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Magnesium in PDB 4mzu: Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans

Protein crystallography data

The structure of Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans, PDB code: 4mzu was solved by D.P.Chantigian, J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 85.314, 109.443, 127.847, 79.23, 79.98, 84.89
R / Rfree (%) 20.4 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans (pdb code 4mzu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans, PDB code: 4mzu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4mzu

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Magnesium binding site 1 out of 5 in the Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans


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 Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:26.7
occ:1.00
 O A:HOH503 2.5 17.9 1.0
O C:HOH505 2.8 12.6 1.0
O A:HOH504 2.9 33.8 1.0
O B:HOH501 2.9 13.6 1.0
OD1 B:ASN76 2.9 14.3 1.0
O B:GLY58 3.0 20.8 1.0
OD1 A:ASN76 3.3 17.6 1.0
CG A:ASN76 3.3 13.2 1.0
CG B:ASN76 3.4 18.0 1.0
ND2 A:ASN76 3.5 20.6 1.0
CB B:ASN76 3.6 16.1 1.0
CA B:ASN76 3.6 15.3 1.0
C B:GLY58 3.9 20.9 1.0
O C:HOH506 3.9 15.7 1.0
CA B:GLY58 4.0 19.7 1.0
CB A:ASN76 4.1 12.4 1.0
O B:ASN76 4.2 14.0 1.0
O A:HOH505 4.2 23.4 1.0
C B:ASN76 4.3 13.4 1.0
MG C:MG404 4.3 20.0 1.0
ND2 B:ASN76 4.3 17.1 1.0
N B:ASN76 4.7 14.1 1.0
NE2 B:GLN60 5.0 26.0 1.0

Magnesium binding site 2 out of 5 in 4mzu

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Magnesium binding site 2 out of 5 in the Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans


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 Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:20.0
occ:1.00
 O B:HOH501 2.0 13.6 1.0
O A:HOH505 2.1 23.4 1.0
OD1 A:ASN108 2.1 13.5 1.0
OD1 B:ASN108 2.1 15.5 1.0
O C:HOH506 2.2 15.7 1.0
OD1 C:ASN108 2.3 17.8 1.0
CG A:ASN108 3.1 15.2 1.0
CG C:ASN108 3.1 16.1 1.0
CG B:ASN108 3.1 17.3 1.0
ND2 C:ASN108 3.3 18.6 1.0
ND2 A:ASN108 3.6 13.6 1.0
ND2 B:ASN108 3.6 15.6 1.0
O B:ASN76 4.2 14.0 1.0
O A:ASN76 4.2 14.7 1.0
O C:ASN76 4.2 16.6 1.0
O A:HOH503 4.3 17.9 1.0
MG B:MG404 4.3 26.7 1.0
CB A:ASN76 4.4 12.4 1.0
CB A:ASN108 4.4 9.1 1.0
CB B:ASN76 4.5 16.1 1.0
CB B:ASN108 4.5 13.3 1.0
CB C:ASN76 4.5 18.2 1.0
CB C:ASN108 4.5 15.3 1.0
O C:HOH505 4.6 12.6 1.0
OG1 B:THR78 4.7 18.0 1.0
OG1 C:THR78 4.8 21.5 1.0
CA A:ASN108 4.8 12.7 1.0
CA B:ASN108 4.9 13.4 1.0
OG1 A:THR78 4.9 18.6 1.0
O B:ASN108 5.0 15.7 1.0
CG A:ASN76 5.0 13.2 1.0

Magnesium binding site 3 out of 5 in 4mzu

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Magnesium binding site 3 out of 5 in the Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans


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 Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:21.6
occ:1.00
 O D:HOH525 2.0 22.9 1.0
OD1 F:ASN108 2.1 19.4 1.0
OD1 D:ASN108 2.2 18.2 1.0
OD1 E:ASN108 2.2 20.5 1.0
O E:HOH540 2.2 19.2 1.0
O F:HOH559 2.3 24.1 1.0
CG F:ASN108 3.1 25.7 1.0
CG D:ASN108 3.2 18.4 1.0
CG E:ASN108 3.2 16.4 1.0
ND2 F:ASN108 3.6 21.5 1.0
ND2 D:ASN108 3.6 18.6 1.0
ND2 E:ASN108 3.6 13.7 1.0
O D:ASN76 4.2 24.3 1.0
O F:HOH556 4.2 21.4 1.0
O F:ASN76 4.2 23.9 1.0
CB F:ASN76 4.3 23.9 1.0
O E:ASN76 4.3 19.5 1.0
CB D:ASN76 4.3 21.1 1.0
O D:HOH524 4.4 21.8 1.0
CB E:ASN76 4.4 18.9 1.0
CB F:ASN108 4.5 23.4 1.0
CB D:ASN108 4.5 16.9 1.0
CB E:ASN108 4.5 16.2 1.0
OG1 F:THR78 4.7 25.7 1.0
OG1 D:THR78 4.7 22.7 1.0
CA F:ASN108 4.9 24.4 1.0
OG1 E:THR78 4.9 19.3 1.0
CG F:ASN76 4.9 30.6 1.0
CA D:ASN108 4.9 17.7 1.0
CG E:ASN76 5.0 22.8 1.0
CA E:ASN108 5.0 17.3 1.0

Magnesium binding site 4 out of 5 in 4mzu

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Magnesium binding site 4 out of 5 in the Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans


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 Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg404

b:27.9
occ:1.00
 O H:HOH542 2.0 36.6 1.0
O G:HOH576 2.0 23.8 1.0
O I:HOH567 2.1 27.2 1.0
OD1 G:ASN108 2.2 19.2 1.0
OD1 H:ASN108 2.2 29.0 1.0
OD1 I:ASN108 2.3 29.0 1.0
CG G:ASN108 3.1 22.9 1.0
CG H:ASN108 3.2 25.4 1.0
CG I:ASN108 3.2 28.5 1.0
ND2 G:ASN108 3.4 22.1 1.0
ND2 I:ASN108 3.5 26.1 1.0
ND2 H:ASN108 3.5 26.7 1.0
O H:ASN76 4.0 31.1 1.0
O I:ASN76 4.2 33.0 1.0
CB H:ASN76 4.3 30.8 1.0
O G:ASN76 4.3 31.0 1.0
CB I:ASN76 4.4 35.8 1.0
CB G:ASN108 4.5 23.4 1.0
CB G:ASN76 4.5 31.5 1.0
CB H:ASN108 4.5 27.6 1.0
CB I:ASN108 4.6 26.9 1.0
OG1 H:THR78 4.8 26.9 1.0
OG1 G:THR78 4.8 33.5 1.0
OG1 I:THR78 4.8 34.0 1.0
CA H:ASN108 4.9 27.9 1.0
CA G:ASN108 4.9 25.3 1.0
CG H:ASN76 5.0 31.1 1.0
CA I:ASN108 5.0 27.0 1.0

Magnesium binding site 5 out of 5 in 4mzu

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Magnesium binding site 5 out of 5 in the Crystal Structure of Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans


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 Fdtd, A Bifunctional Ketoisomerase/N- Acetyltransferase From Shewanella Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg404

b:26.9
occ:1.00
 O K:HOH510 2.0 30.1 1.0
OD1 K:ASN108 2.0 21.2 1.0
OD1 L:ASN108 2.1 18.5 1.0
OD1 J:ASN108 2.2 17.5 1.0
O J:HOH509 2.2 31.0 1.0
O L:HOH513 2.4 23.8 1.0
CG J:ASN108 3.1 17.4 1.0
CG L:ASN108 3.1 23.5 1.0
CG K:ASN108 3.1 20.7 1.0
ND2 J:ASN108 3.4 19.9 1.0
ND2 L:ASN108 3.5 18.9 1.0
ND2 K:ASN108 3.5 22.3 1.0
O L:ASN76 4.2 27.1 1.0
O J:ASN76 4.2 24.5 1.0
O K:ASN76 4.3 25.2 1.0
CB L:ASN76 4.4 25.1 1.0
CB L:ASN108 4.4 24.0 1.0
CB J:ASN108 4.4 17.0 1.0
CB K:ASN108 4.4 21.4 1.0
CB K:ASN76 4.4 28.2 1.0
CB J:ASN76 4.5 26.3 1.0
O J:HOH524 4.5 29.4 1.0
O L:HOH536 4.5 24.7 1.0
OG1 K:THR78 4.8 21.6 1.0
CA L:ASN108 4.8 24.7 1.0
OG1 J:THR78 4.8 23.2 1.0
OG1 L:THR78 4.8 26.5 1.0
CA J:ASN108 4.9 18.4 1.0
CA K:ASN108 4.9 21.5 1.0

Reference:

D.P.Chantigian, J.B.Thoden, H.M.Holden. Structural and Biochemical Characterization of A Bifunctional Ketoisomerase/N-Acetyltransferase From Shewanella Denitrificans. Biochemistry V. 52 8374 2013.
ISSN: ISSN 0006-2960
PubMed: 24128043
DOI: 10.1021/BI401170T
Page generated: Mon Aug 19 23:23:23 2024

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