Magnesium in PDB 6ura: Crystal Structure of Rubisco From Promineofilum Breve

All present enzymatic activity of Crystal Structure of Rubisco From Promineofilum Breve:
4.1.1.39;

The structure of Crystal Structure of Rubisco From Promineofilum Breve, PDB code: 6ura was solved by J.H.Pereira, D.M.Banda, A.K.Liu, P.M.Shih, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.21 / 2.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.060, 162.740, 90.000, 90.00, 109.57, 90.00
R / Rfree (%)	18.8 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of Rubisco From Promineofilum Breve (pdb code 6ura). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Rubisco From Promineofilum Breve, PDB code: 6ura:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Rubisco From Promineofilum Breve


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 Rubisco From Promineofilum Breve within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.9 occ:1.00 OD1 A:ASP207 2.0 33.1 1.0 OE1 A:GLU208 2.0 31.6 1.0 OQ2 A:KCX205 2.1 29.4 1.0 O3 A:CAP501 2.1 26.4 1.0 HO3 A:CAP501 2.3 31.8 1.0 O7 A:CAP501 2.3 25.9 1.0 O2 A:CAP501 2.4 22.9 1.0 HO2 A:CAP501 2.8 27.5 1.0 H A:GLU208 2.9 29.4 1.0 C2 A:CAP501 2.9 28.0 1.0 CD A:GLU208 3.0 31.4 1.0 C A:CAP501 3.0 27.3 1.0 C3 A:CAP501 3.0 27.0 1.0 CX A:KCX205 3.1 26.7 1.0 HG21 A:THR177 3.1 34.7 1.0 CG A:ASP207 3.2 31.8 1.0 HD22 B:ASN127 3.2 34.8 1.0 HZ2 A:LYS181 3.2 45.1 1.0 HZ1 A:LYS181 3.3 45.1 1.0 OQ1 A:KCX205 3.4 26.4 1.0 HE2 A:HIS298 3.4 29.8 1.0 OE2 A:GLU208 3.4 31.2 1.0 HA A:ASP207 3.5 32.9 1.0 H3 A:CAP501 3.5 32.5 1.0 HZ3 A:LYS179 3.6 36.4 1.0 HZ2 A:LYS179 3.6 36.4 1.0 NZ A:LYS181 3.7 37.5 1.0 N A:GLU208 3.8 24.4 1.0 OD2 A:ASP207 3.8 31.5 1.0 HB3 A:GLU208 3.8 34.6 1.0 ND2 B:ASN127 3.9 28.9 1.0 NZ A:LYS179 4.0 30.3 1.0 NE2 A:HIS298 4.0 24.8 1.0 HD21 B:ASN127 4.0 34.8 1.0 CG2 A:THR177 4.1 28.9 1.0 HZ3 A:LYS181 4.1 45.1 1.0 O6 A:CAP501 4.1 26.8 1.0 CA A:ASP207 4.2 27.4 1.0 CB A:ASP207 4.2 30.1 1.0 CG A:GLU208 4.2 32.3 1.0 HZ1 A:LYS179 4.2 36.4 1.0 C4 A:CAP501 4.2 29.4 1.0 OG1 A:THR177 4.3 30.2 1.0 H4 A:CAP501 4.4 35.3 1.0 HG23 A:THR177 4.4 34.7 1.0 NZ A:KCX205 4.4 23.4 1.0 CB A:GLU208 4.4 28.8 1.0 C1 A:CAP501 4.4 28.7 1.0 C A:ASP207 4.5 25.2 1.0 H51 A:CAP501 4.5 31.6 1.0 HZ A:KCX205 4.6 28.2 1.0 HB3 A:ASP207 4.6 36.2 1.0 HG22 A:THR177 4.6 34.7 1.0 HD2 A:HIS298 4.6 26.9 1.0 HG3 A:GLU208 4.7 38.8 1.0 CD2 A:HIS298 4.7 22.4 1.0 HE3 A:LYS181 4.7 44.4 1.0 CB A:THR177 4.7 28.4 1.0 CA A:GLU208 4.7 25.2 1.0 CE1 A:HIS298 4.8 23.3 1.0 CE A:LYS181 4.8 36.9 1.0 HB A:THR177 4.8 34.1 1.0 C5 A:CAP501 4.8 26.3 1.0 H11 A:CAP501 4.9 34.5 1.0 HG2 A:GLU208 4.9 38.8 1.0 H52 A:CAP501 4.9 31.6 1.0 HE1 A:HIS298 4.9 28.0 1.0 HG2 A:LYS181 4.9 42.3 1.0 HG1 A:THR177 4.9 36.3 1.0 H12 A:CAP501 5.0 34.5 1.0 HB2 A:ASP207 5.0 36.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Rubisco From Promineofilum Breve


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 Rubisco From Promineofilum Breve within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:20.9 occ:1.00 HO2 B:CAP501 1.8 36.6 1.0 OD1 B:ASP207 1.9 27.7 1.0 OE1 B:GLU208 2.0 30.0 1.0 O3 B:CAP501 2.1 23.6 1.0 OQ1 B:KCX205 2.1 25.1 1.0 O6 B:CAP501 2.2 22.6 1.0 O2 B:CAP501 2.4 30.5 1.0 HO3 B:CAP501 2.4 28.4 1.0 C2 B:CAP501 2.9 27.4 1.0 C B:CAP501 2.9 26.8 1.0 H B:GLU208 3.0 33.0 1.0 C3 B:CAP501 3.0 24.8 1.0 CD B:GLU208 3.0 30.2 1.0 CX B:KCX205 3.0 24.0 1.0 HD21 A:ASN127 3.1 35.1 1.0 CG B:ASP207 3.2 27.4 1.0 HG21 B:THR177 3.2 41.5 1.0 OQ2 B:KCX205 3.2 25.6 1.0 HE2 B:HIS298 3.3 23.6 1.0 HZ1 B:LYS181 3.3 45.9 1.0 HA B:ASP207 3.4 28.9 1.0 OE2 B:GLU208 3.4 31.8 1.0 HZ1 B:LYS179 3.5 33.4 1.0 H3 B:CAP501 3.5 29.8 1.0 HZ2 B:LYS181 3.6 45.9 1.0 HZ3 B:LYS179 3.7 33.4 1.0 NZ B:LYS181 3.8 38.2 1.0 ND2 A:ASN127 3.8 29.2 1.0 HD22 A:ASN127 3.8 35.1 1.0 N B:GLU208 3.8 27.5 1.0 HZ3 B:LYS181 3.8 45.9 1.0 OD2 B:ASP207 3.9 27.3 1.0 NE2 B:HIS298 3.9 19.7 1.0 HB3 B:GLU208 4.0 33.5 1.0 NZ B:LYS179 4.0 27.8 1.0 O7 B:CAP501 4.1 29.5 1.0 CG2 B:THR177 4.1 34.6 1.0 CA B:ASP207 4.1 24.0 1.0 C4 B:CAP501 4.2 25.8 1.0 CB B:ASP207 4.2 26.3 1.0 H52 B:CAP501 4.2 31.8 1.0 H4 B:CAP501 4.2 31.0 1.0 CG B:GLU208 4.3 28.0 1.0 HZ2 B:LYS179 4.3 33.4 1.0 OG1 B:THR177 4.3 31.2 1.0 NZ B:KCX205 4.3 22.8 1.0 C1 B:CAP501 4.4 28.4 1.0 HG23 B:THR177 4.4 41.5 1.0 HZ B:KCX205 4.5 27.4 1.0 HD2 B:HIS298 4.5 21.9 1.0 CB B:GLU208 4.5 27.9 1.0 C B:ASP207 4.5 23.7 1.0 CD2 B:HIS298 4.5 18.2 1.0 HB3 B:ASP207 4.6 31.6 1.0 C5 B:CAP501 4.6 26.5 1.0 HG22 B:THR177 4.7 41.5 1.0 HG3 B:GLU208 4.7 33.6 1.0 H11 B:CAP501 4.8 34.1 1.0 CB B:THR177 4.8 31.5 1.0 CA B:GLU208 4.8 24.9 1.0 O1 B:CAP501 4.8 29.3 1.0 H51 B:CAP501 4.8 31.8 1.0 CE1 B:HIS298 4.8 20.3 1.0 H12 B:CAP501 4.9 34.1 1.0 HG2 B:GLU208 4.9 33.6 1.0 HG1 B:THR177 4.9 37.5 1.0 HB B:THR177 5.0 37.9 1.0 HB2 B:ASP207 5.0 31.6 1.0 CG A:ASN127 5.0 28.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Rubisco From Promineofilum Breve


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 Rubisco From Promineofilum Breve within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:24.2 occ:1.00 O7 C:CAP501 1.9 27.9 1.0 OQ2 C:KCX205 2.0 32.1 1.0 O2 C:CAP501 2.1 24.2 1.0 OE1 C:GLU208 2.2 31.7 1.0 O3 C:CAP501 2.2 24.5 1.0 OD1 C:ASP207 2.4 36.0 1.0 HO3 C:CAP501 2.5 29.4 1.0 C C:CAP501 2.6 26.8 1.0 C2 C:CAP501 2.6 25.7 1.0 HO2 C:CAP501 2.7 29.1 1.0 C3 C:CAP501 3.0 26.6 1.0 CG C:ASP207 3.0 32.1 1.0 HG21 C:THR177 3.1 38.3 1.0 HZ1 C:LYS181 3.1 27.3 1.0 CX C:KCX205 3.1 30.7 1.0 H C:GLU208 3.1 25.7 1.0 HZ3 C:LYS181 3.2 27.3 1.0 HD22 D:ASN127 3.2 39.9 1.0 CD C:GLU208 3.2 29.1 1.0 HZ3 C:LYS179 3.2 33.1 1.0 HZ2 C:LYS179 3.3 33.1 1.0 OD2 C:ASP207 3.3 34.6 1.0 OQ1 C:KCX205 3.4 30.6 1.0 HA C:ASP207 3.5 33.3 1.0 NZ C:LYS181 3.5 22.7 1.0 HG1 C:THR177 3.5 37.7 1.0 H3 C:CAP501 3.5 31.9 1.0 HE2 C:HIS298 3.6 34.8 1.0 NZ C:LYS179 3.7 27.5 1.0 OE2 C:GLU208 3.7 25.9 1.0 HZ2 C:LYS181 3.8 27.3 1.0 O6 C:CAP501 3.8 27.8 1.0 ND2 D:ASN127 3.8 33.2 1.0 HD21 D:ASN127 3.9 39.9 1.0 N C:GLU208 3.9 21.4 1.0 CG2 C:THR177 4.0 31.9 1.0 HZ1 C:LYS179 4.0 33.1 1.0 C1 C:CAP501 4.1 28.8 1.0 C4 C:CAP501 4.1 27.9 1.0 HB3 C:GLU208 4.1 30.4 1.0 CB C:ASP207 4.2 30.7 1.0 CA C:ASP207 4.2 27.7 1.0 H4 C:CAP501 4.2 33.6 1.0 NE2 C:HIS298 4.2 28.9 1.0 OG1 C:THR177 4.3 31.4 1.0 NZ C:KCX205 4.3 28.8 1.0 HG23 C:THR177 4.3 38.3 1.0 H51 C:CAP501 4.4 34.7 1.0 HZ C:KCX205 4.5 34.6 1.0 CG C:GLU208 4.5 28.1 1.0 H12 C:CAP501 4.5 34.6 1.0 O1 C:CAP501 4.5 29.9 1.0 HG22 C:THR177 4.5 38.3 1.0 C C:ASP207 4.6 24.5 1.0 H11 C:CAP501 4.7 34.6 1.0 CB C:THR177 4.7 30.5 1.0 HD2 C:HIS298 4.7 35.3 1.0 CB C:GLU208 4.7 25.3 1.0 C5 C:CAP501 4.7 28.8 1.0 HB3 C:ASP207 4.7 36.9 1.0 HB2 C:ASP207 4.7 36.9 1.0 CD2 C:HIS298 4.8 29.4 1.0 HB C:THR177 4.8 36.6 1.0 CE C:LYS181 4.8 22.8 1.0 O C:HOH699 4.9 28.9 1.0 HE3 C:LYS181 4.9 27.5 1.0 HG3 C:GLU208 4.9 33.8 1.0 HG2 C:LYS181 4.9 30.1 1.0 HE2 C:LYS179 4.9 36.0 1.0 H52 C:CAP501 4.9 34.7 1.0 CA C:GLU208 4.9 21.5 1.0 CE C:LYS179 5.0 30.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Rubisco From Promineofilum Breve


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 Rubisco From Promineofilum Breve within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:23.9 occ:1.00 OD1 D:ASP207 1.9 34.1 1.0 OQ1 D:KCX205 2.1 28.4 1.0 O6 D:CAP501 2.1 24.0 1.0 O2 D:CAP501 2.1 26.6 1.0 OE1 D:GLU208 2.2 32.0 1.0 O3 D:CAP501 2.3 32.7 1.0 C2 D:CAP501 2.7 29.2 1.0 C D:CAP501 2.8 25.9 1.0 HO3 D:CAP501 2.8 39.3 1.0 HO2 D:CAP501 2.9 31.9 1.0 HD22 C:ASN127 3.0 41.4 1.0 CG D:ASP207 3.0 31.9 1.0 HZ3 D:LYS181 3.1 35.4 1.0 HZ2 D:LYS181 3.1 35.4 1.0 C3 D:CAP501 3.1 33.3 1.0 H D:GLU208 3.1 30.2 1.0 CX D:KCX205 3.2 29.0 1.0 CD D:GLU208 3.2 29.1 1.0 HG21 D:THR177 3.2 44.7 1.0 HZ3 D:LYS179 3.2 41.5 1.0 HE2 D:HIS298 3.4 25.7 1.0 NZ D:LYS181 3.4 29.5 1.0 OQ2 D:KCX205 3.5 29.6 1.0 OE2 D:GLU208 3.5 30.2 1.0 HA D:ASP207 3.6 29.3 1.0 HZ2 D:LYS179 3.6 41.5 1.0 HZ1 D:LYS181 3.6 35.4 1.0 OD2 D:ASP207 3.7 33.8 1.0 ND2 C:ASN127 3.7 34.4 1.0 H3 D:CAP501 3.7 40.0 1.0 HD21 C:ASN127 3.7 41.4 1.0 NZ D:LYS179 3.8 34.5 1.0 N D:GLU208 4.0 25.1 1.0 O7 D:CAP501 4.0 26.7 1.0 NE2 D:HIS298 4.0 21.4 1.0 HB3 D:GLU208 4.1 32.9 1.0 CG2 D:THR177 4.1 37.2 1.0 H4 D:CAP501 4.1 39.4 1.0 HG23 D:THR177 4.2 44.7 1.0 CB D:ASP207 4.2 28.0 1.0 C4 D:CAP501 4.2 32.8 1.0 C1 D:CAP501 4.2 30.0 1.0 HZ1 D:LYS179 4.2 41.5 1.0 CA D:ASP207 4.3 24.4 1.0 OG1 D:THR177 4.3 38.6 1.0 NZ D:KCX205 4.4 26.3 1.0 CG D:GLU208 4.4 28.5 1.0 H52 D:CAP501 4.4 36.8 1.0 HB3 D:ASP207 4.5 33.7 1.0 H11 D:CAP501 4.6 36.1 1.0 HZ D:KCX205 4.6 31.6 1.0 CB D:GLU208 4.6 27.4 1.0 C D:ASP207 4.7 24.4 1.0 O1 D:CAP501 4.7 29.8 1.0 HG22 D:THR177 4.8 44.7 1.0 HG2 D:LYS181 4.8 38.7 1.0 H12 D:CAP501 4.8 36.1 1.0 CB D:THR177 4.8 37.5 1.0 CD2 D:HIS298 4.8 20.9 1.0 CE D:LYS181 4.8 29.3 1.0 HD2 D:HIS298 4.8 25.1 1.0 C5 D:CAP501 4.8 30.6 1.0 HG3 D:GLU208 4.9 34.2 1.0 CE1 D:HIS298 4.9 22.3 1.0 HB2 D:ASP207 4.9 33.7 1.0 CG C:ASN127 4.9 32.2 1.0 HE3 D:LYS181 4.9 35.2 1.0 HE1 D:HIS298 4.9 26.8 1.0 CA D:GLU208 5.0 24.9 1.0 HG1 D:THR177 5.0 46.3 1.0 HB D:THR177 5.0 45.0 1.0 O C:HOH636 5.0 36.5 1.0

D.M.Banda, J.H.Pereira, A.K.Liu, D.J.Orr, M.Hammel, C.He, M.A.J.Parry, E.Carmo-Silva, P.D.Adams, J.F.Banfield, P.M.Shih. Novel Bacterial Clade Reveals Origin of Form I Rubisco. Nat.Plants V. 6 1158 2020.
ISSN: ESSN 2055-0278
PubMed: 32868887
DOI: 10.1038/S41477-020-00762-4