Magnesium in PDB 8yeb: Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30

The structure of Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30, PDB code: 8yeb was solved by M.Watanabe, Y.Nakamich, S.Mine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.12 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	130.095, 148.264, 136.707, 90, 94.97, 90
R / Rfree (%)	20.1 / 24

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 (pdb code 8yeb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30, PDB code: 8yeb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:7.5 occ:1.00 O A:HOH577 2.0 46.0 1.0 OE2 A:GLU146 2.1 29.0 1.0 OD2 A:ASP179 2.2 29.3 1.0 ND1 A:HIS205 2.3 30.2 1.0 OE2 A:GLU240 2.3 27.5 1.0 CD A:GLU146 3.1 28.9 1.0 CE1 A:HIS205 3.1 28.1 1.0 CD A:GLU240 3.2 32.5 1.0 CG A:ASP179 3.3 26.3 1.0 OE1 A:GLU240 3.3 32.0 1.0 CG A:HIS205 3.4 26.1 1.0 OE1 A:GLU146 3.4 29.9 1.0 NH1 A:ARG211 3.8 29.5 1.0 CB A:HIS205 3.8 26.6 1.0 CB A:ASP179 3.9 25.4 1.0 O A:HOH527 3.9 27.6 1.0 NE2 A:HIS182 4.1 18.6 1.0 CD2 A:HIS182 4.2 20.0 1.0 NE2 A:HIS205 4.3 24.5 1.0 OD1 A:ASP179 4.4 28.9 1.0 CG A:GLU146 4.4 25.1 1.0 CD2 A:HIS205 4.5 24.4 1.0 CG A:GLU240 4.6 30.4 1.0 O A:HOH580 4.6 25.8 1.0 CE1 A:HIS177 4.6 26.7 1.0 NE2 A:HIS177 4.7 28.1 1.0 CB A:GLU240 4.9 26.1 1.0

Magnesium binding site 2 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:9.3 occ:1.00 OE2 E:GLU146 2.1 34.7 1.0 OD2 E:ASP179 2.2 24.4 1.0 ND1 E:HIS205 2.2 32.6 1.0 O E:HOH516 2.3 38.4 1.0 OE1 E:GLU240 2.5 36.4 1.0 CD E:GLU146 3.1 35.0 1.0 O E:HOH571 3.1 34.6 1.0 CE1 E:HIS205 3.1 31.1 1.0 CG E:ASP179 3.3 26.3 1.0 OE1 E:GLU146 3.3 29.3 1.0 CD E:GLU240 3.3 36.2 1.0 CG E:HIS205 3.3 32.2 1.0 OE2 E:GLU240 3.4 37.1 1.0 CB E:HIS205 3.7 27.6 1.0 CB E:ASP179 3.8 26.4 1.0 NH1 E:ARG211 4.0 39.0 1.0 O E:HOH544 4.1 28.4 1.0 NE2 E:HIS205 4.2 30.7 1.0 OD1 E:ASP179 4.3 33.7 1.0 CD2 E:HIS182 4.3 23.6 1.0 NE2 E:HIS182 4.3 24.1 1.0 CD2 E:HIS205 4.4 29.0 1.0 CG E:GLU146 4.4 33.2 1.0 CE1 E:HIS177 4.5 29.8 1.0 NE2 E:HIS177 4.6 28.9 1.0 CG E:GLU240 4.7 38.1 1.0

Magnesium binding site 3 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:10.2 occ:1.00 O B:HOH540 1.7 46.5 1.0 OE2 B:GLU146 2.1 35.4 1.0 OD2 B:ASP179 2.2 32.4 1.0 ND1 B:HIS205 2.2 28.9 1.0 OE1 B:GLU240 2.3 27.9 1.0 CE1 B:HIS205 3.0 31.5 1.0 CD B:GLU240 3.1 34.7 1.0 CD B:GLU146 3.1 37.1 1.0 OE2 B:GLU240 3.2 32.7 1.0 CG B:ASP179 3.3 29.9 1.0 CG B:HIS205 3.4 30.1 1.0 OE1 B:GLU146 3.4 32.4 1.0 NH1 B:ARG211 3.7 32.7 1.0 CB B:HIS205 3.8 29.1 1.0 CB B:ASP179 4.0 29.9 1.0 O B:HOH516 4.0 24.8 1.0 NE2 B:HIS182 4.2 23.2 1.0 NE2 B:HIS205 4.2 29.3 1.0 CD2 B:HIS182 4.3 24.2 1.0 OD1 B:ASP179 4.3 33.3 1.0 O B:HOH557 4.4 28.5 1.0 CD2 B:HIS205 4.4 28.7 1.0 CG B:GLU146 4.5 33.6 1.0 CG B:GLU240 4.5 33.5 1.0 CE1 B:HIS177 4.6 33.2 1.0 NE2 B:HIS177 4.7 32.6 1.0 CB B:GLU240 4.9 31.0 1.0

Magnesium binding site 4 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:9.9 occ:1.00 OE2 C:GLU146 2.1 30.2 1.0 OD2 C:ASP179 2.1 26.0 1.0 O C:HOH570 2.1 43.8 1.0 ND1 C:HIS205 2.2 30.5 1.0 OE1 C:GLU240 2.4 31.1 1.0 CD C:GLU146 3.0 31.2 1.0 CE1 C:HIS205 3.1 29.4 1.0 CD C:GLU240 3.3 35.2 1.0 CG C:ASP179 3.3 24.3 1.0 CG C:HIS205 3.3 29.0 1.0 OE1 C:GLU146 3.3 31.4 1.0 OE2 C:GLU240 3.4 37.1 1.0 CB C:HIS205 3.7 24.8 1.0 CB C:ASP179 3.9 25.2 1.0 NH1 C:ARG211 4.1 37.5 1.0 O C:HOH545 4.1 24.0 1.0 NE2 C:HIS205 4.2 27.5 1.0 OD1 C:ASP179 4.3 27.2 1.0 CD2 C:HIS205 4.3 28.8 1.0 CD2 C:HIS182 4.4 28.2 1.0 CG C:GLU146 4.4 29.3 1.0 NE2 C:HIS182 4.4 27.4 1.0 CE1 C:HIS177 4.5 27.9 1.0 NE2 C:HIS177 4.5 28.4 1.0 CG C:GLU240 4.7 36.5 1.0 O C:HOH501 4.9 33.6 1.0

Magnesium binding site 5 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:9.0 occ:1.00 OE2 D:GLU146 1.8 34.6 1.0 OE1 D:GLU240 1.9 33.7 1.0 OD2 D:ASP179 2.0 28.5 1.0 ND1 D:HIS205 2.0 30.7 1.0 O D:HOH567 2.5 37.8 1.0 CE1 D:HIS205 2.8 33.9 1.0 CD D:GLU146 2.8 38.4 1.0 CD D:GLU240 2.9 31.4 1.0 CG D:ASP179 3.2 28.1 1.0 CG D:HIS205 3.2 30.8 1.0 OE2 D:GLU240 3.2 34.2 1.0 OE1 D:GLU146 3.3 38.7 1.0 CB D:HIS205 3.8 31.9 1.0 CB D:ASP179 3.9 28.9 1.0 O D:HOH511 3.9 26.6 1.0 NH1 D:ARG211 3.9 30.4 1.0 NE2 D:HIS205 4.0 28.5 1.0 CG D:GLU146 4.2 36.9 1.0 OD1 D:ASP179 4.2 30.2 1.0 CD2 D:HIS205 4.2 27.7 1.0 CG D:GLU240 4.3 30.9 1.0 CD2 D:HIS182 4.3 26.1 1.0 NE2 D:HIS182 4.4 26.8 1.0 NE2 D:HIS177 4.6 33.2 1.0 O D:HOH518 4.7 26.8 1.0 CE1 D:HIS177 4.7 34.7 1.0 CB D:GLU240 4.9 29.0 1.0

Magnesium binding site 6 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:11.6 occ:1.00 OE2 F:GLU146 1.8 29.3 1.0 OD2 F:ASP179 2.0 34.9 1.0 O F:HOH560 2.0 34.1 1.0 OE1 F:GLU240 2.0 34.0 1.0 ND1 F:HIS205 2.0 32.8 1.0 CE1 F:HIS205 2.8 32.7 1.0 CD F:GLU146 2.8 37.7 1.0 CD F:GLU240 3.0 40.2 1.0 CG F:ASP179 3.1 33.1 1.0 CG F:HIS205 3.2 32.2 1.0 OE1 F:GLU146 3.3 35.3 1.0 OE2 F:GLU240 3.3 42.7 1.0 O F:HOH573 3.7 32.6 1.0 CB F:HIS205 3.7 29.7 1.0 CB F:ASP179 3.8 33.6 1.0 NE2 F:HIS205 4.0 28.3 1.0 NH1 F:ARG211 4.0 40.1 1.0 O F:HOH534 4.1 35.1 1.0 OD1 F:ASP179 4.2 33.3 1.0 CG F:GLU146 4.2 35.6 1.0 CD2 F:HIS205 4.2 30.9 1.0 NE2 F:HIS182 4.3 26.1 1.0 CD2 F:HIS182 4.4 26.3 1.0 CG F:GLU240 4.4 37.8 1.0 NE2 F:HIS177 4.6 28.5 1.0 CE1 F:HIS177 4.7 34.6 1.0

Magnesium binding site 7 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg401 b:8.5 occ:1.00 OE2 G:GLU146 1.8 26.3 1.0 OE2 G:GLU240 1.9 28.7 1.0 OD2 G:ASP179 1.9 26.1 1.0 O G:HOH563 2.1 40.1 1.0 ND1 G:HIS205 2.1 24.4 1.0 CE1 G:HIS205 2.8 29.5 1.0 CD G:GLU240 2.9 28.5 1.0 CD G:GLU146 2.9 26.9 1.0 CG G:ASP179 3.1 25.9 1.0 OE1 G:GLU240 3.2 24.3 1.0 CG G:HIS205 3.3 25.6 1.0 OE1 G:GLU146 3.4 27.4 1.0 CB G:HIS205 3.8 22.7 1.0 NH1 G:ARG211 3.9 25.0 1.0 O G:HOH550 3.9 22.4 1.0 CB G:ASP179 3.9 24.8 1.0 NE2 G:HIS205 4.1 26.3 1.0 OD1 G:ASP179 4.1 30.9 1.0 CG G:GLU146 4.2 26.4 1.0 CG G:GLU240 4.2 29.4 1.0 CD2 G:HIS205 4.3 25.2 1.0 CD2 G:HIS182 4.3 23.4 1.0 NE2 G:HIS182 4.3 23.0 1.0 O G:HOH593 4.4 26.4 1.0 NE2 G:HIS177 4.5 31.7 1.0 CE1 G:HIS177 4.7 31.4 1.0 CB G:GLU240 4.9 26.5 1.0

Magnesium binding site 8 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg401 b:9.9 occ:1.00 OE1 H:GLU146 1.8 22.7 1.0 O H:HOH511 1.9 37.8 1.0 OE2 H:GLU240 1.9 30.1 1.0 OD2 H:ASP179 2.0 31.9 1.0 ND1 H:HIS205 2.0 42.5 1.0 CE1 H:HIS205 2.8 44.7 1.0 CD H:GLU146 2.8 32.5 1.0 CD H:GLU240 2.9 40.2 1.0 CG H:ASP179 3.1 29.9 1.0 OE2 H:GLU146 3.2 35.8 1.0 CG H:HIS205 3.2 37.4 1.0 OE1 H:GLU240 3.3 48.0 1.0 CB H:HIS205 3.8 32.0 1.0 CB H:ASP179 3.8 25.9 1.0 NH1 H:ARG211 3.8 36.1 1.0 NE2 H:HIS205 4.0 37.3 1.0 O H:HOH543 4.0 33.5 1.0 CG H:GLU146 4.2 33.0 1.0 OD1 H:ASP179 4.2 33.4 1.0 CD2 H:HIS205 4.2 36.7 1.0 NE2 H:HIS182 4.3 26.2 1.0 CD2 H:HIS182 4.3 25.0 1.0 CG H:GLU240 4.3 39.0 1.0 O H:HOH513 4.4 36.6 1.0 NE2 H:HIS177 4.6 26.8 1.0 CE1 H:HIS177 4.8 26.8 1.0 CB H:GLU240 5.0 35.9 1.0

Magnesium binding site 9 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg401 b:22.8 occ:1.00 OE2 I:GLU146 1.7 43.1 1.0 OE1 I:GLU240 1.9 37.2 1.0 OD2 I:ASP179 1.9 48.8 1.0 ND1 I:HIS205 2.2 46.1 1.0 O I:HOH522 2.2 47.2 1.0 CD I:GLU146 2.8 52.0 1.0 CD I:GLU240 2.9 48.8 1.0 CE1 I:HIS205 2.9 48.6 1.0 CG I:ASP179 3.1 45.8 1.0 OE2 I:GLU240 3.2 57.0 1.0 OE1 I:GLU146 3.2 53.0 1.0 CG I:HIS205 3.3 45.5 1.0 O I:HOH505 3.8 45.9 1.0 CB I:ASP179 3.8 41.8 1.0 CB I:HIS205 3.9 39.2 1.0 NH1 I:ARG211 4.0 61.4 1.0 O I:HOH525 4.0 49.1 1.0 OD1 I:ASP179 4.1 48.6 1.0 CG I:GLU146 4.1 51.3 1.0 NE2 I:HIS205 4.1 46.6 1.0 CD2 I:HIS182 4.2 38.7 1.0 NE2 I:HIS182 4.2 39.0 1.0 CG I:GLU240 4.3 44.9 1.0 CD2 I:HIS205 4.3 47.5 1.0 NE2 I:HIS177 4.7 54.6 1.0 CE1 I:HIS177 4.9 50.2 1.0 CB I:GLU240 5.0 46.2 1.0

Magnesium binding site 10 out of 16 in the Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30


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 L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg401 b:18.1 occ:1.00 ND1 J:HIS205 1.9 45.2 1.0 OD2 J:ASP179 2.0 49.1 1.0 OE1 J:GLU240 2.1 58.2 1.0 OE2 J:GLU146 2.1 43.1 1.0 CE1 J:HIS205 2.7 49.0 1.0 CD J:GLU146 2.9 46.1 1.0 CD J:GLU240 3.1 51.1 1.0 CG J:ASP179 3.1 42.2 1.0 CG J:HIS205 3.1 47.6 1.0 OE1 J:GLU146 3.2 50.2 1.0 OE2 J:GLU240 3.4 64.2 1.0 CB J:HIS205 3.7 42.1 1.0 CB J:ASP179 3.7 40.1 1.0 NE2 J:HIS205 3.9 41.5 1.0 CD2 J:HIS205 4.1 44.5 1.0 NH1 J:ARG211 4.1 60.8 1.0 OD1 J:ASP179 4.1 43.6 1.0 O J:HOH514 4.2 49.0 1.0 CG J:GLU146 4.2 45.9 1.0 NE2 J:HIS177 4.4 38.7 1.0 CD2 J:HIS182 4.4 29.7 1.0 NE2 J:HIS182 4.4 31.4 1.0 CG J:GLU240 4.5 54.0 1.0 CE1 J:HIS177 4.5 42.6 1.0

M.Watanabe, Y.Nakamich, S.Mine. Crystal Structure of L-Ribulose 3-Epimerase From Arthrobacter Globiformis M30 To Be Published.