Magnesium in PDB 8qj0: Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco

Enzymatic activity of Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco

All present enzymatic activity of Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco:
4.1.1.39;

Protein crystallography data

The structure of Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco, PDB code: 8qj0 was solved by M.Bjelcic, R.Neutze, O.Aurelius, J.Nan, T.Ursby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.78 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 158.6, 157.12, 202.74, 90, 90, 90
R / Rfree (%) 18.1 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco (pdb code 8qj0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco, PDB code: 8qj0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8qj0

Go back to Magnesium Binding Sites List in 8qj0
Magnesium binding site 1 out of 4 in the Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg501

b:17.4
occ:1.00
 OE1 L:GLU204 2.0 14.7 1.0
OD1 L:ASP203 2.1 16.4 1.0
O L:HOH611 2.1 17.9 1.0
OQ2 L:KCX201 2.1 19.0 1.0
O L:HOH674 2.1 19.0 1.0
O L:HOH732 2.2 16.5 1.0
CD L:GLU204 3.1 14.8 1.0
CG L:ASP203 3.1 17.3 1.0
CX L:KCX201 3.1 19.7 1.0
HE2 L:HIS294 3.2 15.6 0.0
H L:GLU204 3.3 11.6 1.0
OQ1 L:KCX201 3.4 23.5 1.0
HG21 L:THR173 3.4 20.4 1.0
OE2 L:GLU204 3.4 14.6 1.0
HZ2 L:LYS177 3.5 23.8 1.0
HA L:ASP203 3.5 13.3 1.0
OD2 L:ASP203 3.8 16.6 1.0
HZ3 L:LYS177 3.9 23.8 1.0
NE2 L:HIS294 4.0 15.9 1.0
CB L:ASP203 4.1 16.6 1.0
N L:GLU204 4.2 11.3 1.0
NZ L:KCX201 4.2 17.0 1.0
NZ L:LYS177 4.2 22.5 1.0
CA L:ASP203 4.2 13.0 1.0
HB2 L:ASP203 4.3 15.8 1.0
CG2 L:THR173 4.4 20.1 1.0
CG L:GLU204 4.4 15.0 1.0
HB3 L:GLU204 4.5 12.9 1.0
HZ1 L:LYS177 4.7 23.8 1.0
HG23 L:THR173 4.7 20.4 1.0
C L:ASP203 4.7 12.9 1.0
HG22 L:THR173 4.8 20.4 1.0
O L:HOH606 4.8 30.7 1.0
CD2 L:HIS294 4.8 15.7 1.0
HG2 L:GLU204 4.8 14.4 1.0
CB L:GLU204 4.9 13.0 1.0
CE1 L:HIS294 4.9 15.9 1.0
HD2 L:HIS294 4.9 15.5 1.0
HE1 L:HIS294 4.9 15.1 1.0
HB3 L:ASP203 5.0 15.8 1.0

Magnesium binding site 2 out of 4 in 8qj0

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Magnesium binding site 2 out of 4 in the Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg501

b:18.7
occ:1.00
 OQ2 M:KCX201 1.9 15.0 1.0
OE1 M:GLU204 2.1 15.5 1.0
OD1 M:ASP203 2.1 16.2 1.0
O M:HOH714 2.1 25.1 1.0
O M:HOH604 2.1 17.9 1.0
O M:HOH686 2.1 20.9 1.0
CX M:KCX201 3.0 16.5 1.0
CG M:ASP203 3.1 15.3 1.0
CD M:GLU204 3.1 14.9 1.0
H M:GLU204 3.2 13.8 1.0
HG21 M:THR173 3.3 17.9 1.0
OQ1 M:KCX201 3.3 17.7 1.0
HE2 M:HIS294 3.4 16.5 0.0
HA M:ASP203 3.4 14.6 1.0
HZ3 M:LYS177 3.4 21.8 1.0
OE2 M:GLU204 3.5 14.3 1.0
OD2 M:ASP203 3.7 16.3 1.0
CB M:ASP203 4.0 15.9 1.0
NE2 M:HIS294 4.1 16.2 1.0
N M:GLU204 4.1 13.5 1.0
CA M:ASP203 4.1 14.3 1.0
NZ M:KCX201 4.1 15.3 1.0
HZ1 M:LYS177 4.1 21.8 1.0
HB2 M:ASP203 4.1 15.4 1.0
NZ M:LYS177 4.2 21.0 1.0
HE2 M:LYS175 4.3 56.0 1.0
CG2 M:THR173 4.3 17.6 1.0
HE2 M:LYS177 4.4 23.8 1.0
CG M:GLU204 4.5 13.7 1.0
HB3 M:GLU204 4.5 13.9 1.0
HG22 M:THR173 4.6 17.9 1.0
HE3 M:LYS175 4.6 56.2 1.0
HG23 M:THR173 4.7 17.9 1.0
C M:ASP203 4.7 16.0 1.0
HD2 M:HIS294 4.8 16.9 1.0
CD2 M:HIS294 4.8 17.8 1.0
HZ2 M:LYS177 4.8 21.8 1.0
HB3 M:ASP203 4.9 15.4 1.0
CE M:LYS177 4.9 23.6 1.0
OG1 M:THR173 4.9 19.5 1.0
CB M:GLU204 4.9 14.7 1.0
HG2 M:GLU204 4.9 14.2 1.0
CE1 M:HIS294 4.9 15.8 1.0
CE M:LYS175 5.0 54.8 1.0
HE1 M:HIS294 5.0 16.0 1.0

Magnesium binding site 3 out of 4 in 8qj0

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Magnesium binding site 3 out of 4 in the Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg501

b:16.6
occ:1.00
 OQ2 N:KCX201 1.9 16.5 1.0
OE1 N:GLU204 2.0 15.7 1.0
OD1 N:ASP203 2.1 19.6 1.0
O N:HOH680 2.1 18.1 1.0
O N:HOH682 2.1 21.2 1.0
O N:HOH616 2.1 20.6 1.0
CG N:ASP203 3.0 18.9 1.0
CX N:KCX201 3.0 20.1 1.0
CD N:GLU204 3.1 16.3 1.0
H N:GLU204 3.1 12.8 1.0
HA N:ASP203 3.3 15.6 1.0
HE2 N:HIS294 3.4 14.6 0.0
OQ1 N:KCX201 3.4 21.5 1.0
HG21 N:THR173 3.4 21.1 1.0
OE2 N:GLU204 3.5 16.2 1.0
HZ3 N:LYS177 3.6 20.1 1.0
OD2 N:ASP203 3.7 18.1 1.0
CB N:ASP203 3.9 18.9 1.0
N N:GLU204 4.0 12.2 1.0
CA N:ASP203 4.0 15.9 1.0
NZ N:KCX201 4.0 17.0 1.0
NE2 N:HIS294 4.1 15.3 1.0
HB2 N:ASP203 4.1 18.1 1.0
HZ1 N:LYS177 4.2 20.1 1.0
NZ N:LYS177 4.3 19.5 1.0
CG2 N:THR173 4.4 21.2 1.0
CG N:GLU204 4.4 15.1 1.0
HE2 N:LYS177 4.4 20.8 1.0
HB3 N:GLU204 4.5 13.6 1.0
C N:ASP203 4.6 14.0 1.0
HG22 N:THR173 4.7 21.0 1.0
HG23 N:THR173 4.7 21.0 1.0
HB3 N:ASP203 4.8 18.1 1.0
HG2 N:GLU204 4.8 14.9 1.0
CD2 N:HIS294 4.8 15.9 1.0
CB N:GLU204 4.8 13.4 1.0
HD2 N:HIS294 4.8 15.1 1.0
CE1 N:HIS294 4.9 13.0 1.0
CE N:LYS177 4.9 21.3 1.0
H N:ASN205 5.0 12.1 1.0
HZ2 N:LYS177 5.0 20.1 1.0

Magnesium binding site 4 out of 4 in 8qj0

Go back to Magnesium Binding Sites List in 8qj0
Magnesium binding site 4 out of 4 in the Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg501

b:20.4
occ:1.00
 OQ2 O:KCX201 1.9 21.5 1.0
O O:HOH762 2.1 25.0 1.0
OD1 O:ASP203 2.1 18.1 1.0
O O:HOH647 2.1 23.0 1.0
OE1 O:GLU204 2.2 13.9 1.0
O O:HOH604 2.2 22.1 1.0
CX O:KCX201 3.0 16.3 1.0
CG O:ASP203 3.2 20.2 1.0
CD O:GLU204 3.2 16.2 1.0
HG21 O:THR173 3.3 20.3 1.0
OQ1 O:KCX201 3.3 15.0 1.0
H O:GLU204 3.3 14.9 1.0
HE2 O:HIS294 3.4 18.1 0.0
HA O:ASP203 3.5 16.3 1.0
HZ3 O:LYS177 3.5 24.3 1.0
OE2 O:GLU204 3.6 18.1 1.0
HZ1 O:LYS175 3.7 63.1 1.0
O O:HOH786 3.9 25.9 1.0
OD2 O:ASP203 3.9 17.3 1.0
HZ3 O:LYS175 4.1 63.1 1.0
NZ O:KCX201 4.1 15.7 1.0
NE2 O:HIS294 4.1 17.7 1.0
CB O:ASP203 4.1 17.6 1.0
HZ1 O:LYS177 4.1 24.4 1.0
CA O:ASP203 4.2 16.7 1.0
N O:GLU204 4.2 14.9 1.0
NZ O:LYS177 4.2 24.1 1.0
HE2 O:LYS175 4.2 55.9 1.0
CG2 O:THR173 4.2 20.6 1.0
HB2 O:ASP203 4.3 17.9 1.0
NZ O:LYS175 4.3 66.8 1.0
HE2 O:LYS177 4.4 25.3 1.0
HG22 O:THR173 4.5 20.2 1.0
CG O:GLU204 4.5 16.4 1.0
HB3 O:GLU204 4.6 14.0 1.0
HG23 O:THR173 4.6 20.2 1.0
OG1 O:THR173 4.7 21.7 1.0
C O:ASP203 4.8 16.9 1.0
CE O:LYS175 4.8 55.6 1.0
HD2 O:HIS294 4.8 17.7 1.0
CD2 O:HIS294 4.8 18.8 1.0
CE O:LYS177 4.9 24.8 1.0
HZ2 O:LYS177 4.9 24.3 1.0
CE1 O:HIS294 4.9 18.3 1.0
CB O:GLU204 5.0 13.4 1.0
HG1 O:THR173 5.0 21.6 0.0

Reference:

M.Bjelcic, O.Aurelius, J.Nan, T.Ursby, T.Neutze. Room-Temperature Serial Synchrotron Crystallography Structure of Spinacia Oleracea Rubisco To Be Published.
Page generated: Fri Oct 4 16:45:04 2024

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