU219 3.4 22.7 1.0
CG B:ASP244 3.4 11.4 1.0
OD1 B:ASP191 3.6 10.9 1.0
NZ B:LYS160 3.7 17.2 1.0
OD1 B:ASN193 3.8 27.8 1.0
OE2 B:GLU219 3.9 18.7 1.0
ND2 B:ASN266 3.9 23.4 1.0
NZ B:LYS162 4.0 15.1 1.0
CB B:ASP244 4.0 11.7 1.0
NZ B:LYS268 4.2 23.7 1.0
CB B:GLU219 4.3 20.8 1.0
CA B:GLU2473 4.3 26.5 1.0
CG B:GLU219 4.3 24.9 1.0
OE1 B:GLU245 4.4 23.8 1.0
CB B:ASP191 4.4 16.3 1.0
O B:HOH2572 4.4 32.3 1.0
OD1 B:ASP244 4.4 16.0 1.0
CE B:LYS160 4.6 20.2 1.0
O B:HOH2484 4.7 25.0 1.0
CG B:ASN193 4.7 23.4 1.0
CE B:LYS268 4.9 22.4 1.0
CD B:GLU245 4.9 23.1 1.0
CG B:ASN266 5.0 22.1 1.0
OE2 B:GLU245 5.0 25.6 1.0

Magnesium binding site 3 out of 8 in 1tkk

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Magnesium binding site 3 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1603

b:27.5
occ:1.00
 OD2 C:ASP244 2.1 20.4 1.0
OE1 C:GLU219 2.3 15.3 1.0
O C:HOH2476 2.3 14.4 1.0
OD2 C:ASP191 2.4 21.6 1.0
O C:GLU2475 2.6 25.2 1.0
C C:GLU2475 3.0 28.2 1.0
CG C:ASP244 3.2 19.9 1.0
CG C:ASP191 3.3 25.7 1.0
CD C:GLU219 3.4 20.0 1.0
OD1 C:ASP191 3.5 20.4 1.0
NZ C:LYS160 3.6 13.1 1.0
CB C:ASP244 3.8 17.9 1.0
OD1 C:ASN193 3.8 25.2 1.0
OE2 C:GLU219 4.0 20.9 1.0
NZ C:LYS268 4.0 19.8 1.0
ND2 C:ASN266 4.0 18.6 1.0
NZ C:LYS162 4.1 17.0 1.0
OD1 C:ASP244 4.2 23.5 1.0
OE1 C:GLU245 4.4 20.5 1.0
CG C:GLU219 4.4 18.8 1.0
CB C:GLU219 4.5 16.6 1.0
CA C:GLU2475 4.5 26.9 1.0
CE C:LYS160 4.6 11.5 1.0
CG C:ASN193 4.6 22.9 1.0
O C:HOH2479 4.7 20.8 1.0
CB C:ASP191 4.7 24.3 1.0
CD C:GLU245 4.8 19.1 1.0
OE2 C:GLU245 4.8 16.6 1.0
ND2 C:ASN193 4.9 11.1 1.0
CG C:ASN266 5.0 16.3 1.0
CE C:LYS268 5.0 18.9 1.0

Magnesium binding site 4 out of 8 in 1tkk

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Magnesium binding site 4 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:22.3
occ:1.00
 O D:HOH2478 2.2 21.6 1.0
OD2 D:ASP191 2.4 23.1 1.0
OE1 D:GLU219 2.4 19.2 1.0
OD2 D:ASP244 2.4 26.5 1.0
O D:GLU2477 2.8 30.4 1.0
CG D:ASP191 3.1 22.6 1.0
OD1 D:ASP191 3.3 23.0 1.0
CD D:GLU219 3.3 22.6 1.0
C D:GLU2477 3.3 26.9 1.0
CG D:ASP244 3.4 20.9 1.0
OD1 D:ASN193 3.6 20.5 1.0
CB D:ASP244 3.7 17.6 1.0
NZ D:LYS160 3.8 28.6 1.0
OE2 D:GLU219 3.9 24.0 1.0
CB D:GLU219 4.0 18.4 1.0
NZ D:LYS162 4.2 15.4 1.0
CG D:GLU219 4.2 18.5 1.0
ND2 D:ASN266 4.3 19.6 1.0
OE1 D:GLU245 4.3 13.1 1.0
CB D:ASP191 4.4 21.1 1.0
NZ D:LYS268 4.5 23.8 1.0
OD1 D:ASP244 4.5 24.6 1.0
CG D:ASN193 4.5 17.9 1.0
CE D:LYS160 4.5 30.4 1.0
OE2 D:GLU245 4.7 21.6 1.0
CD D:GLU245 4.7 21.4 1.0
CA D:GLU2477 4.8 27.9 1.0
ND2 D:ASN193 4.8 8.7 1.0

Magnesium binding site 5 out of 8 in 1tkk

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Magnesium binding site 5 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1605

b:28.7
occ:1.00
 OD2 E:ASP244 2.2 18.9 1.0
OE1 E:GLU219 2.4 21.7 1.0
O E:HOH2480 2.4 19.7 1.0
OD2 E:ASP191 2.6 22.6 1.0
O E:GLU2479 2.9 19.3 1.0
CG E:ASP244 3.1 15.2 1.0
CG E:ASP191 3.2 23.8 1.0
CD E:GLU219 3.2 24.4 1.0
C E:GLU2479 3.3 23.0 1.0
OD1 E:ASP191 3.3 22.5 1.0
CB E:ASP244 3.5 19.1 1.0
OD1 E:ASN193 3.7 27.7 1.0
NZ E:LYS160 3.8 17.5 1.0
OE2 E:GLU219 3.9 19.7 1.0
CB E:GLU219 4.0 22.9 1.0
CG E:GLU219 4.1 24.9 1.0
ND2 E:ASN266 4.2 7.2 1.0
OD1 E:ASP244 4.2 19.3 1.0
NZ E:LYS268 4.3 21.5 1.0
OE1 E:GLU245 4.3 17.1 1.0
NZ E:LYS162 4.4 20.2 1.0
CB E:ASP191 4.5 22.1 1.0
O E:HOH2628 4.6 31.7 1.0
CE E:LYS160 4.7 18.1 1.0
CG E:ASN193 4.7 22.7 1.0
CA E:GLU2479 4.7 25.1 1.0
O E:HOH2571 4.8 24.0 1.0
OE2 E:GLU245 4.8 22.2 1.0
CD E:GLU245 4.8 22.4 1.0
O E:HOH2526 4.8 21.4 1.0
CG E:ASN266 5.0 13.9 1.0

Magnesium binding site 6 out of 8 in 1tkk

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Magnesium binding site 6 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1606

b:37.8
occ:1.00
 OD2 F:ASP244 2.3 17.5 1.0
O F:HOH2482 2.3 24.5 1.0
OE1 F:GLU219 2.3 26.9 1.0
OD2 F:ASP191 2.4 12.1 1.0
O F:GLU2481 2.7 24.9 1.0
CG F:ASP191 3.1 22.1 1.0
OD1 F:ASP191 3.1 28.6 1.0
C F:GLU2481 3.2 27.0 1.0
CD F:GLU219 3.2 26.0 1.0
CG F:ASP244 3.3 19.0 1.0
NZ F:LYS160 3.7 27.2 1.0
CB F:ASP244 3.8 19.9 1.0
OE2 F:GLU219 3.9 25.3 1.0
OD1 F:ASN193 3.9 28.1 1.0
CB F:GLU219 3.9 22.7 1.0
NZ F:LYS268 4.1 26.1 1.0
CG F:GLU219 4.2 26.2 1.0
NZ F:LYS162 4.3 24.4 1.0
OE1 F:GLU245 4.4 20.6 1.0
OD1 F:ASP244 4.4 22.5 1.0
CB F:ASP191 4.5 20.0 1.0
ND2 F:ASN266 4.5 23.0 1.0
CG F:ASN193 4.7 28.2 1.0
CA F:GLU2481 4.7 28.6 1.0
CE F:LYS160 4.8 26.2 1.0
O F:HOH2608 4.8 33.9 1.0
ND2 F:ASN193 4.9 22.1 1.0
O F:HOH2539 4.9 32.8 1.0
O F:HOH2581 5.0 27.3 1.0
CD F:GLU245 5.0 18.8 1.0

Magnesium binding site 7 out of 8 in 1tkk

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Magnesium binding site 7 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1607

b:22.5
occ:1.00
 O G:HOH2484 2.3 13.2 1.0
OD2 G:ASP244 2.4 23.5 1.0
OD2 G:ASP191 2.4 17.0 1.0
OE1 G:GLU219 2.5 26.1 1.0
O G:GLU2483 2.6 26.1 1.0
C G:GLU2483 3.1 24.7 1.0
CG G:ASP191 3.3 27.2 1.0
CG G:ASP244 3.3 24.5 1.0
CD G:GLU219 3.3 26.6 1.0
OD1 G:ASP191 3.4 28.5 1.0
NZ G:LYS160 3.6 18.0 1.0
CB G:ASP244 3.6 18.9 1.0
OE2 G:GLU219 3.8 25.1 1.0
NZ G:LYS268 4.0 19.2 1.0
ND2 G:ASN266 4.0 23.6 1.0
OD1 G:ASN193 4.1 26.2 1.0
CB G:GLU219 4.1 22.7 1.0
CG G:GLU219 4.3 25.1 1.0
NZ G:LYS162 4.3 17.4 1.0
OD1 G:ASP244 4.4 24.4 1.0
OE1 G:GLU245 4.4 27.4 1.0
CE G:LYS160 4.5 20.9 1.0
CB G:ASP191 4.6 25.3 1.0
CA G:GLU2483 4.6 22.8 1.0
O G:HOH2519 4.6 28.5 1.0
CG G:ASN193 4.7 25.8 1.0
O G:HOH2581 4.7 30.9 1.0
ND2 G:ASN193 4.8 19.8 1.0
CG G:ASN266 4.9 25.0 1.0
CD G:GLU245 4.9 24.1 1.0

Magnesium binding site 8 out of 8 in 1tkk

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Magnesium binding site 8 out of 8 in the The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase 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 The Structure of A Substrate-Liganded Complex of the L-Ala- D/L-Glu Epimerase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1608

b:25.5
occ:1.00
 OE1 H:GLU219 2.3 22.1 1.0
O H:HOH2486 2.3 18.8 1.0
OD2 H:ASP191 2.3 23.8 1.0
OD2 H:ASP244 2.3 25.1 1.0
O H:GLU2485 2.6 17.9 1.0
CD H:GLU219 3.1 25.4 1.0
C H:GLU2485 3.1 26.5 1.0
CG H:ASP191 3.2 18.7 1.0
CG H:ASP244 3.3 23.9 1.0
OD1 H:ASP191 3.4 23.0 1.0
NZ H:LYS160 3.5 23.5 1.0
OE2 H:GLU219 3.7 27.6 1.0
CB H:ASP244 3.8 24.4 1.0
CB H:GLU219 4.0 22.7 1.0
CG H:GLU219 4.0 23.3 1.0
ND2 H:ASN266 4.2 25.9 1.0
NZ H:LYS162 4.3 22.9 1.0
OD1 H:ASN193 4.3 23.1 1.0
NZ H:LYS268 4.3 28.4 1.0
OD1 H:ASP244 4.4 28.7 1.0
OE1 H:GLU245 4.4 23.5 1.0
CB H:ASP191 4.5 18.4 1.0
CE H:LYS160 4.5 21.2 1.0
O H:HOH2493 4.6 19.3 1.0
CA H:GLU2485 4.7 25.3 1.0
CG H:ASN266 4.8 22.0 1.0
O H:HOH2567 4.8 29.0 1.0

Reference:

V.A.Klenchin, D.M.Schmidt, J.A.Gerlt, I.Rayment. Evolution of Enzymatic Activities in the Enolase Superfamily: Structure of A Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase From Bacillus Subtilis(,). Biochemistry V. 43 10370 2004.
ISSN: ISSN 0006-2960
PubMed: 15301535
DOI: 10.1021/BI049197O
Page generated: Tue Aug 13 14:35:40 2024

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