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Magnesium in PDB 8qmw: Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N

Enzymatic activity of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N

All present enzymatic activity of Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N:
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 L8S8 Complex with Substitutions R269W, E271R, L273N, PDB code: 8qmw 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) 24.88 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 206.01, 106.44, 108.49, 90, 113.09, 90
R / Rfree (%) 14.5 / 17.5

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 L8S8 Complex with Substitutions R269W, E271R, L273N (pdb code 8qmw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N, PDB code: 8qmw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8qmw

Go back to Magnesium Binding Sites List in 8qmw
Magnesium binding site 1 out of 4 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N


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 L8S8 Complex with Substitutions R269W, E271R, L273N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:12.4
occ:1.00
 OD1 A:ASP189 2.0 12.5 1.0
OQ1 A:KCX187 2.0 12.4 1.0
OE1 A:GLU190 2.1 12.3 1.0
O6 A:CAP501 2.1 12.5 1.0
O3 A:CAP501 2.2 12.4 1.0
O2 A:CAP501 2.3 12.6 1.0
C2 A:CAP501 2.8 12.6 1.0
C A:CAP501 2.8 12.6 1.0
CX A:KCX187 3.0 12.4 1.0
C3 A:CAP501 3.0 12.5 1.0
CD A:GLU190 3.1 12.3 1.0
CG A:ASP189 3.2 12.5 1.0
OQ2 A:KCX187 3.3 12.4 1.0
OE2 A:GLU190 3.5 12.3 1.0
NZ A:LYS163 3.7 12.5 1.0
ND2 B:ASN109 3.8 13.1 1.0
N A:GLU190 3.8 12.3 1.0
NZ A:LYS161 3.9 12.7 1.0
CG2 A:THR159 4.0 12.6 1.0
OD2 A:ASP189 4.0 12.6 1.0
CA A:ASP189 4.1 12.4 1.0
CB A:ASP189 4.1 12.4 1.0
O7 A:CAP501 4.1 13.1 1.0
NE2 A:HIS280 4.1 12.3 1.0
NZ A:KCX187 4.2 12.3 1.0
OG1 A:THR159 4.2 12.6 1.0
C1 A:CAP501 4.3 13.1 1.0
C4 A:CAP501 4.3 12.5 1.0
CG A:GLU190 4.4 12.2 1.0
C A:ASP189 4.5 12.3 1.0
CB A:THR159 4.7 12.6 1.0
CB A:GLU190 4.7 12.2 1.0
O1 A:CAP501 4.7 12.7 1.0
CD2 A:HIS280 4.8 12.2 1.0
C5 A:CAP501 4.8 12.8 1.0
CA A:GLU190 4.9 12.2 1.0
O B:HOH687 4.9 14.3 1.0
CG B:ASN109 5.0 12.4 1.0
O B:HOH731 5.0 13.2 1.0

Magnesium binding site 2 out of 4 in 8qmw

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Magnesium binding site 2 out of 4 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N


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 L8S8 Complex with Substitutions R269W, E271R, L273N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:13.3
occ:1.00
 OE1 B:GLU190 2.0 12.3 1.0
OD1 B:ASP189 2.0 12.4 1.0
OQ2 B:KCX187 2.1 12.3 1.0
O7 B:CAP501 2.1 12.6 1.0
O3 B:CAP501 2.2 12.8 1.0
O2 B:CAP501 2.3 12.7 1.0
C B:CAP501 2.8 14.2 1.0
C2 B:CAP501 2.8 12.5 1.0
CD B:GLU190 3.0 12.2 1.0
C3 B:CAP501 3.0 12.6 1.0
CX B:KCX187 3.1 12.3 1.0
CG B:ASP189 3.2 13.3 1.0
OQ1 B:KCX187 3.4 12.3 1.0
OE2 B:GLU190 3.4 13.7 1.0
ND2 A:ASN109 3.7 13.1 1.0
NZ B:LYS163 3.7 12.4 1.0
N B:GLU190 3.8 12.4 1.0
NZ B:LYS161 3.9 12.8 1.0
OD2 B:ASP189 4.0 14.2 1.0
NE2 B:HIS280 4.0 12.2 1.0
CG2 B:THR159 4.1 12.8 1.0
CA B:ASP189 4.1 12.2 1.0
O6 B:CAP501 4.1 13.7 1.0
CB B:ASP189 4.1 12.3 1.0
NZ B:KCX187 4.3 12.3 1.0
C4 B:CAP501 4.3 12.5 1.0
CG B:GLU190 4.3 12.2 1.0
C1 B:CAP501 4.3 12.9 1.0
OG1 B:THR159 4.4 12.5 1.0
C B:ASP189 4.5 12.2 1.0
CB B:GLU190 4.6 12.1 1.0
CD2 B:HIS280 4.7 12.2 1.0
CB B:THR159 4.8 12.5 1.0
O1 B:CAP501 4.8 12.7 1.0
C5 B:CAP501 4.8 12.8 1.0
O A:HOH727 4.8 16.5 1.0
CA B:GLU190 4.9 12.1 1.0
CG A:ASN109 4.9 12.3 1.0
CE1 B:HIS280 5.0 12.2 1.0
O B:HOH726 5.0 13.8 1.0

Magnesium binding site 3 out of 4 in 8qmw

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Magnesium binding site 3 out of 4 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N


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 L8S8 Complex with Substitutions R269W, E271R, L273N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:12.6
occ:1.00
 OQ2 C:KCX187 2.0 12.4 1.0
OD1 C:ASP189 2.0 12.5 1.0
OE1 C:GLU190 2.0 12.4 1.0
O7 C:CAP501 2.2 12.6 1.0
O3 C:CAP501 2.2 12.5 1.0
O2 C:CAP501 2.3 12.6 1.0
C2 C:CAP501 2.8 12.7 1.0
C C:CAP501 2.8 13.2 1.0
CX C:KCX187 3.0 12.4 1.0
C3 C:CAP501 3.1 12.6 1.0
CD C:GLU190 3.1 12.4 1.0
CG C:ASP189 3.2 12.5 1.0
OQ1 C:KCX187 3.3 12.5 1.0
OE2 C:GLU190 3.5 13.3 1.0
NZ C:LYS163 3.6 12.6 1.0
ND2 D:ASN109 3.7 12.5 1.0
N C:GLU190 3.8 12.3 1.0
NZ C:LYS161 3.9 12.7 1.0
CG2 C:THR159 4.0 12.6 1.0
OD2 C:ASP189 4.0 12.6 1.0
CA C:ASP189 4.1 12.4 1.0
NE2 C:HIS280 4.1 12.3 1.0
CB C:ASP189 4.1 13.5 1.0
O6 C:CAP501 4.2 13.8 1.0
NZ C:KCX187 4.2 12.4 1.0
OG1 C:THR159 4.3 12.6 1.0
C4 C:CAP501 4.3 12.6 1.0
C1 C:CAP501 4.3 12.7 1.0
CG C:GLU190 4.4 12.3 1.0
C C:ASP189 4.5 12.3 1.0
CB C:GLU190 4.6 12.3 1.0
CB C:THR159 4.7 12.7 1.0
CD2 C:HIS280 4.7 12.3 1.0
O1 C:CAP501 4.8 12.8 1.0
C5 C:CAP501 4.8 13.1 1.0
O D:HOH695 4.8 15.4 1.0
CA C:GLU190 4.9 12.3 1.0
CG D:ASN109 4.9 12.5 1.0
CE1 C:HIS280 4.9 12.3 1.0
CE C:LYS163 5.0 12.6 1.0

Magnesium binding site 4 out of 4 in 8qmw

Go back to Magnesium Binding Sites List in 8qmw
Magnesium binding site 4 out of 4 in the Non-Obligately L8S8-Complex Forming Rubisco Derived From Ancestral Sequence Reconstruction and Rational Engineering in L8S8 Complex with Substitutions R269W, E271R, L273N


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 L8S8 Complex with Substitutions R269W, E271R, L273N within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:12.9
occ:1.00
 OQ1 D:KCX187 2.0 12.4 1.0
OE1 D:GLU190 2.0 12.3 1.0
OD1 D:ASP189 2.0 12.4 1.0
O3 D:CAP501 2.1 12.4 1.0
O6 D:CAP501 2.2 12.5 1.0
O2 D:CAP501 2.3 12.9 1.0
C2 D:CAP501 2.8 13.4 1.0
C D:CAP501 2.8 13.9 1.0
CX D:KCX187 2.9 12.4 1.0
C3 D:CAP501 3.0 12.5 1.0
CD D:GLU190 3.1 12.3 1.0
CG D:ASP189 3.3 13.2 1.0
OQ2 D:KCX187 3.3 12.4 1.0
OE2 D:GLU190 3.5 13.8 1.0
ND2 C:ASN109 3.7 12.4 1.0
NZ D:LYS163 3.8 12.5 1.0
N D:GLU190 3.8 12.6 1.0
NE2 D:HIS280 4.0 12.3 1.0
NZ D:LYS161 4.0 12.7 1.0
CG2 D:THR159 4.0 12.5 1.0
OD2 D:ASP189 4.1 13.4 1.0
CA D:ASP189 4.1 12.3 1.0
O7 D:CAP501 4.1 14.0 1.0
NZ D:KCX187 4.1 12.3 1.0
CB D:ASP189 4.2 12.3 1.0
C4 D:CAP501 4.2 12.6 1.0
OG1 D:THR159 4.2 12.8 1.0
C1 D:CAP501 4.3 12.8 1.0
CG D:GLU190 4.4 12.2 1.0
C D:ASP189 4.5 12.2 1.0
CB D:GLU190 4.6 12.2 1.0
CD2 D:HIS280 4.7 12.3 1.0
CB D:THR159 4.7 13.6 1.0
O1 D:CAP501 4.7 12.7 1.0
C5 D:CAP501 4.8 12.5 1.0
CA D:GLU190 4.9 12.2 1.0
CE1 D:HIS280 4.9 12.2 1.0
CG C:ASN109 4.9 12.4 1.0

Reference:

L.Schulz, J.Zarzycki, W.Steinchen, T.J.Erb, G.K.A.Hochberg. Layered Entrenchment Maintains Essentiality in Protein-Protein Interactions Embo J. 2024.
ISSN: ESSN 1460-2075
Page generated: Thu Oct 31 21:59:11 2024

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