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Magnesium in PDB 4rub: A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State

Enzymatic activity of A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State

All present enzymatic activity of A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State:
4.1.1.39;

Protein crystallography data

The structure of A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State, PDB code: 4rub was solved by H.Schreuder, D.Cascio, P.M.G.Curmi, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 204.600, 204.600, 117.400, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State (pdb code 4rub). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State, PDB code: 4rub:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4rub

Go back to Magnesium Binding Sites List in 4rub
Magnesium binding site 1 out of 4 in the A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg491

b:15.5
occ:1.00
 OE1 A:GLU204 1.9 17.4 1.0
O4 A:CAP490 2.1 19.4 1.0
O7 A:CAP490 2.2 20.1 1.0
OD1 A:ASP203 2.3 23.8 1.0
O1 A:FMT492 2.3 12.7 1.0
O2 A:CAP490 2.3 19.3 1.0
O2 A:FMT492 2.5 15.0 1.0
C A:FMT492 2.9 12.7 1.0
C A:CAP490 3.0 20.1 1.0
CD A:GLU204 3.1 17.6 1.0
C2 A:CAP490 3.1 19.9 1.0
NE2 A:HIS294 3.2 15.4 1.0
CG A:ASP203 3.4 23.2 1.0
C4 A:CAP490 3.5 19.5 1.0
C3 A:CAP490 3.8 19.8 1.0
ND2 D:ASN123 3.8 15.8 1.0
CD2 A:HIS294 3.9 14.5 1.0
OE2 A:GLU204 3.9 18.5 1.0
N A:GLU204 3.9 15.3 1.0
CG2 A:THR173 4.0 11.4 1.0
NZ A:LYS201 4.1 11.2 1.0
O6 A:CAP490 4.1 20.6 1.0
OD2 A:ASP203 4.1 24.7 1.0
CE1 A:HIS294 4.2 14.3 1.0
CG A:GLU204 4.2 16.8 1.0
CA A:ASP203 4.3 16.3 1.0
CB A:ASP203 4.3 21.2 1.0
CB A:GLU204 4.3 15.7 1.0
C5 A:CAP490 4.5 18.8 1.0
C1 A:CAP490 4.5 19.5 1.0
NZ A:LYS177 4.5 18.4 1.0
C A:ASP203 4.6 16.1 1.0
CA A:GLU204 4.8 14.2 1.0
NZ A:LYS175 4.8 12.7 1.0
O3 A:CAP490 5.0 19.8 1.0

Magnesium binding site 2 out of 4 in 4rub

Go back to Magnesium Binding Sites List in 4rub
Magnesium binding site 2 out of 4 in the A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg491

b:15.2
occ:1.00
 OE1 B:GLU204 1.9 17.6 1.0
O4 B:CAP490 2.1 19.4 1.0
O7 B:CAP490 2.2 20.4 1.0
O2 B:CAP490 2.2 19.4 1.0
OD1 B:ASP203 2.2 23.9 1.0
O1 B:FMT492 2.5 13.1 1.0
C B:CAP490 2.8 20.2 1.0
O2 B:FMT492 2.9 15.0 1.0
C2 B:CAP490 3.0 19.7 1.0
C B:FMT492 3.0 12.9 1.0
CD B:GLU204 3.1 17.9 1.0
CG B:ASP203 3.4 23.7 1.0
NE2 B:HIS294 3.4 15.4 1.0
C4 B:CAP490 3.4 19.4 1.0
C3 B:CAP490 3.8 19.5 1.0
O6 B:CAP490 3.9 20.5 1.0
OE2 B:GLU204 3.9 19.1 1.0
ND2 C:ASN123 3.9 15.7 1.0
N B:GLU204 4.0 15.2 1.0
CG2 B:THR173 4.0 10.8 1.0
CD2 B:HIS294 4.0 14.4 1.0
CG B:GLU204 4.2 17.2 1.0
OD2 B:ASP203 4.2 25.6 1.0
NZ B:LYS201 4.2 11.3 1.0
C1 B:CAP490 4.3 19.6 1.0
CE1 B:HIS294 4.4 14.4 1.0
CB B:ASP203 4.4 21.4 1.0
CA B:ASP203 4.4 16.6 1.0
CB B:GLU204 4.4 15.6 1.0
C5 B:CAP490 4.5 18.8 1.0
NZ B:LYS177 4.6 19.3 1.0
NZ B:LYS175 4.7 12.4 1.0
C B:ASP203 4.7 16.2 1.0
CA B:GLU204 4.8 14.1 1.0
O1 B:CAP490 4.8 19.1 1.0
O3 B:CAP490 4.8 20.2 1.0

Magnesium binding site 3 out of 4 in 4rub

Go back to Magnesium Binding Sites List in 4rub
Magnesium binding site 3 out of 4 in the A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg491

b:16.4
occ:1.00
 OE1 C:GLU204 2.1 18.2 1.0
O2 C:CAP490 2.1 19.8 1.0
O4 C:CAP490 2.1 19.8 1.0
O1 C:FMT492 2.2 13.6 1.0
OD1 C:ASP203 2.4 24.4 1.0
O7 C:CAP490 2.5 20.2 1.0
C C:FMT492 2.6 13.3 1.0
O2 C:FMT492 2.6 15.0 1.0
C C:CAP490 3.1 20.3 1.0
C2 C:CAP490 3.1 20.1 1.0
CD C:GLU204 3.3 18.3 1.0
NE2 C:HIS294 3.3 15.5 1.0
C4 C:CAP490 3.5 19.6 1.0
CG C:ASP203 3.5 24.0 1.0
CG2 C:THR173 3.7 11.5 1.0
C3 C:CAP490 3.8 19.9 1.0
CD2 C:HIS294 3.9 14.3 1.0
NZ C:LYS201 3.9 11.6 1.0
N C:GLU204 3.9 15.8 1.0
ND2 B:ASN123 4.0 16.5 1.0
OE2 C:GLU204 4.1 19.5 1.0
CA C:ASP203 4.2 16.4 1.0
O6 C:CAP490 4.2 21.0 1.0
OD2 C:ASP203 4.3 25.9 1.0
CG C:GLU204 4.3 17.4 1.0
C1 C:CAP490 4.4 20.0 1.0
CE1 C:HIS294 4.4 14.6 1.0
CB C:GLU204 4.4 15.8 1.0
CB C:ASP203 4.4 21.2 1.0
C5 C:CAP490 4.6 19.0 1.0
NZ C:LYS177 4.7 18.6 1.0
C C:ASP203 4.7 16.4 1.0
O3 C:CAP490 4.7 20.4 1.0
OG1 C:THR173 4.8 14.1 1.0
NZ C:LYS175 4.8 13.1 1.0
CA C:GLU204 4.9 14.7 1.0
CB C:THR173 4.9 13.0 1.0
O1 C:CAP490 4.9 19.7 1.0

Magnesium binding site 4 out of 4 in 4rub

Go back to Magnesium Binding Sites List in 4rub
Magnesium binding site 4 out of 4 in the A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum in the Activated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg491

b:14.9
occ:1.00
 OE1 D:GLU204 1.8 17.9 1.0
O4 D:CAP490 2.0 19.9 1.0
O1 D:FMT492 2.3 13.9 1.0
OD1 D:ASP203 2.4 23.9 1.0
O2 D:CAP490 2.5 19.5 1.0
O2 D:FMT492 2.5 14.8 1.0
C D:FMT492 2.6 13.6 1.0
O7 D:CAP490 2.7 20.8 1.0
CD D:GLU204 3.0 18.4 1.0
NE2 D:HIS294 3.2 15.9 1.0
C D:CAP490 3.3 20.4 1.0
C2 D:CAP490 3.4 20.0 1.0
C4 D:CAP490 3.5 20.0 1.0
CG D:ASP203 3.5 23.9 1.0
CD2 D:HIS294 3.7 14.5 1.0
N D:GLU204 3.7 15.6 1.0
NZ D:LYS201 3.8 11.1 1.0
ND2 A:ASN123 3.9 15.9 1.0
C3 D:CAP490 4.0 20.1 1.0
OE2 D:GLU204 4.0 19.5 1.0
CG D:GLU204 4.0 16.9 1.0
CG2 D:THR173 4.0 11.2 1.0
CB D:GLU204 4.0 15.7 1.0
CE1 D:HIS294 4.1 14.6 1.0
CA D:ASP203 4.2 16.6 1.0
OD2 D:ASP203 4.3 25.6 1.0
CB D:ASP203 4.4 21.3 1.0
O6 D:CAP490 4.4 20.8 1.0
CA D:GLU204 4.5 14.5 1.0
C5 D:CAP490 4.5 19.3 1.0
C D:ASP203 4.5 16.2 1.0
C1 D:CAP490 4.7 19.9 1.0
CG D:HIS294 4.8 13.8 1.0
NZ D:LYS177 4.8 19.1 1.0
CE D:LYS201 5.0 8.2 1.0
ND1 D:HIS294 5.0 14.1 1.0

Reference:

S.W.Suh, D.Cascio, M.S.Chapman, D.Eisenberg. A Crystal Form of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase From Nicotiana Tabacum in the Activated State. J.Mol.Biol. V. 197 363 1987.
ISSN: ISSN 0022-2836
PubMed: 3681999
DOI: 10.1016/0022-2836(87)90129-X
Page generated: Tue Aug 20 03:30:01 2024

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