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Magnesium in PDB 6z1f: Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)

Enzymatic activity of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)

All present enzymatic activity of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120):
4.1.1.39;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) (pdb code 6z1f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120), PDB code: 6z1f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6z1f

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Magnesium binding site 1 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg302

b:23.6
occ:1.00
 O2G 2:AGS301 1.9 43.3 1.0
O2B 2:AGS301 2.3 39.6 1.0
OG1 2:THR44 2.4 45.4 1.0
O2A 2:AGS301 3.1 38.0 1.0
PG 2:AGS301 3.2 42.8 1.0
PB 2:AGS301 3.5 39.1 1.0
O3B 2:AGS301 3.6 40.7 1.0
CB 2:THR44 3.6 45.0 1.0
S1G 2:AGS301 4.0 44.2 1.0
ND2 2:ASN101 4.1 82.4 1.0
OD1 2:ASN101 4.1 80.1 1.0
NH2 3:ARG172 4.2 46.4 1.0
PA 2:AGS301 4.3 38.2 1.0
O3A 2:AGS301 4.3 38.9 1.0
CG2 2:THR44 4.3 47.6 1.0
O3G 2:AGS301 4.3 42.1 1.0
N 2:THR44 4.6 42.4 1.0
CG 2:ASN101 4.6 78.3 1.0
CA 2:THR44 4.7 44.0 1.0
O1B 2:AGS301 4.7 39.4 1.0
OD2 3:ASP132 4.8 75.2 1.0
NH2 3:ARG169 4.8 56.6 1.0
O1A 2:AGS301 4.8 38.5 1.0
CG2 2:THR156 4.9 39.7 1.0

Magnesium binding site 2 out of 12 in 6z1f

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Magnesium binding site 2 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg302

b:37.7
occ:1.00
 O2G 3:AGS301 2.2 60.7 1.0
OG1 3:THR44 2.7 46.0 1.0
O2A 3:AGS301 2.9 46.0 1.0
O2B 3:AGS301 3.0 46.6 1.0
O3B 3:AGS301 3.4 53.5 1.0
PG 3:AGS301 3.4 60.0 1.0
CB 3:THR44 3.5 45.6 1.0
NH2 4:ARG172 3.6 56.3 1.0
ND2 3:ASN101 3.7 86.1 1.0
PB 3:AGS301 3.8 47.2 1.0
OD2 4:ASP132 3.9 82.5 1.0
CG2 3:THR44 4.2 45.2 1.0
S1G 3:AGS301 4.2 61.7 1.0
PA 3:AGS301 4.3 45.7 1.0
OD1 3:ASN101 4.4 83.5 1.0
CG 3:ASN101 4.6 81.8 1.0
O3A 3:AGS301 4.6 46.5 1.0
O3G 3:AGS301 4.6 59.0 1.0
CZ 4:ARG172 4.7 55.9 1.0
CA 3:THR44 4.8 45.5 1.0
N 3:THR44 4.8 45.1 1.0
O1A 3:AGS301 4.8 46.4 1.0
NH1 4:ARG169 4.9 52.7 1.0

Magnesium binding site 3 out of 12 in 6z1f

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Magnesium binding site 3 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg302

b:72.2
occ:1.00
 O2G 4:AGS301 1.9 72.2 1.0
O2A 4:AGS301 1.9 52.0 1.0
O3B 4:AGS301 2.1 62.6 1.0
PG 4:AGS301 2.5 71.8 1.0
O2B 4:AGS301 2.6 56.4 1.0
OG1 4:THR44 2.7 45.2 1.0
PB 4:AGS301 2.9 55.5 1.0
PA 4:AGS301 3.2 51.2 1.0
CB 4:THR44 3.4 44.6 1.0
O3G 4:AGS301 3.5 72.4 1.0
O3A 4:AGS301 3.5 53.8 1.0
NH1 5:ARG169 3.6 77.6 1.0
NH2 5:ARG169 3.9 74.1 1.0
O1A 4:AGS301 4.0 51.7 1.0
S1G 4:AGS301 4.1 75.2 1.0
OD2 5:ASP132 4.2 82.1 1.0
NH2 5:ARG172 4.2 44.4 1.0
CZ 5:ARG169 4.2 75.3 1.0
O1B 4:AGS301 4.3 56.1 1.0
CG2 4:THR44 4.3 44.2 1.0
OD1 5:ASP132 4.3 79.7 1.0
N 4:THR44 4.4 45.1 1.0
O5' 4:AGS301 4.4 51.3 1.0
CA 4:THR44 4.5 44.9 1.0
CG 5:ASP132 4.6 79.0 1.0
CZ 5:ARG172 5.0 44.4 1.0

Magnesium binding site 4 out of 12 in 6z1f

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Magnesium binding site 4 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Mg302

b:28.3
occ:1.00
 O2G 5:AGS301 1.8 44.6 1.0
O2A 5:AGS301 2.4 40.1 1.0
O2B 5:AGS301 2.4 41.6 1.0
OG1 5:THR44 2.7 32.2 1.0
PG 5:AGS301 3.0 44.2 1.0
O3B 5:AGS301 3.0 42.6 1.0
PB 5:AGS301 3.3 41.6 1.0
OD2 6:ASP132 3.4 65.8 1.0
CB 5:THR44 3.5 32.3 1.0
PA 5:AGS301 3.6 40.6 1.0
O3A 5:AGS301 4.0 41.5 1.0
S1G 5:AGS301 4.0 47.0 1.0
O1A 5:AGS301 4.1 40.8 1.0
O3G 5:AGS301 4.1 44.6 1.0
NH2 6:ARG172 4.1 36.6 1.0
OD1 5:ASN101 4.4 62.8 1.0
CG2 5:THR44 4.4 32.7 1.0
N 5:THR44 4.4 34.1 1.0
CG 6:ASP132 4.4 65.9 1.0
O1B 5:AGS301 4.6 41.7 1.0
CA 5:THR44 4.6 33.8 1.0
OD1 6:ASP132 4.8 67.3 1.0
NH1 6:ARG169 4.8 53.5 1.0
ND2 5:ASN101 4.9 62.2 1.0
NH1 6:ARG172 4.9 37.3 1.0
O5' 5:AGS301 4.9 40.7 1.0
CZ 6:ARG172 5.0 37.4 1.0

Magnesium binding site 5 out of 12 in 6z1f

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Magnesium binding site 5 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:52.9
occ:1.00
 OQ2 A:KCX202 2.2 42.1 1.0
OD1 A:ASP204 2.5 52.8 1.0
O2 A:CAP502 2.6 80.6 1.0
O7 A:CAP502 2.7 81.3 1.0
OE1 A:GLU205 2.8 52.5 1.0
O3 A:CAP502 2.8 81.0 1.0
CD A:GLU205 3.4 52.6 1.0
OE2 A:GLU205 3.4 52.9 1.0
CG A:ASP204 3.4 52.2 1.0
C2 A:CAP502 3.4 80.9 1.0
C A:CAP502 3.5 81.8 1.0
CX A:KCX202 3.5 42.1 1.0
CB A:ASP204 3.6 50.7 1.0
CA A:ASP204 3.7 49.4 1.0
C3 A:CAP502 3.7 81.1 1.0
N A:GLU205 3.9 49.5 1.0
OQ1 A:KCX202 4.1 42.4 1.0
NZ A:LYS176 4.1 47.5 1.0
CE A:LYS178 4.3 56.0 1.0
CG2 A:THR174 4.3 42.4 1.0
C A:ASP204 4.4 49.4 1.0
NZ A:KCX202 4.4 42.1 1.0
NZ A:LYS178 4.5 57.5 1.0
OD2 A:ASP204 4.6 53.1 1.0
O6 A:CAP502 4.7 82.6 1.0
NE2 A:HIS295 4.7 32.1 1.0
CG A:GLU205 4.7 51.6 1.0
C1 A:CAP502 4.8 80.2 1.0
N A:ASP204 4.9 48.4 1.0
CB A:GLU205 4.9 50.5 1.0
C4 A:CAP502 4.9 81.7 1.0
CG A:LYS178 5.0 53.9 1.0
ND2 B:ASN124 5.0 54.4 1.0

Magnesium binding site 6 out of 12 in 6z1f

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Magnesium binding site 6 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:37.8
occ:1.00
 OQ1 B:KCX202 2.2 40.4 1.0
OE1 B:GLU205 2.6 49.9 1.0
CD B:GLU205 3.4 49.5 1.0
OE2 B:GLU205 3.5 50.0 1.0
CX B:KCX202 3.5 40.4 1.0
OD1 B:ASP204 3.9 48.4 1.0
OQ2 B:KCX202 3.9 41.0 1.0
ND2 A:ASN124 4.3 53.1 1.0
NZ B:LYS176 4.4 65.7 1.0
CD B:LYS178 4.5 65.6 1.0
NE2 B:HIS295 4.5 31.6 1.0
NZ B:KCX202 4.5 39.6 1.0
CB B:ASP204 4.8 46.3 1.0
CG2 B:THR174 4.8 46.0 1.0
CG B:ASP204 4.8 48.0 1.0
N B:GLU205 4.8 45.7 1.0
CG B:GLU205 4.9 48.5 1.0
CA B:ASP204 4.9 44.6 1.0
NZ B:LYS178 5.0 68.0 1.0

Magnesium binding site 7 out of 12 in 6z1f

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Magnesium binding site 7 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:69.0
occ:1.00
 OQ2 C:KCX202 2.1 44.0 1.0
O7 C:CAP502 2.6 71.0 1.0
OE1 C:GLU205 2.6 52.1 1.0
O2 C:CAP502 2.8 69.2 1.0
OD1 C:ASP204 2.9 50.8 1.0
NZ C:LYS176 3.4 41.2 1.0
CD C:GLU205 3.5 52.2 1.0
CX C:KCX202 3.5 43.9 1.0
C C:CAP502 3.5 70.7 1.0
OE2 C:GLU205 3.6 52.6 1.0
O3 C:CAP502 3.6 68.1 1.0
CB C:ASP204 3.7 49.6 1.0
C2 C:CAP502 3.7 69.5 1.0
CG C:ASP204 3.7 51.0 1.0
CA C:ASP204 3.8 48.2 1.0
CD C:LYS178 4.1 42.6 1.0
CG2 C:THR174 4.1 40.6 1.0
OQ1 C:KCX202 4.1 44.1 1.0
N C:GLU205 4.1 48.3 1.0
CG C:LYS178 4.3 42.8 1.0
NZ C:KCX202 4.3 43.1 1.0
C3 C:CAP502 4.3 68.9 1.0
C C:ASP204 4.5 48.0 1.0
O6 C:CAP502 4.6 71.3 1.0
CE C:LYS176 4.8 41.2 1.0
NZ C:LYS178 4.9 43.9 1.0
CG C:GLU205 4.9 51.0 1.0
OD2 C:ASP204 4.9 51.5 1.0
C1 C:CAP502 5.0 69.4 1.0
O1 C:CAP502 5.0 68.2 1.0
N C:ASP204 5.0 47.1 1.0

Magnesium binding site 8 out of 12 in 6z1f

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Magnesium binding site 8 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:45.0
occ:1.00
 OQ1 D:KCX202 2.2 40.0 1.0
O6 D:CAP502 2.6 77.3 1.0
OE1 D:GLU205 2.6 50.6 1.0
O2 D:CAP502 2.8 76.0 1.0
OD1 D:ASP204 2.9 48.0 1.0
NZ D:LYS176 3.3 39.0 1.0
CX D:KCX202 3.5 39.8 1.0
C D:CAP502 3.5 77.1 1.0
CD D:GLU205 3.5 50.0 1.0
OE2 D:GLU205 3.6 50.1 1.0
CB D:ASP204 3.6 46.3 1.0
O3 D:CAP502 3.7 76.2 1.0
CG D:ASP204 3.7 47.8 1.0
C2 D:CAP502 3.7 76.4 1.0
CA D:ASP204 3.8 45.0 1.0
CD D:LYS178 4.1 40.6 1.0
CG2 D:THR174 4.1 39.4 1.0
OQ2 D:KCX202 4.1 40.0 1.0
N D:GLU205 4.1 46.0 1.0
CG D:LYS178 4.3 40.6 1.0
NZ D:KCX202 4.3 39.4 1.0
C3 D:CAP502 4.4 76.4 1.0
C D:ASP204 4.5 45.6 1.0
O7 D:CAP502 4.6 77.3 1.0
CE D:LYS176 4.8 39.2 1.0
NZ D:LYS178 4.9 41.4 1.0
CG D:GLU205 4.9 48.8 1.0
OD2 D:ASP204 4.9 48.3 1.0
C1 D:CAP502 5.0 75.6 1.0
O1 D:CAP502 5.0 73.7 1.0
N D:ASP204 5.0 43.4 1.0

Magnesium binding site 9 out of 12 in 6z1f

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Magnesium binding site 9 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:77.3
occ:1.00
 OQ2 E:KCX202 2.2 43.8 1.0
O2 E:CAP502 2.6 89.2 1.0
OE1 E:GLU205 2.7 54.4 1.0
OD1 E:ASP204 2.8 51.0 1.0
O7 E:CAP502 2.9 89.8 1.0
O3 E:CAP502 3.1 87.2 1.0
CD E:GLU205 3.4 54.4 1.0
OE2 E:GLU205 3.5 54.6 1.0
CX E:KCX202 3.5 43.5 1.0
C2 E:CAP502 3.5 89.4 1.0
NZ E:LYS176 3.6 50.7 1.0
C E:CAP502 3.6 89.8 1.0
CG E:ASP204 3.6 51.3 1.0
CB E:ASP204 3.6 50.3 1.0
CA E:ASP204 3.8 49.5 1.0
CD E:LYS178 3.9 53.1 1.0
N E:GLU205 4.0 50.6 1.0
C3 E:CAP502 4.0 87.9 1.0
CG2 E:THR174 4.2 47.5 1.0
OQ1 E:KCX202 4.3 43.7 1.0
NZ E:KCX202 4.3 42.8 1.0
C E:ASP204 4.4 50.0 1.0
CG E:LYS178 4.7 52.9 1.0
CG E:GLU205 4.7 53.8 1.0
NZ E:LYS178 4.7 53.6 1.0
O6 E:CAP502 4.8 89.9 1.0
C1 E:CAP502 4.8 90.1 1.0
OD2 E:ASP204 4.8 51.9 1.0
CE E:LYS178 4.9 53.1 1.0
CE E:LYS176 4.9 50.5 1.0
ND2 F:ASN124 4.9 64.5 1.0
NE2 E:HIS295 4.9 34.6 1.0
N E:ASP204 4.9 48.0 1.0

Magnesium binding site 10 out of 12 in 6z1f

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Magnesium binding site 10 out of 12 in the Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryoem Structure of Rubisco Activase with Its Substrate Rubisco From Nostoc Sp. (Strain PCC7120) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:50.1
occ:1.00
 OQ1 F:KCX202 2.2 40.1 1.0
O6 F:CAP502 2.6 91.4 1.0
O2 F:CAP502 2.7 91.2 1.0
OD1 F:ASP204 2.7 50.2 1.0
OE1 F:GLU205 2.8 49.3 1.0
O3 F:CAP502 3.3 89.8 1.0
OE2 F:GLU205 3.3 49.1 1.0
CD F:GLU205 3.4 49.0 1.0
C F:CAP502 3.5 91.7 1.0
CX F:KCX202 3.5 40.1 1.0
C2 F:CAP502 3.6 91.0 1.0
CG F:ASP204 3.6 50.0 1.0
NZ F:LYS176 3.6 51.3 1.0
CB F:ASP204 3.6 48.2 1.0
CA F:ASP204 3.8 46.8 1.0
CD F:LYS178 3.8 52.4 1.0
N F:GLU205 4.0 46.8 1.0
C3 F:CAP502 4.1 90.6 1.0
OQ2 F:KCX202 4.1 40.5 1.0
CG2 F:THR174 4.2 47.7 1.0
NZ F:KCX202 4.3 39.7 1.0
C F:ASP204 4.5 46.9 1.0
O7 F:CAP502 4.7 92.7 1.0
CG F:LYS178 4.7 52.1 1.0
NZ F:LYS178 4.7 53.1 1.0
CG F:GLU205 4.8 48.1 1.0
CE F:LYS176 4.8 51.7 1.0
OD2 F:ASP204 4.8 51.0 1.0
CE F:LYS178 4.9 52.5 1.0
C1 F:CAP502 4.9 90.7 1.0
NE2 F:HIS295 4.9 35.6 1.0
N F:ASP204 5.0 45.3 1.0

Reference:

M.Flecken, H.Wang, L.Popilka, F.U.Hartl, A.Bracher, M.Hayer-Hartl. Dual Role of Rca-Like Protein in Rubisco Metabolic Repair and Carboxysome Organization To Be Published.
Page generated: Wed Oct 2 02:01:09 2024

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