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Magnesium in PDB 5jyd: Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia

Protein crystallography data

The structure of Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia, PDB code: 5jyd was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.800, 107.820, 117.690, 90.00, 97.63, 90.00
R / Rfree (%) 14.1 / 17.4

Other elements in 5jyd:

The structure of Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia also contains other interesting chemical elements:

Iodine (I) 54 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia (pdb code 5jyd). 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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia, PDB code: 5jyd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5jyd

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Magnesium binding site 1 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:15.2
occ:1.00
 OD2 A:ASP78 2.0 16.4 1.0
OE2 A:GLU104 2.0 23.2 1.0
O A:HOH1052 2.1 18.8 1.0
O A:HOH1011 2.1 18.9 1.0
OG A:SER79 2.1 13.6 1.0
O3B A:NAD901 2.3 20.3 1.0
CG A:ASP78 3.0 16.4 1.0
CD A:GLU104 3.0 20.4 1.0
CB A:SER79 3.1 14.3 1.0
C3B A:NAD901 3.2 25.2 1.0
OD1 A:ASP78 3.4 17.4 1.0
OE1 A:GLU104 3.8 17.7 1.0
CG A:GLU104 3.9 19.1 1.0
O2A A:NAD901 4.0 20.8 1.0
C2B A:NAD901 4.0 27.4 1.0
O2B A:NAD901 4.0 26.0 1.0
O A:GLY45 4.1 19.6 1.0
O1A A:NAD901 4.2 18.8 1.0
N A:SER79 4.3 12.8 1.0
CA A:SER79 4.3 14.7 1.0
CB A:ASP78 4.3 14.2 1.0
CB A:GLU104 4.4 16.7 1.0
OD2 A:ASP107 4.4 18.2 1.0
PA A:NAD901 4.4 20.0 1.0
O5B A:NAD901 4.5 23.6 1.0
C4B A:NAD901 4.5 26.4 1.0
CG A:PRO255 4.7 20.5 1.0
O A:PRO44 4.7 16.6 1.0
C A:ASP78 4.7 12.0 1.0
CB A:PRO44 4.8 19.7 1.0
C A:SER79 5.0 14.9 1.0
C5B A:NAD901 5.0 27.7 1.0

Magnesium binding site 2 out of 8 in 5jyd

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Magnesium binding site 2 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:15.8
occ:1.00
 OD1 B:ASP78 1.9 23.3 1.0
O B:HOH1036 2.0 19.6 1.0
OE1 B:GLU104 2.0 24.6 1.0
O B:HOH1013 2.1 23.5 1.0
OG B:SER79 2.2 20.6 1.0
O3B B:NAD901 2.2 20.7 1.0
CG B:ASP78 2.9 23.6 1.0
CD B:GLU104 3.0 22.4 1.0
CB B:SER79 3.2 22.2 1.0
OD2 B:ASP78 3.3 21.1 1.0
C3B B:NAD901 3.3 18.8 1.0
OE2 B:GLU104 3.7 25.4 1.0
CG B:GLU104 3.8 22.8 1.0
O2B B:NAD901 4.0 20.9 1.0
O B:GLY45 4.0 24.9 1.0
C2B B:NAD901 4.1 18.1 1.0
O2A B:NAD901 4.1 20.4 1.0
O1A B:NAD901 4.1 18.7 1.0
N B:SER79 4.2 18.5 1.0
CB B:ASP78 4.3 19.4 1.0
CA B:SER79 4.3 18.0 1.0
CB B:GLU104 4.4 23.1 1.0
OD2 B:ASP107 4.4 22.9 1.0
PA B:NAD901 4.5 19.1 1.0
C4B B:NAD901 4.5 19.8 1.0
O5B B:NAD901 4.6 18.5 1.0
O B:PRO44 4.7 20.4 1.0
C B:ASP78 4.8 18.5 1.0
CB B:PRO44 4.9 22.2 1.0
CG B:PRO255 5.0 29.5 1.0

Magnesium binding site 3 out of 8 in 5jyd

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Magnesium binding site 3 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:10.7
occ:1.00
 OD2 C:ASP78 2.0 14.9 1.0
OE1 C:GLU104 2.1 14.4 1.0
O C:HOH1025 2.1 14.7 1.0
O C:HOH1040 2.1 11.1 1.0
OG C:SER79 2.1 11.6 1.0
O3B C:NAD901 2.2 10.5 1.0
CD C:GLU104 3.0 15.8 1.0
CG C:ASP78 3.0 11.9 1.0
CB C:SER79 3.2 10.4 1.0
C3B C:NAD901 3.2 11.9 1.0
OD1 C:ASP78 3.3 13.3 1.0
OE2 C:GLU104 3.7 14.6 1.0
CG C:GLU104 3.8 14.8 1.0
O C:GLY45 4.0 14.5 1.0
C2B C:NAD901 4.0 11.0 1.0
O2B C:NAD901 4.1 13.2 1.0
O2A C:NAD901 4.1 11.1 1.0
O1A C:NAD901 4.2 11.3 1.0
N C:SER79 4.3 11.7 1.0
CA C:SER79 4.3 10.1 1.0
CB C:ASP78 4.4 11.1 1.0
PA C:NAD901 4.4 10.8 1.0
CB C:GLU104 4.4 13.8 1.0
OD1 C:ASP107 4.5 13.6 1.0
C4B C:NAD901 4.5 11.2 1.0
O5B C:NAD901 4.5 12.1 1.0
CG C:PRO255 4.7 14.4 1.0
O C:PRO44 4.7 12.0 1.0
C C:ASP78 4.8 13.2 1.0
CB C:PRO44 5.0 15.9 1.0
C C:SER79 5.0 10.7 1.0

Magnesium binding site 4 out of 8 in 5jyd

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Magnesium binding site 4 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:10.6
occ:1.00
 O D:HOH1031 2.0 11.4 1.0
OD2 D:ASP78 2.0 11.6 1.0
OE2 D:GLU104 2.1 15.4 1.0
O D:HOH1019 2.1 12.2 1.0
OG D:SER79 2.1 11.5 1.0
O3B D:NAD901 2.2 10.7 1.0
CG D:ASP78 3.0 12.5 1.0
CD D:GLU104 3.0 15.4 1.0
C3B D:NAD901 3.2 10.5 1.0
CB D:SER79 3.2 12.2 1.0
OD1 D:ASP78 3.3 12.9 1.0
OE1 D:GLU104 3.7 13.8 1.0
CG D:GLU104 3.9 14.2 1.0
C2B D:NAD901 4.0 12.4 1.0
O D:GLY45 4.0 14.4 1.0
O2B D:NAD901 4.0 13.1 1.0
O1A D:NAD901 4.1 11.1 1.0
O2A D:NAD901 4.1 11.1 1.0
N D:SER79 4.3 10.9 1.0
CA D:SER79 4.3 11.8 1.0
CB D:ASP78 4.4 12.6 1.0
PA D:NAD901 4.4 10.2 1.0
C4B D:NAD901 4.4 12.0 1.0
O5B D:NAD901 4.5 9.6 1.0
CB D:GLU104 4.5 12.9 1.0
OD2 D:ASP107 4.5 13.2 1.0
CG D:PRO255 4.6 16.8 1.0
O D:PRO44 4.7 11.8 1.0
C D:ASP78 4.8 11.5 1.0
CB D:PRO44 4.9 13.2 1.0
C5B D:NAD901 4.9 9.6 1.0

Magnesium binding site 5 out of 8 in 5jyd

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Magnesium binding site 5 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg902

b:14.8
occ:1.00
 OD2 E:ASP78 1.9 17.6 1.0
O E:HOH1022 2.0 17.5 1.0
OE2 E:GLU104 2.1 19.9 1.0
OG E:SER79 2.1 15.3 1.0
O E:HOH1011 2.2 17.0 1.0
O3B E:NAD901 2.2 19.3 1.0
CG E:ASP78 2.9 16.2 1.0
CD E:GLU104 3.0 18.8 1.0
CB E:SER79 3.2 14.1 1.0
C3B E:NAD901 3.2 21.6 1.0
OD1 E:ASP78 3.3 15.0 1.0
OE1 E:GLU104 3.7 16.7 1.0
CG E:GLU104 3.8 21.2 1.0
O2B E:NAD901 4.0 17.4 1.0
O2A E:NAD901 4.0 19.1 1.0
C2B E:NAD901 4.0 18.4 1.0
O1A E:NAD901 4.1 16.7 1.0
O E:GLY45 4.2 19.9 1.0
N E:SER79 4.2 13.3 1.0
CA E:SER79 4.3 12.8 1.0
CB E:ASP78 4.3 15.0 1.0
CB E:GLU104 4.4 19.5 1.0
PA E:NAD901 4.4 19.1 1.0
OD1 E:ASP107 4.4 20.0 1.0
C4B E:NAD901 4.5 18.5 1.0
O5B E:NAD901 4.5 16.7 1.0
CG E:PRO255 4.7 22.4 1.0
O E:PRO44 4.7 18.6 1.0
C E:ASP78 4.7 14.3 1.0
C E:SER79 5.0 13.8 1.0
CB E:PRO44 5.0 20.2 1.0

Magnesium binding site 6 out of 8 in 5jyd

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Magnesium binding site 6 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg902

b:24.1
occ:1.00
 OE1 F:GLU104 2.0 39.8 1.0
O F:HOH1036 2.1 25.5 1.0
O F:HOH1031 2.1 29.8 1.0
OD1 F:ASP78 2.1 35.8 1.0
OG F:SER79 2.2 26.4 1.0
O3B F:NAD901 2.3 36.6 1.0
CD F:GLU104 2.9 39.1 1.0
CG F:ASP78 3.2 31.9 1.0
CB F:SER79 3.2 26.7 1.0
C3B F:NAD901 3.2 36.0 1.0
OD2 F:ASP78 3.5 29.4 1.0
OE2 F:GLU104 3.7 34.3 1.0
CG F:GLU104 3.7 33.0 1.0
O F:GLY45 3.9 36.6 1.0
O1A F:NAD901 4.0 31.7 1.0
C2B F:NAD901 4.0 36.1 1.0
O2B F:NAD901 4.1 36.4 1.0
O2A F:NAD901 4.2 28.4 1.0
N F:SER79 4.4 25.5 1.0
CA F:SER79 4.4 25.4 1.0
CB F:GLU104 4.4 30.7 1.0
PA F:NAD901 4.4 30.3 1.0
CB F:ASP78 4.5 28.1 1.0
OD2 F:ASP107 4.5 32.8 1.0
O5B F:NAD901 4.5 30.5 1.0
C4B F:NAD901 4.5 37.8 1.0
O F:PRO44 4.6 35.3 1.0
CG F:PRO255 4.6 33.0 1.0
C F:ASP78 4.9 26.8 1.0
CB F:PRO44 4.9 36.3 1.0
C5B F:NAD901 5.0 36.7 1.0
C F:GLY45 5.0 37.3 1.0

Magnesium binding site 7 out of 8 in 5jyd

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Magnesium binding site 7 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg902

b:13.0
occ:1.00
 OD2 G:ASP78 1.9 19.8 1.0
O G:HOH1015 2.0 19.0 1.0
O G:HOH1042 2.0 17.9 1.0
OE2 G:GLU104 2.1 23.3 1.0
OG G:SER79 2.2 17.1 1.0
O3B G:NAD901 2.2 16.9 1.0
CG G:ASP78 2.9 19.4 1.0
CD G:GLU104 3.0 22.5 1.0
CB G:SER79 3.2 17.3 1.0
C3B G:NAD901 3.2 21.6 1.0
OD1 G:ASP78 3.3 17.6 1.0
OE1 G:GLU104 3.7 22.7 1.0
CG G:GLU104 3.8 25.6 1.0
O2B G:NAD901 4.0 16.7 1.0
C2B G:NAD901 4.0 17.6 1.0
O2A G:NAD901 4.0 18.8 1.0
O G:GLY45 4.1 22.8 1.0
O1A G:NAD901 4.1 17.9 1.0
N G:SER79 4.2 15.8 1.0
CB G:ASP78 4.3 20.5 1.0
CA G:SER79 4.3 18.8 1.0
CB G:GLU104 4.4 21.1 1.0
PA G:NAD901 4.4 18.2 1.0
OD2 G:ASP107 4.5 22.9 1.0
C4B G:NAD901 4.5 19.7 1.0
O5B G:NAD901 4.6 17.1 1.0
C G:ASP78 4.7 16.7 1.0
CG G:PRO255 4.8 24.1 1.0
O G:PRO44 4.8 19.4 1.0
CB G:PRO44 4.9 17.7 1.0
C G:SER79 5.0 15.7 1.0

Magnesium binding site 8 out of 8 in 5jyd

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Magnesium binding site 8 out of 8 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg902

b:23.0
occ:1.00
 O H:HOH1035 1.9 25.6 1.0
OE2 H:GLU104 2.0 33.1 1.0
OD2 H:ASP78 2.1 35.2 1.0
O H:HOH1009 2.1 31.6 1.0
OG H:SER79 2.2 29.9 1.0
O3B H:NAD901 2.4 29.4 1.0
CD H:GLU104 3.0 31.6 1.0
CG H:ASP78 3.0 30.8 1.0
C3B H:NAD901 3.2 30.6 1.0
CB H:SER79 3.3 32.9 1.0
OD1 H:ASP78 3.3 29.9 1.0
CG H:GLU104 3.8 33.9 1.0
OE1 H:GLU104 3.8 31.5 1.0
O H:GLY45 3.8 35.4 1.0
O1A H:NAD901 4.0 26.8 1.0
C2B H:NAD901 4.1 28.9 1.0
O2B H:NAD901 4.1 27.5 1.0
O2A H:NAD901 4.3 26.7 1.0
N H:SER79 4.4 30.1 1.0
CB H:GLU104 4.4 33.5 1.0
CA H:SER79 4.4 30.1 1.0
CB H:ASP78 4.4 31.5 1.0
PA H:NAD901 4.4 24.3 1.0
OD2 H:ASP107 4.4 33.8 1.0
O5B H:NAD901 4.5 23.2 1.0
O H:PRO44 4.5 30.7 1.0
C4B H:NAD901 4.6 25.0 1.0
CB H:PRO44 4.8 30.6 1.0
CG H:PRO255 4.8 32.1 1.0
C H:ASP78 4.9 31.0 1.0
C H:GLY45 4.9 37.1 1.0

Reference:

Ssgcid, J.Y.Yano, D.Lorimer, T.E.Edwards. Tbd To Be Published.
Page generated: Tue Aug 12 12:27:34 2025

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