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Magnesium in PDB 7qsx: Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex

Enzymatic activity of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex

All present enzymatic activity of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex:
4.1.1.39;

Protein crystallography data

The structure of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex, PDB code: 7qsx 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) 29.89 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.599, 159.197, 127.91, 90, 107.9, 90
R / Rfree (%) 21.8 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex (pdb code 7qsx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex, PDB code: 7qsx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7qsx

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Magnesium binding site 1 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:34.5
occ:1.00
 O6 A:CAP501 2.0 22.4 1.0
O3 A:CAP501 2.1 26.2 1.0
OE1 A:GLU190 2.1 24.3 1.0
OD1 A:ASP189 2.1 28.9 1.0
OQ1 A:KCX187 2.2 25.8 1.0
O2 A:CAP501 2.3 25.4 1.0
C A:CAP501 2.8 23.5 1.0
C2 A:CAP501 2.8 26.4 1.0
C3 A:CAP501 2.9 25.9 1.0
CD A:GLU190 3.1 25.3 1.0
CX A:KCX187 3.2 23.9 1.0
CG A:ASP189 3.3 24.1 1.0
OQ2 A:KCX187 3.5 24.0 1.0
OE2 A:GLU190 3.5 29.8 1.0
ND2 F:ASN109 3.6 22.1 1.0
NZ A:LYS163 3.9 22.8 1.0
NZ A:LYS161 4.0 22.7 1.0
N A:GLU190 4.0 25.6 1.0
O7 A:CAP501 4.0 25.6 1.0
NE2 A:HIS280 4.1 25.4 1.0
CG2 A:THR159 4.1 21.6 1.0
C4 A:CAP501 4.1 26.4 1.0
OD2 A:ASP189 4.1 22.2 1.0
CA A:ASP189 4.2 26.4 1.0
CB A:ASP189 4.2 24.6 1.0
OG1 A:THR159 4.3 23.3 1.0
C1 A:CAP501 4.3 23.8 1.0
NZ A:KCX187 4.4 22.4 1.0
CG A:GLU190 4.4 23.9 1.0
C5 A:CAP501 4.6 24.9 1.0
O A:HOH636 4.6 26.8 1.0
C A:ASP189 4.6 25.4 1.0
CB A:THR159 4.7 25.2 1.0
CB A:GLU190 4.7 23.2 1.0
O1 A:CAP501 4.7 22.5 1.0
CD2 A:HIS280 4.7 23.9 1.0
CG F:ASN109 4.9 26.9 1.0
CA A:GLU190 5.0 23.7 1.0

Magnesium binding site 2 out of 8 in 7qsx

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Magnesium binding site 2 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:21.3
occ:1.00
 O3 B:CAP501 1.9 25.5 1.0
OD1 B:ASP189 2.0 23.3 1.0
OE1 B:GLU190 2.1 21.5 1.0
OQ2 B:KCX187 2.1 23.6 1.0
O7 B:CAP501 2.3 22.4 1.0
O2 B:CAP501 2.4 22.5 1.0
C3 B:CAP501 2.8 25.8 1.0
C2 B:CAP501 2.9 25.7 1.0
C B:CAP501 3.0 22.4 1.0
CX B:KCX187 3.1 23.9 1.0
CD B:GLU190 3.2 24.2 1.0
CG B:ASP189 3.3 22.7 1.0
OQ1 B:KCX187 3.3 24.9 1.0
OE2 B:GLU190 3.6 22.6 1.0
ND2 E:ASN109 3.7 19.7 1.0
NE2 B:HIS280 3.9 22.7 1.0
OD2 B:ASP189 4.0 26.1 1.0
NZ B:LYS163 4.0 21.5 1.0
C4 B:CAP501 4.1 22.3 1.0
N B:GLU190 4.1 24.9 1.0
NZ B:LYS161 4.1 21.2 1.0
CG2 B:THR159 4.2 18.9 1.0
O6 B:CAP501 4.3 23.4 1.0
NZ B:KCX187 4.3 20.7 1.0
CA B:ASP189 4.3 22.7 1.0
CB B:ASP189 4.3 20.3 1.0
C1 B:CAP501 4.4 22.4 1.0
OG1 B:THR159 4.4 19.9 1.0
CG B:GLU190 4.5 23.0 1.0
C5 B:CAP501 4.5 22.2 1.0
CD2 B:HIS280 4.7 22.9 1.0
C B:ASP189 4.8 23.4 1.0
CB B:GLU190 4.8 18.8 1.0
CE1 B:HIS280 4.8 25.6 1.0
CB B:THR159 4.8 24.8 1.0
CG E:ASN109 4.9 24.3 1.0
O1 B:CAP501 4.9 22.9 1.0

Magnesium binding site 3 out of 8 in 7qsx

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Magnesium binding site 3 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:26.2
occ:1.00
 O2 C:CAP501 2.0 28.0 1.0
OD1 C:ASP189 2.1 23.8 1.0
O3 C:CAP501 2.1 29.8 1.0
OE1 C:GLU190 2.2 25.2 1.0
O7 C:CAP501 2.2 29.2 1.0
OQ2 C:KCX187 2.3 27.2 1.0
C2 C:CAP501 2.7 29.4 1.0
C C:CAP501 2.8 31.9 1.0
C3 C:CAP501 2.9 24.8 1.0
CD C:GLU190 3.2 24.7 1.0
CX C:KCX187 3.2 28.0 1.0
CG C:ASP189 3.2 24.5 1.0
OQ1 C:KCX187 3.4 28.4 1.0
ND2 D:ASN109 3.5 25.4 1.0
OE2 C:GLU190 3.5 24.0 1.0
NZ C:LYS163 3.7 24.4 1.0
NE2 C:HIS280 3.9 24.2 1.0
NZ C:LYS161 4.0 28.9 1.0
O6 C:CAP501 4.0 32.1 1.0
OD2 C:ASP189 4.0 25.8 1.0
N C:GLU190 4.1 22.5 1.0
C4 C:CAP501 4.1 25.6 1.0
C1 C:CAP501 4.1 27.7 1.0
CB C:ASP189 4.2 22.6 1.0
CG2 C:THR159 4.2 23.0 1.0
CA C:ASP189 4.3 25.6 1.0
NZ C:KCX187 4.4 20.5 1.0
CG C:GLU190 4.5 21.7 1.0
OG1 C:THR159 4.5 25.4 1.0
CD2 C:HIS280 4.7 24.4 1.0
C5 C:CAP501 4.7 24.6 1.0
CG D:ASN109 4.7 24.4 1.0
C C:ASP189 4.8 23.1 1.0
O1 C:CAP501 4.8 25.8 1.0
CB C:GLU190 4.8 20.9 1.0
O D:HOH620 4.8 22.9 1.0
CE1 C:HIS280 4.9 24.9 1.0
CB C:THR159 4.9 26.7 1.0
O C:HOH607 5.0 22.9 1.0

Magnesium binding site 4 out of 8 in 7qsx

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Magnesium binding site 4 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:24.7
occ:1.00
 OD1 D:ASP189 2.0 19.5 1.0
O3 D:CAP501 2.0 24.5 1.0
OE1 D:GLU190 2.0 23.9 1.0
O7 D:CAP501 2.0 21.7 1.0
OQ1 D:KCX187 2.1 23.2 1.0
O2 D:CAP501 2.1 24.6 1.0
C2 D:CAP501 2.5 25.1 1.0
C D:CAP501 2.6 24.8 1.0
C3 D:CAP501 2.7 21.9 1.0
CX D:KCX187 3.0 21.3 1.0
CD D:GLU190 3.2 21.9 1.0
CG D:ASP189 3.2 21.3 1.0
OQ2 D:KCX187 3.3 21.6 1.0
OE2 D:GLU190 3.6 24.5 1.0
NZ D:LYS163 3.7 23.6 1.0
ND2 C:ASN109 3.7 21.6 1.0
O6 D:CAP501 3.8 25.8 1.0
NZ D:LYS161 3.9 21.9 1.0
N D:GLU190 4.0 22.0 1.0
C4 D:CAP501 4.0 23.5 1.0
C1 D:CAP501 4.0 27.6 1.0
OD2 D:ASP189 4.1 28.7 1.0
NE2 D:HIS280 4.1 24.3 1.0
CB D:ASP189 4.1 19.2 1.0
NZ D:KCX187 4.2 18.9 1.0
CA D:ASP189 4.2 23.5 1.0
CG2 D:THR159 4.3 20.5 1.0
OG1 D:THR159 4.4 23.9 1.0
CG D:GLU190 4.4 19.5 1.0
O1 D:CAP501 4.5 25.4 1.0
O D:HOH607 4.5 23.8 1.0
C5 D:CAP501 4.6 23.7 1.0
C D:ASP189 4.7 24.3 1.0
CB D:GLU190 4.7 22.7 1.0
CD2 D:HIS280 4.7 21.1 1.0
CB D:THR159 4.9 22.5 1.0
CG C:ASN109 4.9 26.7 1.0

Magnesium binding site 5 out of 8 in 7qsx

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Magnesium binding site 5 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:26.6
occ:1.00
 OQ1 E:KCX187 2.0 24.5 1.0
OE1 E:GLU190 2.1 23.5 1.0
OD1 E:ASP189 2.1 23.9 1.0
O3 E:CAP501 2.2 27.6 1.0
O2 E:CAP501 2.5 25.3 1.0
O6 E:CAP501 2.5 27.6 1.0
CX E:KCX187 3.0 22.9 1.0
C2 E:CAP501 3.1 27.5 1.0
CD E:GLU190 3.2 24.2 1.0
C3 E:CAP501 3.2 30.3 1.0
C E:CAP501 3.2 26.9 1.0
CG E:ASP189 3.3 26.3 1.0
OQ2 E:KCX187 3.4 26.8 1.0
ND2 B:ASN109 3.6 23.3 1.0
N E:GLU190 3.7 20.6 1.0
OE2 E:GLU190 3.7 27.0 1.0
NZ E:LYS163 3.7 24.0 1.0
CA E:ASP189 4.0 22.3 1.0
NE2 E:HIS280 4.1 23.0 1.0
CB E:ASP189 4.1 23.9 1.0
CG2 E:THR159 4.1 22.3 1.0
NZ E:LYS161 4.2 25.5 1.0
NZ E:KCX187 4.2 22.0 1.0
OD2 E:ASP189 4.2 27.1 1.0
CG E:GLU190 4.3 20.3 1.0
C E:ASP189 4.4 20.4 1.0
CB E:GLU190 4.4 19.9 1.0
C4 E:CAP501 4.4 26.5 1.0
O7 E:CAP501 4.4 28.9 1.0
C1 E:CAP501 4.6 27.4 1.0
OG1 E:THR159 4.7 23.8 1.0
CD2 E:HIS280 4.7 20.3 1.0
CA E:GLU190 4.7 19.8 1.0
C5 E:CAP501 4.8 25.7 1.0
CG B:ASN109 4.9 24.4 1.0
CB E:THR159 4.9 23.1 1.0
O1 E:CAP501 5.0 23.2 1.0
O B:HOH612 5.0 30.0 1.0

Magnesium binding site 6 out of 8 in 7qsx

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Magnesium binding site 6 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:29.4
occ:1.00
 O3 F:CAP501 2.0 23.4 1.0
OE1 F:GLU190 2.0 23.9 1.0
O2 F:CAP501 2.0 23.4 1.0
OD1 F:ASP189 2.0 27.3 1.0
O6 F:CAP501 2.1 23.1 1.0
OQ1 F:KCX187 2.4 24.9 1.0
C2 F:CAP501 2.5 25.8 1.0
C F:CAP501 2.7 25.6 1.0
C3 F:CAP501 2.7 29.7 1.0
CD F:GLU190 3.1 24.1 1.0
CG F:ASP189 3.2 27.3 1.0
CX F:KCX187 3.3 25.2 1.0
OE2 F:GLU190 3.5 21.3 1.0
ND2 A:ASN109 3.5 22.1 1.0
OQ2 F:KCX187 3.6 26.0 1.0
O7 F:CAP501 3.9 28.5 1.0
NZ F:LYS163 3.9 22.9 1.0
C4 F:CAP501 4.0 30.6 1.0
C1 F:CAP501 4.0 27.6 1.0
NZ F:LYS161 4.0 24.4 1.0
N F:GLU190 4.0 25.5 1.0
OD2 F:ASP189 4.1 29.8 1.0
CB F:ASP189 4.2 23.1 1.0
NE2 F:HIS280 4.2 26.0 1.0
CA F:ASP189 4.2 24.1 1.0
CG2 F:THR159 4.3 21.4 1.0
CG F:GLU190 4.4 20.1 1.0
OG1 F:THR159 4.4 23.0 1.0
O1 F:CAP501 4.5 32.0 1.0
NZ F:KCX187 4.5 21.8 1.0
C5 F:CAP501 4.6 26.2 1.0
C F:ASP189 4.7 23.5 1.0
O F:HOH628 4.7 32.8 1.0
CB F:GLU190 4.7 20.6 1.0
CD2 F:HIS280 4.8 23.1 1.0
CG A:ASN109 4.8 26.0 1.0
CB F:THR159 4.8 24.3 1.0

Magnesium binding site 7 out of 8 in 7qsx

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Magnesium binding site 7 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:43.9
occ:1.00
 O3 G:CAP501 2.0 34.6 1.0
OQ2 G:KCX187 2.1 28.8 1.0
OE1 G:GLU190 2.1 29.3 1.0
O2 G:CAP501 2.1 26.6 1.0
OD1 G:ASP189 2.1 31.0 1.0
O7 G:CAP501 2.1 28.4 1.0
C2 G:CAP501 2.6 28.5 1.0
C G:CAP501 2.7 29.8 1.0
C3 G:CAP501 2.8 29.1 1.0
CX G:KCX187 3.1 28.5 1.0
CD G:GLU190 3.1 30.8 1.0
CG G:ASP189 3.3 28.0 1.0
ND2 H:ASN109 3.4 29.0 1.0
OQ1 G:KCX187 3.4 33.4 1.0
OE2 G:GLU190 3.5 28.4 1.0
NZ G:LYS163 3.8 25.9 1.0
NZ G:LYS161 3.9 27.6 1.0
O6 G:CAP501 4.0 33.3 1.0
C4 G:CAP501 4.0 28.8 1.0
NE2 G:HIS280 4.0 25.2 1.0
OD2 G:ASP189 4.1 28.6 1.0
C1 G:CAP501 4.1 27.7 1.0
N G:GLU190 4.2 24.2 1.0
O G:HOH604 4.2 22.9 1.0
CB G:ASP189 4.3 24.1 1.0
NZ G:KCX187 4.3 25.6 1.0
CG2 G:THR159 4.4 25.9 1.0
CA G:ASP189 4.4 25.3 1.0
CG G:GLU190 4.5 27.8 1.0
C5 G:CAP501 4.5 27.9 1.0
OG1 G:THR159 4.5 27.2 1.0
O1 G:CAP501 4.6 27.7 1.0
CG H:ASN109 4.6 33.5 1.0
CD2 G:HIS280 4.8 23.5 1.0
CB G:GLU190 4.8 25.5 1.0
C G:ASP189 4.8 26.3 1.0
CB G:THR159 4.9 29.5 1.0
CE1 G:HIS280 5.0 28.0 1.0

Magnesium binding site 8 out of 8 in 7qsx

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Magnesium binding site 8 out of 8 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:29.6
occ:1.00
 O3 H:CAP501 2.0 31.2 1.0
OE1 H:GLU190 2.0 28.9 1.0
OQ1 H:KCX187 2.1 31.3 1.0
O2 H:CAP501 2.1 33.8 1.0
O7 H:CAP501 2.1 34.3 1.0
OD1 H:ASP189 2.1 32.3 1.0
C2 H:CAP501 2.6 33.3 1.0
C H:CAP501 2.7 35.8 1.0
C3 H:CAP501 2.8 31.9 1.0
CX H:KCX187 3.0 29.9 1.0
CD H:GLU190 3.1 31.5 1.0
OQ2 H:KCX187 3.2 28.2 1.0
CG H:ASP189 3.3 31.6 1.0
OE2 H:GLU190 3.6 34.1 1.0
NZ H:LYS163 3.7 30.9 1.0
ND2 G:ASN109 3.7 43.9 1.0
O6 H:CAP501 4.0 38.7 1.0
NZ H:LYS161 4.0 30.9 1.0
C4 H:CAP501 4.0 32.3 1.0
OD2 H:ASP189 4.0 30.5 1.0
CG2 H:THR159 4.0 24.7 1.0
N H:GLU190 4.1 23.6 1.0
C1 H:CAP501 4.1 36.0 1.0
NE2 H:HIS280 4.1 25.8 1.0
NZ H:KCX187 4.2 27.1 1.0
OG1 H:THR159 4.4 31.7 1.0
CB H:ASP189 4.4 27.2 1.0
CA H:ASP189 4.4 25.3 1.0
CG H:GLU190 4.4 28.1 1.0
O G:HOH613 4.4 34.3 1.0
C5 H:CAP501 4.5 29.3 1.0
O1 H:CAP501 4.7 41.3 1.0
CB H:THR159 4.7 30.8 1.0
CB H:GLU190 4.7 23.7 1.0
CD2 H:HIS280 4.7 27.6 1.0
C H:ASP189 4.8 21.3 1.0
CG G:ASN109 4.9 41.4 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 06:45:18 2024

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