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Magnesium in PDB 7yyo: Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution

Enzymatic activity of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution

All present enzymatic activity of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution:
4.1.1.39;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution (pdb code 7yyo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution, PDB code: 7yyo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7yyo

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Magnesium binding site 1 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:55.8
occ:1.00
 NE2 A:HIS378 2.3 45.9 1.0
O A:GLY373 2.8 47.4 1.0
CD2 A:HIS378 2.8 45.9 1.0
CE1 A:HIS378 3.5 45.9 1.0
C A:GLY373 3.9 47.4 1.0
O A:VAL323 4.0 51.0 1.0
CD2 A:HIS375 4.0 47.8 1.0
CG A:HIS378 4.1 45.9 1.0
CA A:VAL324 4.3 55.3 1.0
ND1 A:HIS378 4.4 45.9 1.0
CA A:GLY325 4.5 55.4 1.0
CB A:VAL324 4.6 55.3 1.0
CA A:ILE374 4.6 45.0 1.0
N A:ILE374 4.7 45.0 1.0
N A:HIS375 4.8 47.8 1.0
C A:VAL323 4.8 51.0 1.0
NE2 A:HIS375 4.8 47.8 1.0
CA A:GLY373 4.9 47.4 1.0
C A:ILE374 5.0 45.0 1.0

Magnesium binding site 2 out of 8 in 7yyo

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Magnesium binding site 2 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg500

b:51.3
occ:1.00
 NE2 C:HIS378 2.3 45.7 1.0
O C:GLY373 2.8 47.9 1.0
CD2 C:HIS378 2.8 45.7 1.0
CE1 C:HIS378 3.5 45.7 1.0
C C:GLY373 3.9 47.9 1.0
O C:VAL323 4.0 52.0 1.0
CD2 C:HIS375 4.0 48.3 1.0
CG C:HIS378 4.1 45.7 1.0
CA C:VAL324 4.3 55.8 1.0
ND1 C:HIS378 4.4 45.7 1.0
CA C:GLY325 4.5 56.0 1.0
CB C:VAL324 4.6 55.8 1.0
CA C:ILE374 4.6 45.5 1.0
N C:ILE374 4.7 45.5 1.0
N C:HIS375 4.8 48.3 1.0
C C:VAL323 4.8 52.0 1.0
NE2 C:HIS375 4.8 48.3 1.0
CA C:GLY373 4.9 47.9 1.0
C C:ILE374 5.0 45.5 1.0

Magnesium binding site 3 out of 8 in 7yyo

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Magnesium binding site 3 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg500

b:59.3
occ:1.00
 NE2 E:HIS378 2.3 47.8 1.0
O E:GLY373 2.8 50.8 1.0
CD2 E:HIS378 2.8 47.8 1.0
CE1 E:HIS378 3.5 47.8 1.0
C E:GLY373 4.0 50.8 1.0
O E:VAL323 4.0 55.3 1.0
CD2 E:HIS375 4.0 50.5 1.0
CG E:HIS378 4.1 47.8 1.0
CA E:VAL324 4.3 59.4 1.0
ND1 E:HIS378 4.4 47.8 1.0
CA E:GLY325 4.5 60.2 1.0
CB E:VAL324 4.6 59.4 1.0
CA E:ILE374 4.6 48.7 1.0
N E:ILE374 4.7 48.7 1.0
N E:HIS375 4.8 50.5 1.0
C E:VAL323 4.8 55.3 1.0
NE2 E:HIS375 4.8 50.5 1.0
CA E:GLY373 4.9 50.8 1.0
C E:ILE374 5.0 48.7 1.0

Magnesium binding site 4 out of 8 in 7yyo

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Magnesium binding site 4 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg500

b:56.1
occ:1.00
 NE2 G:HIS378 2.3 45.6 1.0
O G:GLY373 2.8 47.5 1.0
CD2 G:HIS378 2.8 45.6 1.0
CE1 G:HIS378 3.5 45.6 1.0
C G:GLY373 3.9 47.5 1.0
O G:VAL323 4.0 50.4 1.0
CD2 G:HIS375 4.0 48.7 1.0
CG G:HIS378 4.1 45.6 1.0
CA G:VAL324 4.3 55.1 1.0
ND1 G:HIS378 4.4 45.6 1.0
CA G:GLY325 4.5 54.8 1.0
CB G:VAL324 4.6 55.1 1.0
CA G:ILE374 4.6 45.3 1.0
N G:ILE374 4.7 45.3 1.0
N G:HIS375 4.8 48.7 1.0
C G:VAL323 4.8 50.4 1.0
NE2 G:HIS375 4.8 48.7 1.0
CA G:GLY373 4.9 47.5 1.0
C G:ILE374 5.0 45.3 1.0

Magnesium binding site 5 out of 8 in 7yyo

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Magnesium binding site 5 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg500

b:59.5
occ:1.00
 NE2 I:HIS378 2.3 49.1 1.0
O I:GLY373 2.8 51.8 1.0
CD2 I:HIS378 2.8 49.1 1.0
CE1 I:HIS378 3.5 49.1 1.0
C I:GLY373 3.9 51.8 1.0
O I:VAL323 4.0 55.0 1.0
CD2 I:HIS375 4.0 52.0 1.0
CG I:HIS378 4.1 49.1 1.0
CA I:VAL324 4.3 58.9 1.0
ND1 I:HIS378 4.4 49.1 1.0
CA I:GLY325 4.5 59.6 1.0
CB I:VAL324 4.6 58.9 1.0
CA I:ILE374 4.6 49.3 1.0
N I:ILE374 4.7 49.3 1.0
N I:HIS375 4.8 52.0 1.0
C I:VAL323 4.8 55.0 1.0
NE2 I:HIS375 4.8 52.0 1.0
CA I:GLY373 4.9 51.8 1.0
C I:ILE374 5.0 49.3 1.0

Magnesium binding site 6 out of 8 in 7yyo

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Magnesium binding site 6 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg500

b:54.4
occ:1.00
 NE2 K:HIS378 2.3 45.8 1.0
O K:GLY373 2.8 47.5 1.0
CD2 K:HIS378 2.8 45.8 1.0
CE1 K:HIS378 3.5 45.8 1.0
C K:GLY373 3.9 47.5 1.0
O K:VAL323 4.0 50.5 1.0
CD2 K:HIS375 4.0 48.4 1.0
CG K:HIS378 4.1 45.8 1.0
CA K:VAL324 4.3 54.8 1.0
ND1 K:HIS378 4.4 45.8 1.0
CA K:GLY325 4.5 54.6 1.0
CB K:VAL324 4.6 54.8 1.0
CA K:ILE374 4.6 45.6 1.0
N K:ILE374 4.7 45.6 1.0
N K:HIS375 4.8 48.4 1.0
C K:VAL323 4.8 50.5 1.0
NE2 K:HIS375 4.8 48.4 1.0
CA K:GLY373 4.9 47.5 1.0
C K:ILE374 5.0 45.6 1.0

Magnesium binding site 7 out of 8 in 7yyo

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Magnesium binding site 7 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg500

b:55.5
occ:1.00
 NE2 M:HIS378 2.3 46.4 1.0
O M:GLY373 2.8 47.2 1.0
CD2 M:HIS378 2.8 46.4 1.0
CE1 M:HIS378 3.5 46.4 1.0
C M:GLY373 4.0 47.2 1.0
O M:VAL323 4.0 51.3 1.0
CD2 M:HIS375 4.0 48.2 1.0
CG M:HIS378 4.1 46.4 1.0
CA M:VAL324 4.3 56.2 1.0
ND1 M:HIS378 4.4 46.4 1.0
CA M:GLY325 4.5 55.8 1.0
CB M:VAL324 4.6 56.2 1.0
CA M:ILE374 4.6 45.7 1.0
N M:ILE374 4.7 45.7 1.0
N M:HIS375 4.8 48.2 1.0
C M:VAL323 4.8 51.3 1.0
NE2 M:HIS375 4.8 48.2 1.0
CA M:GLY373 4.9 47.2 1.0
C M:ILE374 5.0 45.7 1.0

Magnesium binding site 8 out of 8 in 7yyo

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Magnesium binding site 8 out of 8 in the Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of An A-Carboxysome Rubisco Enzyme at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg500

b:56.7
occ:1.00
 NE2 O:HIS378 2.3 49.5 1.0
O O:GLY373 2.8 51.0 1.0
CD2 O:HIS378 2.8 49.5 1.0
CE1 O:HIS378 3.5 49.5 1.0
C O:GLY373 3.9 51.0 1.0
O O:VAL323 4.0 54.6 1.0
CD2 O:HIS375 4.0 51.7 1.0
CG O:HIS378 4.1 49.5 1.0
CA O:VAL324 4.3 58.5 1.0
ND1 O:HIS378 4.4 49.5 1.0
CA O:GLY325 4.5 59.0 1.0
CB O:VAL324 4.6 58.5 1.0
CA O:ILE374 4.6 48.5 1.0
N O:ILE374 4.7 48.5 1.0
N O:HIS375 4.8 51.7 1.0
C O:VAL323 4.8 54.6 1.0
NE2 O:HIS375 4.8 51.7 1.0
CA O:GLY373 4.9 51.0 1.0
C O:ILE374 5.0 48.5 1.0

Reference:

S.L.Evans, M.M.J.Al-Hazeem, D.Mann, N.Smetacek, A.Beavil, Y.Sun, T.Chen, G.F.Dykes, L.Liu, J.R.C.Bergeron. Cryo-Em Analysis of the Shell Architecture and Internal Organization of An Intact A-Carboxysome To Be Published.
Page generated: Thu Oct 3 15:45:01 2024

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