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Magnesium in PDB 7qsw: L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos

Enzymatic activity of L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos

All present enzymatic activity of L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos:
4.1.1.39;

Protein crystallography data

The structure of L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos, PDB code: 7qsw was solved by J.Zarzycki, L.Schulz, T.J.Erb, G.K.A.Hochberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 131.873, 131.873, 305.463, 90, 90, 90
R / Rfree (%) 14.1 / 15.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos (pdb code 7qsw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos, PDB code: 7qsw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7qsw

Go back to Magnesium Binding Sites List in 7qsw
Magnesium binding site 1 out of 4 in the L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:17.5
occ:1.00
OQ2 A:KCX199 2.0 18.1 1.0
OD1 A:ASP201 2.0 17.4 1.0
OE1 A:GLU202 2.0 18.8 1.0
O7 A:CAP501 2.1 16.8 1.0
O3 A:CAP501 2.2 16.2 1.0
O2 A:CAP501 2.2 18.1 1.0
C2 A:CAP501 2.8 17.8 1.0
C A:CAP501 2.8 17.4 1.0
CX A:KCX199 3.0 16.1 1.0
C3 A:CAP501 3.0 16.7 1.0
CD A:GLU202 3.1 17.6 1.0
CG A:ASP201 3.2 16.4 1.0
OQ1 A:KCX199 3.4 17.9 1.0
OE2 A:GLU202 3.5 19.2 1.0
NZ A:LYS175 3.7 18.3 1.0
N A:GLU202 3.8 15.7 1.0
OD2 A:ASP201 3.9 17.9 1.0
CG2 A:THR171 3.9 16.7 1.0
NZ A:LYS173 4.0 16.4 1.0
NE2 A:HIS292 4.0 16.6 1.0
O6 A:CAP501 4.0 16.1 1.0
NZ A:KCX199 4.2 16.0 1.0
CA A:ASP201 4.2 16.1 1.0
C4 A:CAP501 4.2 18.0 1.0
C1 A:CAP501 4.3 17.1 1.0
CB A:ASP201 4.3 16.3 1.0
CG A:GLU202 4.3 15.9 1.0
OG1 A:THR171 4.3 17.5 1.0
CB A:GLU202 4.5 15.0 1.0
C A:ASP201 4.6 16.9 1.0
CD2 A:HIS292 4.6 15.6 1.0
CB A:THR171 4.7 18.2 1.0
C5 A:CAP501 4.7 15.4 1.0
O1 A:CAP501 4.7 18.2 1.0
CA A:GLU202 4.8 15.5 1.0
CE1 A:HIS292 4.9 15.8 1.0

Magnesium binding site 2 out of 4 in 7qsw

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Magnesium binding site 2 out of 4 in the L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:16.6
occ:1.00
OD1 C:ASP201 2.0 16.1 1.0
OQ1 C:KCX199 2.0 15.6 1.0
OE1 C:GLU202 2.0 14.8 1.0
O6 C:CAP501 2.1 16.7 1.0
O3 C:CAP501 2.2 16.9 1.0
O2 C:CAP501 2.3 16.1 1.0
C2 C:CAP501 2.8 16.9 1.0
C C:CAP501 2.8 18.1 1.0
CX C:KCX199 3.0 16.6 1.0
C3 C:CAP501 3.0 15.5 1.0
CD C:GLU202 3.1 15.5 1.0
CG C:ASP201 3.2 18.2 1.0
OQ2 C:KCX199 3.4 15.9 1.0
OE2 C:GLU202 3.5 17.1 1.0
NZ C:LYS175 3.7 16.7 1.0
N C:GLU202 3.8 16.5 1.0
OD2 C:ASP201 3.9 17.2 1.0
CG2 C:THR171 3.9 15.4 1.0
NZ C:LYS173 3.9 15.3 1.0
NE2 C:HIS292 4.0 15.9 1.0
O7 C:CAP501 4.0 18.3 1.0
CA C:ASP201 4.2 16.0 1.0
NZ C:KCX199 4.2 15.5 1.0
CB C:ASP201 4.2 14.6 1.0
C4 C:CAP501 4.3 17.6 1.0
OG1 C:THR171 4.3 17.3 1.0
C1 C:CAP501 4.3 17.5 1.0
CG C:GLU202 4.3 15.9 1.0
CB C:GLU202 4.5 15.5 1.0
C C:ASP201 4.5 15.4 1.0
CD2 C:HIS292 4.6 14.8 1.0
CB C:THR171 4.6 16.6 1.0
C5 C:CAP501 4.7 15.4 1.0
O1 C:CAP501 4.8 17.1 1.0
CA C:GLU202 4.8 14.7 1.0
CE1 C:HIS292 4.9 14.4 1.0

Magnesium binding site 3 out of 4 in 7qsw

Go back to Magnesium Binding Sites List in 7qsw
Magnesium binding site 3 out of 4 in the L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:20.3
occ:1.00
OD1 E:ASP201 2.0 21.2 1.0
OQ2 E:KCX199 2.0 18.2 1.0
OE1 E:GLU202 2.0 19.9 1.0
O7 E:CAP501 2.1 20.2 1.0
O3 E:CAP501 2.2 21.6 1.0
O2 E:CAP501 2.2 20.9 1.0
C2 E:CAP501 2.8 21.2 1.0
C E:CAP501 2.8 20.6 1.0
CX E:KCX199 3.0 19.2 1.0
C3 E:CAP501 3.0 18.0 1.0
CD E:GLU202 3.1 20.3 1.0
CG E:ASP201 3.2 19.6 1.0
OQ1 E:KCX199 3.3 19.6 1.0
OE2 E:GLU202 3.6 22.0 1.0
NZ E:LYS175 3.7 20.7 1.0
N E:GLU202 3.8 20.0 1.0
OD2 E:ASP201 3.9 19.9 1.0
CG2 E:THR171 3.9 19.1 1.0
NZ E:LYS173 3.9 19.5 1.0
NE2 E:HIS292 4.0 19.3 1.0
O6 E:CAP501 4.1 21.1 1.0
CA E:ASP201 4.2 18.4 1.0
NZ E:KCX199 4.2 17.6 1.0
CB E:ASP201 4.3 17.5 1.0
C4 E:CAP501 4.3 21.1 1.0
OG1 E:THR171 4.3 20.1 1.0
CG E:GLU202 4.3 19.0 1.0
C1 E:CAP501 4.3 19.5 1.0
CB E:GLU202 4.5 19.6 1.0
C E:ASP201 4.5 18.4 1.0
CD2 E:HIS292 4.6 18.0 1.0
CB E:THR171 4.7 20.7 1.0
CA E:GLU202 4.7 17.3 1.0
O1 E:CAP501 4.7 21.1 1.0
C5 E:CAP501 4.8 20.6 1.0
CE1 E:HIS292 4.9 20.6 1.0

Magnesium binding site 4 out of 4 in 7qsw

Go back to Magnesium Binding Sites List in 7qsw
Magnesium binding site 4 out of 4 in the L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction of the Last Common Ancestor of Ssu-Bearing Form I Rubiscos within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:17.4
occ:1.00
OE1 G:GLU202 2.0 17.2 1.0
OD1 G:ASP201 2.0 17.1 1.0
OQ1 G:KCX199 2.1 16.8 1.0
O6 G:CAP501 2.1 17.2 1.0
O3 G:CAP501 2.2 17.2 1.0
O2 G:CAP501 2.2 19.2 1.0
C2 G:CAP501 2.8 17.4 1.0
C G:CAP501 2.8 19.6 1.0
CX G:KCX199 3.0 18.7 1.0
CD G:GLU202 3.0 16.9 1.0
C3 G:CAP501 3.0 17.9 1.0
CG G:ASP201 3.2 18.7 1.0
OQ2 G:KCX199 3.4 18.3 1.0
OE2 G:GLU202 3.5 18.7 1.0
NZ G:LYS175 3.7 17.0 1.0
N G:GLU202 3.8 14.8 1.0
OD2 G:ASP201 3.9 18.2 1.0
NZ G:LYS173 3.9 18.5 1.0
CG2 G:THR171 4.0 16.7 1.0
NE2 G:HIS292 4.0 17.7 1.0
O7 G:CAP501 4.0 18.4 1.0
CA G:ASP201 4.2 16.1 1.0
NZ G:KCX199 4.3 16.1 1.0
C4 G:CAP501 4.3 18.6 1.0
CB G:ASP201 4.3 17.2 1.0
CG G:GLU202 4.3 16.1 1.0
C1 G:CAP501 4.3 17.4 1.0
OG1 G:THR171 4.3 17.5 1.0
CB G:GLU202 4.5 17.6 1.0
C G:ASP201 4.6 16.8 1.0
CD2 G:HIS292 4.7 15.4 1.0
CB G:THR171 4.7 18.4 1.0
C5 G:CAP501 4.7 18.6 1.0
O1 G:CAP501 4.7 18.4 1.0
CA G:GLU202 4.8 16.4 1.0
CE1 G:HIS292 4.9 15.9 1.0

Reference:

L.Schulz, Z.Guo, J.Zarzycki, W.Steinchen, J.M.Schuller, T.Heimerl, S.Prinz, O.Mueller-Cajar, T.J.Erb, G.K.A.Hochberg. Evolution of Increased Complexity and Specificity at the Dawn of Form I Rubiscos. Science V. 378 155 2022.
ISSN: ESSN 1095-9203
PubMed: 36227987
DOI: 10.1126/SCIENCE.ABQ1416
Page generated: Thu Oct 3 06:45:12 2024

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