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Magnesium in PDB 5mac: Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate

Enzymatic activity of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate

All present enzymatic activity of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate:
4.1.1.39;

Protein crystallography data

The structure of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate, PDB code: 5mac was solved by L.H.Gunn, K.Valegard, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.37 / 2.60
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 273.760, 273.760, 96.740, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 22.5

Other elements in 5mac:

The structure of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate (pdb code 5mac). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate, PDB code: 5mac:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5mac

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Magnesium binding site 1 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:46.1
occ:1.00
 O7 A:CAP501 1.9 63.3 1.0
O2 A:CAP501 2.0 59.4 1.0
OE1 A:GLU196 2.1 44.9 1.0
O3 A:CAP501 2.2 56.3 1.0
OD1 A:ASP195 2.2 52.4 1.0
OQ2 A:KCX193 2.2 52.2 1.0
C A:CAP501 2.5 60.2 1.0
C2 A:CAP501 2.5 57.6 1.0
C3 A:CAP501 2.9 57.0 1.0
CD A:GLU196 3.1 50.7 1.0
CX A:KCX193 3.3 54.0 1.0
OE2 A:GLU196 3.4 42.1 1.0
CG A:ASP195 3.4 53.9 1.0
ND2 B:ASN115 3.4 60.5 1.0
OQ1 A:KCX193 3.6 54.9 1.0
O6 A:CAP501 3.7 60.1 1.0
NZ A:LYS167 4.0 51.3 1.0
OD2 A:ASP195 4.0 61.1 1.0
C1 A:CAP501 4.0 55.4 1.0
NE2 A:HIS288 4.1 56.1 1.0
C4 A:CAP501 4.1 55.1 1.0
N A:GLU196 4.2 49.2 1.0
NZ A:LYS169 4.3 50.1 1.0
CG A:GLU196 4.4 50.6 1.0
O1 A:CAP501 4.4 54.4 1.0
CB A:ASP195 4.5 49.4 1.0
CA A:ASP195 4.5 49.1 1.0
NZ A:KCX193 4.5 53.9 1.0
CE1 A:HIS288 4.6 55.9 1.0
CG B:ASN115 4.7 68.0 1.0
CG2 A:ILE165 4.7 57.7 1.0
CE A:LYS169 4.7 40.4 1.0
O A:HOH632 4.7 55.4 1.0
C5 A:CAP501 4.8 53.4 1.0
CB A:GLU196 4.8 49.3 1.0
C A:ASP195 4.9 51.2 1.0
O A:HOH627 5.0 45.9 1.0

Magnesium binding site 2 out of 10 in 5mac

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Magnesium binding site 2 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:41.1
occ:1.00
 OD2 A:ASP368 2.2 71.8 1.0
OD2 A:ASP366 2.4 84.8 1.0
OD1 A:ASP366 2.7 88.7 1.0
CG A:ASP366 2.9 85.7 1.0
CG A:ASP368 3.4 70.2 1.0
CB A:ASP368 4.1 66.8 1.0
O A:HOH675 4.2 60.4 1.0
CB A:ASP366 4.4 76.1 1.0
OD1 A:ASP368 4.5 69.6 1.0
NH1 A:ARG389 4.8 54.6 1.0
N A:ASP368 4.9 66.5 1.0

Magnesium binding site 3 out of 10 in 5mac

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Magnesium binding site 3 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:59.5
occ:1.00
 OQ1 B:KCX193 1.9 50.3 1.0
OD1 B:ASP195 2.0 57.8 1.0
OE1 B:GLU196 2.0 65.5 1.0
O6 B:CAP501 2.2 67.9 1.0
O2 B:CAP501 2.3 66.6 1.0
O3 B:CAP501 2.3 64.5 1.0
C B:CAP501 2.9 65.4 1.0
CD B:GLU196 2.9 51.3 1.0
C2 B:CAP501 3.0 64.4 1.0
CG B:ASP195 3.1 54.7 1.0
CX B:KCX193 3.2 49.8 1.0
C3 B:CAP501 3.2 63.6 1.0
NZ B:LYS169 3.2 63.5 1.0
OE2 B:GLU196 3.3 49.0 1.0
ND2 A:ASN115 3.5 47.8 1.0
OD2 B:ASP195 3.7 52.5 1.0
OQ2 B:KCX193 3.7 50.3 1.0
NZ B:LYS167 3.9 59.9 1.0
N B:GLU196 4.0 46.1 1.0
NE2 B:HIS288 4.1 49.3 1.0
O7 B:CAP501 4.1 65.3 1.0
CB B:ASP195 4.2 49.2 1.0
CA B:ASP195 4.2 47.7 1.0
CG B:GLU196 4.2 45.3 1.0
NZ B:KCX193 4.3 48.1 1.0
CG2 B:ILE165 4.3 47.1 1.0
C1 B:CAP501 4.4 62.8 1.0
C4 B:CAP501 4.5 60.0 1.0
C B:ASP195 4.6 50.5 1.0
CB B:GLU196 4.6 46.4 1.0
CE1 B:HIS288 4.6 49.1 1.0
CE B:LYS169 4.7 48.1 1.0
O1 B:CAP501 4.8 60.3 1.0
CG A:ASN115 4.8 53.4 1.0
CE B:LYS167 4.9 50.1 1.0
CA B:GLU196 4.9 45.2 1.0

Magnesium binding site 4 out of 10 in 5mac

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Magnesium binding site 4 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:46.2
occ:1.00
 OD2 B:ASP368 2.2 75.2 1.0
OD1 B:ASP366 2.3 74.6 1.0
OE2 D:GLU179 2.4 64.8 1.0
OD1 D:ASP183 2.5 50.8 1.0
O B:HOH674 2.7 75.0 1.0
OD2 B:ASP366 2.7 73.3 1.0
OD2 D:ASP183 2.8 67.2 1.0
CG B:ASP366 2.9 73.7 1.0
CG D:ASP183 3.0 56.0 1.0
CG B:ASP368 3.4 75.9 1.0
CD D:GLU179 3.5 71.8 1.0
CG D:GLU179 3.8 64.7 1.0
CB B:ASP368 4.1 71.4 1.0
CB B:ASP366 4.4 68.2 1.0
NE2 D:GLN435 4.4 67.0 1.0
OD1 B:ASP368 4.5 75.3 1.0
NH2 B:ARG389 4.5 75.2 1.0
CB D:ASP183 4.5 57.3 1.0
OE1 D:GLU179 4.6 58.6 1.0
N B:ASP368 4.8 70.1 1.0

Magnesium binding site 5 out of 10 in 5mac

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Magnesium binding site 5 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:58.1
occ:1.00
 OQ2 C:KCX193 1.9 63.7 1.0
OD1 C:ASP195 1.9 55.9 1.0
O7 C:CAP501 2.1 73.7 1.0
OE1 C:GLU196 2.1 72.7 1.0
O2 C:CAP501 2.2 73.5 1.0
O3 C:CAP501 2.2 63.8 1.0
C C:CAP501 2.8 72.6 1.0
C2 C:CAP501 2.8 70.4 1.0
CX C:KCX193 3.0 63.7 1.0
C3 C:CAP501 3.0 66.2 1.0
CG C:ASP195 3.1 58.3 1.0
OQ1 C:KCX193 3.2 60.8 1.0
CD C:GLU196 3.3 79.5 1.0
OD2 C:ASP195 3.7 59.5 1.0
ND2 D:ASN115 3.8 68.5 1.0
OE2 C:GLU196 3.9 68.0 1.0
N C:GLU196 3.9 61.5 1.0
O6 C:CAP501 4.0 74.7 1.0
NZ C:LYS167 4.0 54.1 1.0
NE2 C:HIS288 4.1 64.2 1.0
NZ C:KCX193 4.2 63.9 1.0
CA C:ASP195 4.2 59.5 1.0
CB C:ASP195 4.2 60.6 1.0
C1 C:CAP501 4.2 71.0 1.0
CE C:LYS169 4.3 71.6 1.0
CG2 C:ILE165 4.3 58.6 1.0
C4 C:CAP501 4.4 64.7 1.0
CG C:GLU196 4.4 72.5 1.0
C C:ASP195 4.5 64.6 1.0
CB C:GLU196 4.6 62.3 1.0
NZ C:LYS169 4.6 86.2 1.0
O1 C:CAP501 4.6 70.9 1.0
CE1 C:HIS288 4.6 64.0 1.0
CA C:GLU196 4.9 60.9 1.0
CE C:LYS167 4.9 53.1 1.0
C5 C:CAP501 4.9 64.3 1.0
CG1 C:ILE165 5.0 61.3 1.0

Magnesium binding site 6 out of 10 in 5mac

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Magnesium binding site 6 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:50.5
occ:1.00
 OD2 C:ASP368 1.9 77.2 1.0
OD1 C:ASP366 2.3 90.2 1.0
OE2 A:GLU179 2.4 49.4 1.0
OD1 A:ASP183 2.5 65.6 1.0
OD2 A:ASP183 2.7 68.6 1.0
O C:HOH648 2.9 54.4 1.0
OD2 C:ASP366 2.9 94.5 1.0
CG A:ASP183 2.9 64.4 1.0
CG C:ASP366 2.9 90.1 1.0
CG C:ASP368 3.2 80.2 1.0
CD A:GLU179 3.4 66.0 1.0
CG A:GLU179 3.8 56.0 1.0
CB C:ASP368 3.9 74.1 1.0
OD1 C:ASP368 4.2 82.0 1.0
NE2 A:GLN435 4.2 58.1 1.0
CB A:ASP183 4.4 56.2 1.0
CB C:ASP366 4.4 82.2 1.0
OE1 A:GLU179 4.6 63.9 1.0
N C:ASP368 4.6 73.2 1.0
NH2 C:ARG389 4.8 71.0 1.0
CA C:ASP368 4.9 71.9 1.0
O A:GLU179 4.9 58.6 1.0
O A:HOH614 5.0 62.4 1.0

Magnesium binding site 7 out of 10 in 5mac

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Magnesium binding site 7 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:55.7
occ:1.00
 OD1 D:ASP195 1.9 61.0 1.0
OE1 D:GLU196 2.0 52.7 1.0
OQ1 D:KCX193 2.0 48.6 1.0
O2 D:CAP501 2.2 62.4 1.0
O3 D:CAP501 2.3 64.5 1.0
O7 D:CAP501 2.6 59.3 1.0
C2 D:CAP501 2.9 61.5 1.0
C D:CAP501 3.0 59.5 1.0
C3 D:CAP501 3.1 62.8 1.0
CG D:ASP195 3.1 59.8 1.0
CD D:GLU196 3.2 71.2 1.0
CX D:KCX193 3.2 50.9 1.0
NZ D:LYS169 3.3 77.0 1.0
OQ2 D:KCX193 3.5 55.2 1.0
ND2 C:ASN115 3.6 58.8 1.0
N D:GLU196 3.7 54.0 1.0
OD2 D:ASP195 3.8 63.0 1.0
OE2 D:GLU196 3.9 65.9 1.0
NZ D:LYS167 4.1 57.7 1.0
NE2 D:HIS288 4.1 58.1 1.0
CA D:ASP195 4.2 51.1 1.0
O6 D:CAP501 4.2 59.6 1.0
CB D:ASP195 4.2 53.0 1.0
CG D:GLU196 4.3 59.4 1.0
C1 D:CAP501 4.3 61.8 1.0
NZ D:KCX193 4.4 49.8 1.0
CB D:GLU196 4.4 54.9 1.0
CE1 D:HIS288 4.4 57.6 1.0
C4 D:CAP501 4.4 61.0 1.0
C D:ASP195 4.4 56.0 1.0
CE D:LYS169 4.5 63.9 1.0
CG2 D:ILE165 4.5 56.6 1.0
CA D:GLU196 4.7 53.7 1.0
CG C:ASN115 4.7 60.4 1.0
O1 D:CAP501 4.8 60.6 1.0

Magnesium binding site 8 out of 10 in 5mac

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Magnesium binding site 8 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


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 Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:53.6
occ:1.00
 O D:HOH623 2.0 92.2 1.0
OD2 D:ASP368 2.5 87.7 1.0
OD1 D:ASP366 2.7 78.8 1.0
OD2 D:ASP366 2.7 76.3 1.0
CG D:ASP366 3.1 78.0 1.0
CG D:ASP368 3.6 86.4 1.0
CB D:ASP368 4.2 78.0 1.0
CB D:ASP366 4.6 78.2 1.0
OD1 D:ASP368 4.6 87.0 1.0
N D:ASP368 4.8 77.6 1.0
NH2 D:ARG389 4.8 71.5 1.0

Magnesium binding site 9 out of 10 in 5mac

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Magnesium binding site 9 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:62.4
occ:1.00
 OD1 E:ASP195 1.9 73.0 1.0
OQ2 E:KCX193 2.1 63.0 1.0
O7 E:CAP501 2.1 78.2 1.0
OE1 E:GLU196 2.1 77.2 1.0
O2 E:CAP501 2.3 80.3 1.0
O3 E:CAP501 2.4 77.8 1.0
C E:CAP501 2.8 79.5 1.0
C2 E:CAP501 2.9 79.6 1.0
CX E:KCX193 3.0 61.6 1.0
CG E:ASP195 3.0 71.0 1.0
OQ1 E:KCX193 3.0 63.6 1.0
CD E:GLU196 3.2 80.9 1.0
C3 E:CAP501 3.2 78.4 1.0
OD2 E:ASP195 3.7 73.7 1.0
OE2 E:GLU196 3.7 72.8 1.0
N E:GLU196 3.8 60.7 1.0
CA E:ASP195 4.0 61.9 1.0
O6 E:CAP501 4.1 78.8 1.0
NE2 E:HIS288 4.1 66.5 1.0
CB E:ASP195 4.1 63.5 1.0
CG2 E:ILE165 4.1 60.8 1.0
NZ E:KCX193 4.3 59.7 1.0
NZ E:LYS167 4.3 0.4 1.0
CE E:LYS169 4.3 86.7 1.0
C1 E:CAP501 4.3 79.8 1.0
CG E:GLU196 4.4 68.6 1.0
C E:ASP195 4.4 65.1 1.0
C4 E:CAP501 4.5 78.8 1.0
CB E:GLU196 4.5 60.8 1.0
NZ E:LYS169 4.7 96.5 1.0
O1 E:CAP501 4.8 80.1 1.0
CA E:GLU196 4.8 59.8 1.0
CE E:LYS167 4.8 86.7 1.0
CE1 E:HIS288 4.8 66.2 1.0
CD2 E:HIS288 4.9 66.6 1.0
CG1 E:ILE165 4.9 62.2 1.0

Magnesium binding site 10 out of 10 in 5mac

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Magnesium binding site 10 out of 10 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:57.6
occ:1.00
 OD2 E:ASP368 2.3 99.5 1.0
OD1 C:ASP183 2.4 73.4 1.0
OE2 C:GLU179 2.4 66.8 1.0
OD1 E:ASP366 2.5 93.3 1.0
OD2 C:ASP183 2.6 78.8 1.0
OD2 E:ASP366 2.7 0.5 1.0
CG C:ASP183 2.8 71.8 1.0
O E:HOH612 2.9 79.8 1.0
CG E:ASP366 3.0 95.3 1.0
CD C:GLU179 3.5 77.5 1.0
CG E:ASP368 3.5 92.1 1.0
CG C:GLU179 3.8 64.5 1.0
CB E:ASP368 4.1 85.1 1.0
O C:HOH650 4.3 70.4 1.0
CB C:ASP183 4.3 59.9 1.0
OD1 E:ASP368 4.5 90.5 1.0
CB E:ASP366 4.5 88.3 1.0
OE1 C:GLU179 4.6 64.7 1.0
NE2 C:GLN435 4.6 54.2 1.0
N E:ASP368 4.9 84.7 1.0
O C:GLU179 5.0 62.9 1.0

Reference:

L.H.Gunn, K.Valegard, I.Andersson. A Unique Structural Domain in Methanococcoides Burtonii Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Acts As A Small Subunit Mimic. J. Biol. Chem. V. 292 6838 2017.
ISSN: ESSN 1083-351X
PubMed: 28154188
DOI: 10.1074/JBC.M116.767145
Page generated: Mon Dec 14 20:50:58 2020

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