Atomistry » Magnesium » PDB 4rrk-4s1l » 4rub
Atomistry »
  Magnesium »
    PDB 4rrk-4s1l »
      4rub »

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

Last articles

Mg in 3AV0
Mg in 3AUX
Mg in 3AUY
Mg in 3AUW
Mg in 3AUA
Mg in 3AU9
Mg in 3AU6
Mg in 3AU0
Mg in 3ATT
Mg in 3ATS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy