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Magnesium in PDB 3a13: Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca

Enzymatic activity of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca

All present enzymatic activity of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca:
4.1.1.39;

Protein crystallography data

The structure of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca, PDB code: 3a13 was solved by Y.Nishitani, M.Fujihashi, T.Doi, S.Yoshida, H.Atomi, T.Imanaka, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.22 / 2.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 173.678, 247.090, 144.940, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25

Other elements in 3a13:

The structure of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca (pdb code 3a13). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca, PDB code: 3a13:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3a13

Go back to Magnesium Binding Sites List in 3a13
Magnesium binding site 1 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg445

b:32.6
occ:1.00
 O7 A:CAP446 2.0 31.5 1.0
OE1 A:GLU192 2.1 22.7 1.0
OQ1 A:KCX189 2.1 24.2 1.0
OD1 A:ASP191 2.2 26.8 1.0
O3 A:CAP446 2.2 31.5 1.0
O2 A:CAP446 2.3 30.5 1.0
C A:CAP446 2.6 31.1 1.0
C2 A:CAP446 2.7 31.2 1.0
C3 A:CAP446 2.9 30.3 1.0
CG A:ASP191 3.1 25.4 1.0
CX A:KCX189 3.1 22.7 1.0
CD A:GLU192 3.2 24.1 1.0
OQ2 A:KCX189 3.5 23.6 1.0
OD2 A:ASP191 3.6 29.0 1.0
OE2 A:GLU192 3.7 25.0 1.0
O6 A:CAP446 3.8 31.0 1.0
N A:GLU192 3.8 23.3 1.0
NZ A:LYS165 3.8 26.2 1.0
NZ A:LYS163 3.9 29.1 1.0
NE2 A:HIS281 4.0 19.2 1.0
CA A:ASP191 4.1 23.9 1.0
C4 A:CAP446 4.2 29.6 1.0
CB A:ASP191 4.2 24.0 1.0
C1 A:CAP446 4.2 31.0 1.0
NZ A:KCX189 4.3 21.8 1.0
CG A:GLU192 4.4 23.1 1.0
CG1 A:VAL161 4.5 25.2 1.0
C A:ASP191 4.5 23.7 1.0
CB A:GLU192 4.6 23.2 1.0
O1 A:CAP446 4.7 32.1 1.0
CE1 A:HIS281 4.7 19.5 1.0
O A:HOH584 4.7 37.7 1.0
C5 A:CAP446 4.7 28.9 1.0
CD2 A:HIS281 4.7 19.6 1.0
CA A:GLU192 4.8 23.3 1.0
CG2 A:VAL161 4.9 26.1 1.0
CE A:LYS163 5.0 29.1 1.0

Magnesium binding site 2 out of 8 in 3a13

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Magnesium binding site 2 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg445

b:19.9
occ:1.00
 O7 B:CAP446 1.7 30.3 1.0
O2 B:CAP446 2.0 30.3 1.0
O3 B:CAP446 2.2 28.0 1.0
C B:CAP446 2.3 30.7 1.0
OQ1 B:KCX189 2.3 22.1 1.0
OE1 B:GLU192 2.4 20.4 1.0
OD1 B:ASP191 2.4 27.8 1.0
C2 B:CAP446 2.5 30.8 1.0
C3 B:CAP446 2.9 29.2 1.0
CG B:ASP191 3.1 25.1 1.0
CD B:GLU192 3.3 22.4 1.0
OD2 B:ASP191 3.3 29.9 1.0
O6 B:CAP446 3.4 31.6 1.0
CX B:KCX189 3.4 20.9 1.0
NZ B:LYS163 3.5 26.9 1.0
OE2 B:GLU192 3.5 23.6 1.0
NZ B:LYS165 3.6 23.2 1.0
OQ2 B:KCX189 3.8 21.0 1.0
C1 B:CAP446 4.0 30.5 1.0
C4 B:CAP446 4.0 27.2 1.0
CB B:ASP191 4.3 22.2 1.0
N B:GLU192 4.3 21.6 1.0
NE2 B:HIS281 4.3 19.5 1.0
O1 B:CAP446 4.3 33.5 1.0
CA B:ASP191 4.4 22.1 1.0
O B:HOH560 4.5 27.6 1.0
CG1 B:VAL161 4.6 24.9 1.0
CE B:LYS163 4.6 28.0 1.0
NZ B:KCX189 4.6 19.3 1.0
CG B:GLU192 4.7 20.9 1.0
C5 B:CAP446 4.7 26.6 1.0
C B:ASP191 4.9 21.9 1.0

Magnesium binding site 3 out of 8 in 3a13

Go back to Magnesium Binding Sites List in 3a13
Magnesium binding site 3 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg445

b:23.4
occ:1.00
 O2 C:CAP446 2.0 35.6 1.0
O3 C:CAP446 2.2 32.0 1.0
O7 C:CAP446 2.2 36.1 1.0
OE1 C:GLU192 2.3 18.0 1.0
OQ1 C:KCX189 2.3 28.1 1.0
C2 C:CAP446 2.7 35.9 1.0
C C:CAP446 2.7 36.3 1.0
C3 C:CAP446 3.0 34.3 1.0
OD2 C:ASP191 3.1 28.6 1.0
OD1 C:ASP191 3.2 28.9 1.0
CD C:GLU192 3.3 19.9 1.0
CG C:ASP191 3.4 24.6 1.0
CX C:KCX189 3.5 26.4 1.0
OE2 C:GLU192 3.6 21.9 1.0
NZ C:LYS163 3.6 32.7 1.0
NZ C:LYS165 3.8 28.9 1.0
O6 C:CAP446 3.9 37.6 1.0
OQ2 C:KCX189 3.9 25.2 1.0
C4 C:CAP446 4.1 32.1 1.0
C1 C:CAP446 4.1 35.6 1.0
NE2 C:HIS281 4.2 18.5 1.0
N C:GLU192 4.3 21.0 1.0
O1 C:CAP446 4.5 35.9 1.0
CB C:ASP191 4.5 22.5 1.0
NZ C:KCX189 4.5 25.1 1.0
CA C:ASP191 4.6 21.8 1.0
CG C:GLU192 4.6 20.2 1.0
C5 C:CAP446 4.7 32.3 1.0
CG1 C:VAL161 4.7 28.4 1.0
CE C:LYS163 4.9 33.0 1.0
CE1 C:HIS281 4.9 19.0 1.0
CB C:GLU192 5.0 20.8 1.0

Magnesium binding site 4 out of 8 in 3a13

Go back to Magnesium Binding Sites List in 3a13
Magnesium binding site 4 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg445

b:27.2
occ:1.00
 O7 D:CAP446 1.8 29.1 1.0
OE1 D:GLU192 2.1 22.1 1.0
OD1 D:ASP191 2.1 26.8 1.0
O3 D:CAP446 2.2 27.9 1.0
O2 D:CAP446 2.2 28.6 1.0
OQ1 D:KCX189 2.2 26.0 1.0
C D:CAP446 2.5 28.9 1.0
C2 D:CAP446 2.6 29.2 1.0
C3 D:CAP446 2.9 28.7 1.0
CG D:ASP191 3.1 24.5 1.0
CD D:GLU192 3.2 22.4 1.0
CX D:KCX189 3.3 24.6 1.0
OE2 D:GLU192 3.6 24.4 1.0
OD2 D:ASP191 3.7 29.0 1.0
OQ2 D:KCX189 3.7 24.6 1.0
O6 D:CAP446 3.7 28.5 1.0
NZ D:LYS163 3.8 33.8 1.0
N D:GLU192 3.8 21.2 1.0
NZ D:LYS165 3.9 27.5 1.0
CA D:ASP191 4.0 22.2 1.0
NE2 D:HIS281 4.1 15.8 1.0
C4 D:CAP446 4.1 28.2 1.0
C1 D:CAP446 4.1 29.2 1.0
CB D:ASP191 4.1 22.4 1.0
C D:ASP191 4.4 21.7 1.0
NZ D:KCX189 4.4 22.7 1.0
CG D:GLU192 4.5 21.4 1.0
CG1 D:VAL161 4.5 27.1 1.0
O1 D:CAP446 4.6 31.1 1.0
CB D:GLU192 4.7 21.3 1.0
C5 D:CAP446 4.7 27.3 1.0
CD2 D:HIS281 4.8 15.5 1.0
CA D:GLU192 4.9 21.4 1.0
CE1 D:HIS281 4.9 14.7 1.0

Magnesium binding site 5 out of 8 in 3a13

Go back to Magnesium Binding Sites List in 3a13
Magnesium binding site 5 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg445

b:36.6
occ:1.00
 O7 F:CAP446 1.9 34.6 1.0
OQ1 F:KCX189 2.0 27.4 1.0
OD1 F:ASP191 2.0 29.2 1.0
OE1 F:GLU192 2.0 22.9 1.0
O3 F:CAP446 2.2 33.3 1.0
O2 F:CAP446 2.3 33.4 1.0
C F:CAP446 2.5 34.0 1.0
C2 F:CAP446 2.7 34.2 1.0
C3 F:CAP446 2.9 33.5 1.0
CX F:KCX189 3.0 25.6 1.0
CG F:ASP191 3.1 27.4 1.0
CD F:GLU192 3.1 24.7 1.0
OQ2 F:KCX189 3.3 27.4 1.0
OE2 F:GLU192 3.5 25.2 1.0
OD2 F:ASP191 3.7 30.9 1.0
NZ F:LYS165 3.7 27.7 1.0
O6 F:CAP446 3.7 33.5 1.0
NZ F:LYS163 3.8 29.6 1.0
N F:GLU192 3.8 25.2 1.0
NE2 F:HIS281 4.0 19.3 1.0
CA F:ASP191 4.1 26.0 1.0
C4 F:CAP446 4.2 32.6 1.0
C1 F:CAP446 4.2 34.4 1.0
CB F:ASP191 4.2 26.2 1.0
NZ F:KCX189 4.2 24.8 1.0
CG F:GLU192 4.4 23.9 1.0
CG1 F:VAL161 4.4 30.3 1.0
O F:HOH570 4.5 35.4 1.0
C F:ASP191 4.5 25.7 1.0
CB F:GLU192 4.6 25.1 1.0
C5 F:CAP446 4.7 31.9 1.0
O1 F:CAP446 4.7 35.2 1.0
CE1 F:HIS281 4.8 19.6 1.0
CG2 F:VAL161 4.8 30.8 1.0
CD2 F:HIS281 4.8 20.1 1.0
CA F:GLU192 4.9 25.2 1.0

Magnesium binding site 6 out of 8 in 3a13

Go back to Magnesium Binding Sites List in 3a13
Magnesium binding site 6 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg445

b:22.2
occ:1.00
 O7 G:CAP446 1.7 30.0 1.0
O2 G:CAP446 2.1 29.9 1.0
OD1 G:ASP191 2.1 25.1 1.0
OQ1 G:KCX189 2.1 19.4 1.0
O3 G:CAP446 2.2 28.1 1.0
OE1 G:GLU192 2.3 20.7 1.0
C G:CAP446 2.4 30.4 1.0
C2 G:CAP446 2.5 30.5 1.0
C3 G:CAP446 2.9 29.1 1.0
CG G:ASP191 3.1 23.5 1.0
CD G:GLU192 3.2 22.2 1.0
CX G:KCX189 3.2 19.2 1.0
O6 G:CAP446 3.5 31.3 1.0
OE2 G:GLU192 3.5 23.4 1.0
OD2 G:ASP191 3.6 28.6 1.0
OQ2 G:KCX189 3.6 20.5 1.0
NZ G:LYS163 3.6 28.1 1.0
NZ G:LYS165 3.6 21.1 1.0
C4 G:CAP446 3.9 27.7 1.0
C1 G:CAP446 4.0 30.1 1.0
NE2 G:HIS281 4.1 16.7 1.0
N G:GLU192 4.1 20.7 1.0
CB G:ASP191 4.2 21.1 1.0
CA G:ASP191 4.3 20.9 1.0
NZ G:KCX189 4.4 16.4 1.0
O1 G:CAP446 4.5 32.4 1.0
CG1 G:VAL161 4.6 24.1 1.0
CG G:GLU192 4.6 20.1 1.0
C5 G:CAP446 4.6 26.7 1.0
O G:HOH594 4.7 30.8 1.0
C G:ASP191 4.7 20.6 1.0
CE1 G:HIS281 4.8 17.5 1.0
CE G:LYS163 4.8 29.1 1.0
CB G:GLU192 4.9 20.3 1.0
CD2 G:HIS281 5.0 15.9 1.0

Magnesium binding site 7 out of 8 in 3a13

Go back to Magnesium Binding Sites List in 3a13
Magnesium binding site 7 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg445

b:22.5
occ:1.00
 O2 H:CAP446 2.2 36.0 1.0
O7 H:CAP446 2.2 36.9 1.0
OQ1 H:KCX189 2.2 26.7 1.0
OE1 H:GLU192 2.3 18.2 1.0
O3 H:CAP446 2.4 34.8 1.0
C H:CAP446 2.7 37.0 1.0
C2 H:CAP446 2.8 36.8 1.0
OD1 H:ASP191 3.0 27.6 1.0
C3 H:CAP446 3.1 35.5 1.0
OD2 H:ASP191 3.2 28.1 1.0
CD H:GLU192 3.3 19.7 1.0
CG H:ASP191 3.3 24.2 1.0
CX H:KCX189 3.4 25.5 1.0
OE2 H:GLU192 3.5 19.7 1.0
NZ H:LYS165 3.6 26.5 1.0
NZ H:LYS163 3.8 30.3 1.0
OQ2 H:KCX189 3.8 25.1 1.0
O6 H:CAP446 3.9 38.0 1.0
C4 H:CAP446 4.2 33.8 1.0
N H:GLU192 4.2 21.3 1.0
C1 H:CAP446 4.2 36.5 1.0
NE2 H:HIS281 4.3 18.6 1.0
CA H:ASP191 4.4 21.6 1.0
CB H:ASP191 4.4 22.2 1.0
NZ H:KCX189 4.4 25.0 1.0
O1 H:CAP446 4.6 37.4 1.0
CG1 H:VAL161 4.6 28.2 1.0
CG H:GLU192 4.6 19.9 1.0
C5 H:CAP446 4.8 33.2 1.0
C H:ASP191 4.9 21.5 1.0
CB H:GLU192 5.0 21.1 1.0

Magnesium binding site 8 out of 8 in 3a13

Go back to Magnesium Binding Sites List in 3a13
Magnesium binding site 8 out of 8 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg445

b:21.2
occ:1.00
 O7 I:CAP446 1.9 25.6 1.0
OD1 I:ASP191 2.1 27.6 1.0
O2 I:CAP446 2.1 26.3 1.0
OE1 I:GLU192 2.2 20.5 1.0
O3 I:CAP446 2.3 27.2 1.0
OQ1 I:KCX189 2.3 25.5 1.0
C I:CAP446 2.5 26.1 1.0
C2 I:CAP446 2.6 26.4 1.0
CG I:ASP191 2.9 23.6 1.0
C3 I:CAP446 3.0 26.1 1.0
CD I:GLU192 3.2 21.4 1.0
CX I:KCX189 3.3 23.8 1.0
OD2 I:ASP191 3.4 27.7 1.0
NZ I:LYS163 3.6 29.5 1.0
OQ2 I:KCX189 3.6 25.1 1.0
OE2 I:GLU192 3.6 23.3 1.0
NZ I:LYS165 3.7 23.8 1.0
O6 I:CAP446 3.7 26.1 1.0
N I:GLU192 3.9 19.9 1.0
CA I:ASP191 4.1 21.0 1.0
CB I:ASP191 4.1 21.1 1.0
C1 I:CAP446 4.1 25.9 1.0
C4 I:CAP446 4.2 25.8 1.0
NE2 I:HIS281 4.2 16.0 1.0
CG1 I:VAL161 4.4 25.1 1.0
O1 I:CAP446 4.5 26.4 1.0
NZ I:KCX189 4.5 21.5 1.0
C I:ASP191 4.5 20.3 1.0
CG I:GLU192 4.6 20.0 1.0
CB I:GLU192 4.8 19.7 1.0
C5 I:CAP446 4.8 24.9 1.0
CG2 I:VAL161 4.9 25.7 1.0
CE I:LYS163 4.9 29.9 1.0
CD2 I:HIS281 4.9 16.0 1.0
CA I:GLU192 5.0 20.1 1.0

Reference:

Y.Nishitani, M.Fujihashi, T.Doi, S.Yoshida, H.Atomi, T.Imanaka, K.Miki. Sturcture-Based Optimization of A Type III Rubisco From A Hyperthermophile To Be Published.
Page generated: Wed Aug 14 08:25:15 2024

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