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Magnesium in PDB 1rbl: Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301

Enzymatic activity of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301

All present enzymatic activity of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301:
4.1.1.39;

Protein crystallography data

The structure of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301, PDB code: 1rbl was solved by J.Newman, S.Gutteridge, C.-I.Branden, T.A.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 223.900, 111.900, 199.700, 90.00, 90.00, 90.00
R / Rfree (%) 20 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 (pdb code 1rbl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301, PDB code: 1rbl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1rbl

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Magnesium binding site 1 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg477

b:19.9
occ:1.00
 OD1 A:ASP203 2.3 17.1 1.0
OE1 A:GLU204 2.3 19.8 1.0
O3 A:CAP476 2.4 19.1 1.0
O2 A:FMT478 2.4 14.2 1.0
O2 A:CAP476 2.4 19.9 1.0
O7 A:CAP476 2.4 19.2 1.0
C2 A:CAP476 2.9 20.1 1.0
C A:CAP476 3.0 17.9 1.0
O1 A:FMT478 3.1 15.5 1.0
C A:FMT478 3.1 13.9 1.0
C3 A:CAP476 3.2 20.0 1.0
CD A:GLU204 3.3 17.9 1.0
CG A:ASP203 3.5 16.2 1.0
OE2 A:GLU204 3.8 17.1 1.0
NE2 A:HIS294 3.8 17.8 1.0
ND2 B:ASN123 3.9 14.4 1.0
N A:GLU204 3.9 13.5 1.0
CG2 A:THR173 4.0 14.2 1.0
NZ A:LYS177 4.1 8.4 1.0
NZ A:LYS175 4.1 14.8 1.0
CA A:ASP203 4.2 13.2 1.0
OD2 A:ASP203 4.3 19.6 1.0
O6 A:CAP476 4.3 20.5 1.0
C4 A:CAP476 4.3 16.6 1.0
C1 A:CAP476 4.4 16.3 1.0
CB A:ASP203 4.4 12.6 1.0
OG1 A:THR173 4.4 18.5 1.0
CD2 A:HIS294 4.5 15.4 1.0
NZ A:LYS201 4.5 12.8 1.0
CG A:GLU204 4.5 14.2 1.0
CB A:GLU204 4.6 13.3 1.0
C A:ASP203 4.6 13.8 1.0
CE1 A:HIS294 4.7 16.4 1.0
CB A:THR173 4.8 18.4 1.0
C5 A:CAP476 4.8 13.7 1.0
CA A:GLU204 4.9 13.5 1.0

Magnesium binding site 2 out of 8 in 1rbl

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Magnesium binding site 2 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg477

b:19.9
occ:1.00
 OD1 B:ASP203 2.3 17.1 1.0
OE1 B:GLU204 2.3 19.8 1.0
O3 B:CAP476 2.4 19.1 1.0
O2 B:FMT478 2.4 14.2 1.0
O2 B:CAP476 2.4 19.9 1.0
O7 B:CAP476 2.4 19.2 1.0
C2 B:CAP476 2.9 20.1 1.0
C B:CAP476 3.0 17.9 1.0
C B:FMT478 3.1 13.9 1.0
O1 B:FMT478 3.1 15.5 1.0
C3 B:CAP476 3.2 20.0 1.0
CD B:GLU204 3.3 17.9 1.0
CG B:ASP203 3.5 16.2 1.0
OE2 B:GLU204 3.8 17.1 1.0
NE2 B:HIS294 3.8 17.8 1.0
ND2 A:ASN123 3.8 14.4 1.0
N B:GLU204 3.9 13.5 1.0
CG2 B:THR173 4.0 14.2 1.0
NZ B:LYS177 4.1 8.4 1.0
NZ B:LYS175 4.1 14.8 1.0
CA B:ASP203 4.2 13.2 1.0
OD2 B:ASP203 4.3 19.6 1.0
O6 B:CAP476 4.3 20.5 1.0
C4 B:CAP476 4.3 16.6 1.0
C1 B:CAP476 4.4 16.3 1.0
CB B:ASP203 4.4 12.6 1.0
OG1 B:THR173 4.4 18.5 1.0
NZ B:LYS201 4.5 12.8 1.0
CD2 B:HIS294 4.5 15.4 1.0
CG B:GLU204 4.5 14.2 1.0
CB B:GLU204 4.6 13.3 1.0
C B:ASP203 4.6 13.8 1.0
CE1 B:HIS294 4.7 16.4 1.0
CB B:THR173 4.8 18.4 1.0
C5 B:CAP476 4.8 13.7 1.0
CA B:GLU204 4.9 13.5 1.0

Magnesium binding site 3 out of 8 in 1rbl

Go back to Magnesium Binding Sites List in 1rbl
Magnesium binding site 3 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg477

b:19.9
occ:1.00
 OD1 C:ASP203 2.3 17.1 1.0
OE1 C:GLU204 2.3 19.8 1.0
O3 C:CAP476 2.4 19.1 1.0
O2 C:FMT478 2.4 14.2 1.0
O2 C:CAP476 2.4 19.9 1.0
O7 C:CAP476 2.4 19.2 1.0
C2 C:CAP476 2.9 20.1 1.0
C C:CAP476 3.0 17.9 1.0
O1 C:FMT478 3.1 15.5 1.0
C C:FMT478 3.1 13.9 1.0
C3 C:CAP476 3.2 20.0 1.0
CD C:GLU204 3.3 17.9 1.0
CG C:ASP203 3.5 16.2 1.0
OE2 C:GLU204 3.8 17.1 1.0
NE2 C:HIS294 3.8 17.8 1.0
ND2 D:ASN123 3.8 14.4 1.0
N C:GLU204 3.9 13.5 1.0
CG2 C:THR173 4.0 14.2 1.0
NZ C:LYS177 4.1 8.4 1.0
NZ C:LYS175 4.1 14.8 1.0
CA C:ASP203 4.2 13.2 1.0
OD2 C:ASP203 4.3 19.6 1.0
O6 C:CAP476 4.3 20.5 1.0
C4 C:CAP476 4.3 16.6 1.0
C1 C:CAP476 4.4 16.3 1.0
CB C:ASP203 4.4 12.6 1.0
OG1 C:THR173 4.4 18.5 1.0
CD2 C:HIS294 4.5 15.4 1.0
NZ C:LYS201 4.5 12.8 1.0
CG C:GLU204 4.5 14.2 1.0
CB C:GLU204 4.6 13.3 1.0
C C:ASP203 4.6 13.8 1.0
CE1 C:HIS294 4.7 16.4 1.0
CB C:THR173 4.8 18.4 1.0
C5 C:CAP476 4.8 13.7 1.0
CA C:GLU204 4.9 13.5 1.0

Magnesium binding site 4 out of 8 in 1rbl

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Magnesium binding site 4 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg477

b:19.9
occ:1.00
 OD1 D:ASP203 2.3 17.1 1.0
OE1 D:GLU204 2.3 19.8 1.0
O3 D:CAP476 2.4 19.1 1.0
O2 D:FMT478 2.4 14.2 1.0
O2 D:CAP476 2.4 19.9 1.0
O7 D:CAP476 2.4 19.2 1.0
C2 D:CAP476 2.9 20.1 1.0
C D:CAP476 3.0 17.9 1.0
C D:FMT478 3.1 13.9 1.0
O1 D:FMT478 3.1 15.5 1.0
C3 D:CAP476 3.2 20.0 1.0
CD D:GLU204 3.3 17.9 1.0
CG D:ASP203 3.5 16.2 1.0
OE2 D:GLU204 3.8 17.1 1.0
NE2 D:HIS294 3.8 17.8 1.0
ND2 C:ASN123 3.8 14.4 1.0
N D:GLU204 3.9 13.5 1.0
CG2 D:THR173 4.0 14.2 1.0
NZ D:LYS177 4.1 8.4 1.0
NZ D:LYS175 4.1 14.8 1.0
CA D:ASP203 4.2 13.2 1.0
OD2 D:ASP203 4.3 19.6 1.0
O6 D:CAP476 4.3 20.5 1.0
C4 D:CAP476 4.3 16.6 1.0
C1 D:CAP476 4.4 16.3 1.0
CB D:ASP203 4.4 12.6 1.0
OG1 D:THR173 4.4 18.5 1.0
CD2 D:HIS294 4.5 15.4 1.0
NZ D:LYS201 4.5 12.8 1.0
CG D:GLU204 4.5 14.2 1.0
CB D:GLU204 4.6 13.3 1.0
C D:ASP203 4.6 13.8 1.0
CE1 D:HIS294 4.7 16.4 1.0
CB D:THR173 4.8 18.4 1.0
C5 D:CAP476 4.8 13.7 1.0
CA D:GLU204 4.9 13.5 1.0

Magnesium binding site 5 out of 8 in 1rbl

Go back to Magnesium Binding Sites List in 1rbl
Magnesium binding site 5 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg477

b:19.9
occ:1.00
 OD1 E:ASP203 2.3 17.1 1.0
OE1 E:GLU204 2.3 19.8 1.0
O3 E:CAP476 2.4 19.1 1.0
O2 E:FMT478 2.4 14.2 1.0
O2 E:CAP476 2.4 19.9 1.0
O7 E:CAP476 2.4 19.2 1.0
C2 E:CAP476 2.9 20.1 1.0
C E:CAP476 3.0 17.9 1.0
O1 E:FMT478 3.1 15.5 1.0
C E:FMT478 3.1 13.9 1.0
C3 E:CAP476 3.2 20.0 1.0
CD E:GLU204 3.3 17.9 1.0
CG E:ASP203 3.5 16.2 1.0
OE2 E:GLU204 3.8 17.1 1.0
NE2 E:HIS294 3.8 17.8 1.0
ND2 F:ASN123 3.9 14.4 1.0
N E:GLU204 3.9 13.5 1.0
CG2 E:THR173 4.0 14.2 1.0
NZ E:LYS177 4.1 8.4 1.0
NZ E:LYS175 4.1 14.8 1.0
CA E:ASP203 4.2 13.2 1.0
OD2 E:ASP203 4.3 19.6 1.0
O6 E:CAP476 4.3 20.5 1.0
C4 E:CAP476 4.3 16.6 1.0
C1 E:CAP476 4.4 16.3 1.0
CB E:ASP203 4.4 12.6 1.0
OG1 E:THR173 4.4 18.5 1.0
CD2 E:HIS294 4.5 15.4 1.0
NZ E:LYS201 4.5 12.8 1.0
CG E:GLU204 4.5 14.2 1.0
CB E:GLU204 4.6 13.3 1.0
C E:ASP203 4.6 13.8 1.0
CE1 E:HIS294 4.7 16.4 1.0
CB E:THR173 4.8 18.4 1.0
C5 E:CAP476 4.8 13.7 1.0
CA E:GLU204 4.9 13.5 1.0

Magnesium binding site 6 out of 8 in 1rbl

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Magnesium binding site 6 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg477

b:19.9
occ:1.00
 OD1 F:ASP203 2.3 17.1 1.0
OE1 F:GLU204 2.3 19.8 1.0
O3 F:CAP476 2.4 19.1 1.0
O2 F:FMT478 2.4 14.2 1.0
O2 F:CAP476 2.4 19.9 1.0
O7 F:CAP476 2.4 19.2 1.0
C2 F:CAP476 2.9 20.1 1.0
C F:CAP476 3.0 17.9 1.0
C F:FMT478 3.1 13.9 1.0
O1 F:FMT478 3.1 15.5 1.0
C3 F:CAP476 3.2 20.0 1.0
CD F:GLU204 3.3 17.9 1.0
CG F:ASP203 3.5 16.2 1.0
OE2 F:GLU204 3.8 17.1 1.0
NE2 F:HIS294 3.8 17.8 1.0
ND2 E:ASN123 3.8 14.4 1.0
N F:GLU204 3.9 13.5 1.0
CG2 F:THR173 4.0 14.2 1.0
NZ F:LYS177 4.1 8.4 1.0
NZ F:LYS175 4.1 14.8 1.0
CA F:ASP203 4.2 13.2 1.0
OD2 F:ASP203 4.3 19.6 1.0
O6 F:CAP476 4.3 20.5 1.0
C4 F:CAP476 4.3 16.6 1.0
C1 F:CAP476 4.4 16.3 1.0
CB F:ASP203 4.4 12.6 1.0
OG1 F:THR173 4.4 18.5 1.0
CD2 F:HIS294 4.5 15.4 1.0
NZ F:LYS201 4.5 12.8 1.0
CG F:GLU204 4.5 14.2 1.0
CB F:GLU204 4.6 13.3 1.0
C F:ASP203 4.6 13.8 1.0
CE1 F:HIS294 4.7 16.4 1.0
CB F:THR173 4.8 18.4 1.0
C5 F:CAP476 4.8 13.7 1.0
CA F:GLU204 4.9 13.5 1.0
CG E:ASN123 5.0 16.2 1.0

Magnesium binding site 7 out of 8 in 1rbl

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Magnesium binding site 7 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg477

b:19.9
occ:1.00
 OD1 G:ASP203 2.3 17.1 1.0
OE1 G:GLU204 2.3 19.8 1.0
O3 G:CAP476 2.4 19.1 1.0
O2 G:FMT478 2.4 14.2 1.0
O2 G:CAP476 2.4 19.9 1.0
O7 G:CAP476 2.4 19.2 1.0
C2 G:CAP476 2.9 20.1 1.0
C G:CAP476 3.0 17.9 1.0
O1 G:FMT478 3.1 15.5 1.0
C G:FMT478 3.1 13.9 1.0
C3 G:CAP476 3.2 20.0 1.0
CD G:GLU204 3.3 17.9 1.0
CG G:ASP203 3.5 16.2 1.0
OE2 G:GLU204 3.8 17.1 1.0
NE2 G:HIS294 3.8 17.8 1.0
ND2 H:ASN123 3.9 14.4 1.0
N G:GLU204 3.9 13.5 1.0
CG2 G:THR173 4.0 14.2 1.0
NZ G:LYS177 4.1 8.4 1.0
NZ G:LYS175 4.1 14.8 1.0
CA G:ASP203 4.2 13.2 1.0
OD2 G:ASP203 4.3 19.6 1.0
O6 G:CAP476 4.3 20.5 1.0
C4 G:CAP476 4.3 16.6 1.0
C1 G:CAP476 4.4 16.3 1.0
CB G:ASP203 4.4 12.6 1.0
OG1 G:THR173 4.4 18.5 1.0
CD2 G:HIS294 4.5 15.4 1.0
NZ G:LYS201 4.5 12.8 1.0
CG G:GLU204 4.5 14.2 1.0
CB G:GLU204 4.6 13.3 1.0
C G:ASP203 4.6 13.8 1.0
CE1 G:HIS294 4.7 16.4 1.0
CB G:THR173 4.8 18.4 1.0
C5 G:CAP476 4.8 13.7 1.0
CA G:GLU204 4.9 13.5 1.0

Magnesium binding site 8 out of 8 in 1rbl

Go back to Magnesium Binding Sites List in 1rbl
Magnesium binding site 8 out of 8 in the Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure Determination and Refinement of Ribulose 1,5 Bisphosphate Carboxylase(Slash)Oxygenase From Synechococcus PCC6301 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg477

b:19.9
occ:1.00
 OD1 H:ASP203 2.3 17.1 1.0
OE1 H:GLU204 2.3 19.8 1.0
O3 H:CAP476 2.4 19.1 1.0
O2 H:FMT478 2.4 14.2 1.0
O2 H:CAP476 2.4 19.9 1.0
O7 H:CAP476 2.4 19.2 1.0
C2 H:CAP476 2.9 20.1 1.0
C H:CAP476 3.0 17.9 1.0
O1 H:FMT478 3.1 15.5 1.0
C H:FMT478 3.1 13.9 1.0
C3 H:CAP476 3.2 20.0 1.0
CD H:GLU204 3.3 17.9 1.0
CG H:ASP203 3.5 16.2 1.0
OE2 H:GLU204 3.8 17.1 1.0
NE2 H:HIS294 3.8 17.8 1.0
ND2 G:ASN123 3.8 14.4 1.0
N H:GLU204 3.9 13.5 1.0
CG2 H:THR173 4.0 14.2 1.0
NZ H:LYS177 4.1 8.4 1.0
NZ H:LYS175 4.1 14.8 1.0
CA H:ASP203 4.2 13.2 1.0
OD2 H:ASP203 4.3 19.6 1.0
O6 H:CAP476 4.3 20.5 1.0
C4 H:CAP476 4.3 16.6 1.0
C1 H:CAP476 4.4 16.3 1.0
CB H:ASP203 4.4 12.6 1.0
OG1 H:THR173 4.4 18.5 1.0
CD2 H:HIS294 4.5 15.4 1.0
NZ H:LYS201 4.5 12.8 1.0
CG H:GLU204 4.5 14.2 1.0
CB H:GLU204 4.6 13.3 1.0
C H:ASP203 4.6 13.8 1.0
CE1 H:HIS294 4.7 16.4 1.0
CB H:THR173 4.8 18.4 1.0
C5 H:CAP476 4.8 13.7 1.0
CA H:GLU204 4.9 13.5 1.0

Reference:

J.Newman, C.I.Branden, T.A.Jones. Structure Determination and Refinement of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase From Synechococcus PCC6301. Acta Crystallogr.,Sect.D V. 49 548 1993.
ISSN: ISSN 0907-4449
PubMed: 15299492
DOI: 10.1107/S090744499300530X
Page generated: Tue Aug 13 12:07:06 2024

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