Magnesium in PDB 9ck5: Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2

Enzymatic activity of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2

All present enzymatic activity of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2:
4.1.1.39;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 (pdb code 9ck5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2, PDB code: 9ck5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9ck5

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Magnesium binding site 1 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:197.3
occ:1.00
 O6 A:CAP502 1.9 192.5 1.0
OQ2 A:KCX201 2.0 171.8 1.0
O3 A:CAP502 2.0 192.9 1.0
O2 A:CAP502 2.1 196.9 1.0
C2 A:CAP502 2.5 195.9 1.0
C A:CAP502 2.5 195.3 1.0
OE1 A:GLU204 2.6 182.4 1.0
C3 A:CAP502 2.7 192.4 1.0
CX A:KCX201 3.0 170.4 1.0
OQ1 A:KCX201 3.3 172.4 1.0
CD A:GLU204 3.7 179.8 1.0
O7 A:CAP502 3.7 197.0 1.0
OD1 A:ASP203 3.9 180.0 1.0
C4 A:CAP502 3.9 191.8 1.0
OE2 A:GLU204 4.0 182.1 1.0
C1 A:CAP502 4.0 195.9 1.0
NZ A:KCX201 4.1 167.9 1.0
CE1 A:HIS294 4.4 145.2 1.0
C5 A:CAP502 4.4 192.3 1.0
CG A:ASP203 4.4 174.2 1.0
OD2 A:ASP203 4.5 172.9 1.0
O1 A:CAP502 4.5 195.7 1.0
NZ A:LYS175 4.6 154.0 1.0
ND2 B:ASN123 4.7 162.7 1.0
CG A:GLU204 5.0 174.5 1.0

Magnesium binding site 2 out of 8 in 9ck5

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Magnesium binding site 2 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:201.1
occ:1.00
 O3 B:CAP502 2.0 200.5 1.0
O2 B:CAP502 2.1 201.1 1.0
OQ2 B:KCX201 2.1 170.9 1.0
O7 B:CAP502 2.1 201.0 1.0
C B:CAP502 2.3 201.3 1.0
C2 B:CAP502 2.4 200.8 1.0
OE1 B:GLU204 2.6 183.5 1.0
C3 B:CAP502 2.7 198.8 1.0
OE2 B:GLU204 2.9 190.2 1.0
CX B:KCX201 3.1 169.7 1.0
CD B:GLU204 3.1 185.1 1.0
O6 B:CAP502 3.2 203.9 1.0
OQ1 B:KCX201 3.5 173.1 1.0
C1 B:CAP502 3.9 201.0 1.0
C4 B:CAP502 3.9 198.2 1.0
NZ B:KCX201 4.2 167.0 1.0
OD1 B:ASP203 4.3 173.3 1.0
O1 B:CAP502 4.3 202.2 1.0
C5 B:CAP502 4.4 199.3 1.0
NZ B:LYS175 4.5 150.2 1.0
ND2 A:ASN123 4.5 162.2 1.0
OD2 B:ASP203 4.5 183.3 1.0
CG B:ASP203 4.6 175.9 1.0
CG B:GLU204 4.7 179.0 1.0
NZ B:LYS177 4.7 157.8 1.0
CE1 B:HIS294 4.7 146.6 1.0

Magnesium binding site 3 out of 8 in 9ck5

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Magnesium binding site 3 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:200.0
occ:1.00
 O3 C:CAP502 2.0 200.4 1.0
O2 C:CAP502 2.1 201.5 1.0
O7 C:CAP502 2.2 202.0 1.0
C C:CAP502 2.3 202.2 1.0
C2 C:CAP502 2.4 202.0 1.0
OQ2 C:KCX201 2.4 166.6 1.0
OE1 C:GLU204 2.6 187.5 1.0
C3 C:CAP502 2.7 199.6 1.0
OE2 C:GLU204 2.9 191.8 1.0
CD C:GLU204 3.1 188.3 1.0
O6 C:CAP502 3.2 204.4 1.0
CX C:KCX201 3.5 165.6 1.0
C1 C:CAP502 3.9 203.3 1.0
C4 C:CAP502 3.9 199.1 1.0
OQ1 C:KCX201 4.0 167.8 1.0
OD1 C:ASP203 4.1 176.2 1.0
O1 C:CAP502 4.4 203.2 1.0
C5 C:CAP502 4.4 200.4 1.0
NZ C:LYS175 4.5 148.4 1.0
CG C:ASP203 4.6 180.9 1.0
CG C:GLU204 4.6 182.2 1.0
NZ C:KCX201 4.6 161.6 1.0
OD2 C:ASP203 4.6 189.4 1.0
CE1 C:HIS294 4.7 146.9 1.0
ND2 D:ASN123 4.7 161.2 1.0
NZ C:LYS177 4.8 162.2 1.0

Magnesium binding site 4 out of 8 in 9ck5

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Magnesium binding site 4 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:206.4
occ:1.00
 O6 D:CAP502 2.0 199.0 1.0
O3 D:CAP502 2.0 199.8 1.0
OQ2 D:KCX201 2.0 176.7 1.0
O2 D:CAP502 2.0 201.3 1.0
C2 D:CAP502 2.4 200.8 1.0
C D:CAP502 2.5 200.2 1.0
OE1 D:GLU204 2.5 188.4 1.0
C3 D:CAP502 2.7 198.5 1.0
OE2 D:GLU204 2.8 193.3 1.0
CD D:GLU204 3.0 189.4 1.0
CX D:KCX201 3.0 174.7 1.0
OQ1 D:KCX201 3.4 178.2 1.0
O7 D:CAP502 3.7 202.1 1.0
C4 D:CAP502 3.9 197.2 1.0
C1 D:CAP502 3.9 202.2 1.0
NZ D:KCX201 4.1 171.2 1.0
OD2 D:ASP203 4.3 174.9 1.0
O1 D:CAP502 4.4 202.9 1.0
C5 D:CAP502 4.4 198.8 1.0
OD1 D:ASP203 4.5 184.5 1.0
CG D:GLU204 4.5 183.1 1.0
CE1 D:HIS294 4.5 146.6 1.0
ND2 C:ASN123 4.6 160.1 1.0
CG D:ASP203 4.6 176.8 1.0
NZ D:LYS175 4.7 150.0 1.0
NZ D:LYS177 4.8 160.3 1.0

Magnesium binding site 5 out of 8 in 9ck5

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Magnesium binding site 5 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:204.2
occ:1.00
 O6 E:CAP502 1.9 197.2 1.0
OQ2 E:KCX201 1.9 171.5 1.0
O3 E:CAP502 2.0 195.8 1.0
O2 E:CAP502 2.3 200.1 1.0
OE2 E:GLU204 2.3 182.6 1.0
C E:CAP502 2.6 198.0 1.0
C2 E:CAP502 2.6 198.8 1.0
C3 E:CAP502 2.8 194.9 1.0
CX E:KCX201 2.9 171.4 1.0
CD E:GLU204 3.1 178.9 1.0
OE1 E:GLU204 3.3 180.7 1.0
OQ1 E:KCX201 3.3 174.1 1.0
O7 E:CAP502 3.8 199.7 1.0
C4 E:CAP502 4.0 194.4 1.0
NZ E:KCX201 4.0 168.7 1.0
C1 E:CAP502 4.1 199.1 1.0
OD1 E:ASP203 4.3 184.8 1.0
C5 E:CAP502 4.4 195.5 1.0
NE2 E:HIS294 4.4 141.7 1.0
ND2 F:ASN123 4.5 160.1 1.0
CG E:GLU204 4.5 172.9 1.0
O1 E:CAP502 4.6 198.0 1.0
CG E:ASP203 4.7 176.3 1.0
OD2 E:ASP203 4.7 173.0 1.0
NZ E:LYS177 4.8 160.2 1.0
NZ E:LYS175 4.9 153.3 1.0
N E:GLU204 5.0 172.0 1.0

Magnesium binding site 6 out of 8 in 9ck5

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Magnesium binding site 6 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:196.5
occ:1.00
 O6 F:CAP502 1.9 192.9 1.0
OQ2 F:KCX201 1.9 171.1 1.0
O3 F:CAP502 2.0 193.8 1.0
O2 F:CAP502 2.0 196.4 1.0
C2 F:CAP502 2.4 195.0 1.0
C F:CAP502 2.5 194.8 1.0
OE2 F:GLU204 2.6 177.9 1.0
C3 F:CAP502 2.7 192.2 1.0
CX F:KCX201 2.9 170.3 1.0
OQ1 F:KCX201 3.3 173.6 1.0
O7 F:CAP502 3.7 197.2 1.0
CD F:GLU204 3.7 175.9 1.0
OD1 F:ASP203 3.9 172.8 1.0
C1 F:CAP502 3.9 196.3 1.0
C4 F:CAP502 3.9 191.2 1.0
NZ F:KCX201 4.1 167.9 1.0
OE1 F:GLU204 4.3 178.7 1.0
O1 F:CAP502 4.4 197.3 1.0
C5 F:CAP502 4.4 192.6 1.0
CE1 F:HIS294 4.5 145.0 1.0
ND2 E:ASN123 4.6 159.3 1.0
CG F:ASP203 4.7 168.0 1.0
NZ F:LYS175 4.8 151.6 1.0
CG F:GLU204 4.8 172.2 1.0
NZ F:LYS177 4.9 158.3 1.0
OD2 F:ASP203 5.0 167.3 1.0

Magnesium binding site 7 out of 8 in 9ck5

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Magnesium binding site 7 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:199.7
occ:1.00
 O6 G:CAP502 1.9 195.3 1.0
OQ2 G:KCX201 1.9 174.5 1.0
O3 G:CAP502 2.0 196.1 1.0
O2 G:CAP502 2.3 197.4 1.0
OE1 G:GLU204 2.5 179.5 1.0
C G:CAP502 2.6 196.7 1.0
C2 G:CAP502 2.6 197.0 1.0
C3 G:CAP502 2.8 194.1 1.0
CX G:KCX201 2.9 172.9 1.0
OQ1 G:KCX201 3.3 175.6 1.0
CD G:GLU204 3.7 178.1 1.0
O7 G:CAP502 3.8 199.3 1.0
OD1 G:ASP203 3.9 180.3 1.0
C4 G:CAP502 4.0 192.9 1.0
NZ G:KCX201 4.0 170.1 1.0
C1 G:CAP502 4.1 198.4 1.0
C5 G:CAP502 4.4 194.8 1.0
CE1 G:HIS294 4.4 142.8 1.0
OE2 G:GLU204 4.5 181.9 1.0
CG G:ASP203 4.5 175.8 1.0
ND2 H:ASN123 4.6 162.0 1.0
OD2 G:ASP203 4.6 173.2 1.0
CG G:GLU204 4.6 174.9 1.0
O1 G:CAP502 4.6 198.4 1.0
NZ G:LYS175 4.7 155.8 1.0
NZ G:LYS177 4.8 162.0 1.0
N G:GLU204 5.0 172.8 1.0

Magnesium binding site 8 out of 8 in 9ck5

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Magnesium binding site 8 out of 8 in the Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Anthoceros Agrestis Rubisco Assembled with RBCX1, RBCX2, RAF1, RAF2 and BSD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:198.8
occ:1.00
 O6 H:CAP502 1.9 194.4 1.0
OQ2 H:KCX201 1.9 167.8 1.0
O3 H:CAP502 2.0 196.1 1.0
O2 H:CAP502 2.2 197.8 1.0
OE1 H:GLU204 2.5 180.1 1.0
C H:CAP502 2.5 195.8 1.0
C2 H:CAP502 2.6 196.6 1.0
C3 H:CAP502 2.8 194.5 1.0
CX H:KCX201 2.9 167.4 1.0
OQ1 H:KCX201 3.3 171.3 1.0
CD H:GLU204 3.4 177.5 1.0
OE2 H:GLU204 3.7 179.4 1.0
O7 H:CAP502 3.8 197.2 1.0
OD1 H:ASP203 4.0 177.6 1.0
C4 H:CAP502 4.0 193.2 1.0
NZ H:KCX201 4.0 164.6 1.0
C1 H:CAP502 4.0 197.8 1.0
NZ H:LYS175 4.2 157.0 1.0
CE1 H:HIS294 4.4 142.6 1.0
C5 H:CAP502 4.4 194.4 1.0
ND2 G:ASN123 4.5 163.6 1.0
O1 H:CAP502 4.6 197.7 1.0
CG H:ASP203 4.7 171.4 1.0
CG H:GLU204 4.8 174.1 1.0
CE H:LYS175 4.8 158.7 1.0
OD2 H:ASP203 4.9 170.7 1.0
N H:GLU204 5.0 172.6 1.0

Reference:

Z.G.Oh, W.S.L.Ang, F.W.Li, L.H.Gunn. Unique Biogenesis and Kinetics of Hornwort Rubiscos Revealed By Synthetic Biology Systems To Be Published.
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