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Magnesium in PDB 5nv3: Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp

Enzymatic activity of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp

All present enzymatic activity of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp:
4.1.1.39;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp (pdb code 5nv3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp, PDB code: 5nv3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5nv3

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Magnesium binding site 1 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:0.0
occ:1.00
 OQ2 A:KCX203 2.2 0.0 1.0
OE1 A:GLU206 2.3 0.3 1.0
O3 A:CAP1001 2.6 0.9 1.0
O2 A:CAP1001 2.7 0.3 1.0
O7 A:CAP1001 2.9 0.2 1.0
OD2 A:ASP205 2.9 0.6 1.0
CG A:ASP205 3.4 0.5 1.0
CX A:KCX203 3.4 0.7 1.0
CD A:GLU206 3.4 0.2 1.0
C2 A:CAP1001 3.5 0.9 1.0
C3 A:CAP1001 3.6 0.5 1.0
C A:CAP1001 3.6 0.8 1.0
NZ A:LYS179 3.7 0.2 1.0
OD1 A:ASP205 3.7 0.1 1.0
CG2 A:THR175 3.9 0.8 1.0
OE2 A:GLU206 3.9 1.0 1.0
OQ1 A:KCX203 3.9 0.2 1.0
NE2 A:HIS295 4.0 0.5 1.0
N A:GLU206 4.0 0.8 1.0
CA A:ASP205 4.1 0.1 1.0
CB A:ASP205 4.3 0.3 1.0
NZ A:KCX203 4.4 0.5 1.0
ND2 E:ASN125 4.5 0.5 1.0
CE1 A:HIS295 4.6 0.5 1.0
C A:ASP205 4.6 0.2 1.0
CG A:GLU206 4.7 0.6 1.0
NZ A:LYS177 4.7 0.2 1.0
CD2 A:HIS295 4.8 0.3 1.0
OG1 A:THR175 4.8 0.5 1.0
CB A:GLU206 4.8 0.4 1.0
C4 A:CAP1001 4.8 0.6 1.0
O6 A:CAP1001 4.9 0.3 1.0
CE A:LYS179 4.9 0.0 1.0
CB A:THR175 4.9 0.9 1.0
C1 A:CAP1001 4.9 0.2 1.0

Magnesium binding site 2 out of 8 in 5nv3

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Magnesium binding site 2 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:0.4
occ:1.00
 OQ2 B:KCX203 2.2 0.3 1.0
OE1 B:GLU206 2.4 0.7 1.0
O3 B:CAP1001 2.6 0.4 1.0
O2 B:CAP1001 2.7 0.6 1.0
O7 B:CAP1001 2.8 0.9 1.0
OD2 B:ASP205 2.9 0.8 1.0
CG B:ASP205 3.4 0.7 1.0
CX B:KCX203 3.4 0.7 1.0
CD B:GLU206 3.4 0.5 1.0
C2 B:CAP1001 3.5 0.1 1.0
C B:CAP1001 3.6 0.5 1.0
C3 B:CAP1001 3.6 0.3 1.0
NZ B:LYS179 3.6 0.6 1.0
OD1 B:ASP205 3.7 0.5 1.0
OQ1 B:KCX203 3.9 0.9 1.0
OE2 B:GLU206 3.9 0.5 1.0
CG2 B:THR175 3.9 0.3 1.0
NE2 B:HIS295 4.0 1.0 1.0
N B:GLU206 4.0 0.4 1.0
CA B:ASP205 4.1 0.6 1.0
CB B:ASP205 4.3 0.9 1.0
NZ B:KCX203 4.4 0.3 1.0
ND2 F:ASN125 4.5 0.9 1.0
CE1 B:HIS295 4.6 0.7 1.0
C B:ASP205 4.6 0.4 1.0
NZ B:LYS177 4.7 0.9 1.0
CG B:GLU206 4.7 0.9 1.0
OG1 B:THR175 4.8 0.0 1.0
O6 B:CAP1001 4.8 0.1 1.0
CB B:GLU206 4.8 1.0 1.0
CD2 B:HIS295 4.8 0.6 1.0
C4 B:CAP1001 4.8 0.3 1.0
CE B:LYS179 4.8 0.5 1.0
CB B:THR175 4.9 0.3 1.0
C1 B:CAP1001 4.9 0.1 1.0

Magnesium binding site 3 out of 8 in 5nv3

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Magnesium binding site 3 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:0.7
occ:1.00
 OQ2 C:KCX203 2.2 0.8 1.0
OE1 C:GLU206 2.3 0.4 1.0
O3 C:CAP1001 2.6 0.2 1.0
O2 C:CAP1001 2.7 0.1 1.0
O7 C:CAP1001 2.9 0.3 1.0
OD2 C:ASP205 2.9 0.8 1.0
CG C:ASP205 3.4 0.6 1.0
CX C:KCX203 3.4 0.9 1.0
CD C:GLU206 3.4 0.1 1.0
C2 C:CAP1001 3.5 0.9 1.0
C3 C:CAP1001 3.6 0.3 1.0
C C:CAP1001 3.6 0.2 1.0
NZ C:LYS179 3.7 0.9 1.0
OD1 C:ASP205 3.7 0.3 1.0
OE2 C:GLU206 3.9 0.7 1.0
CG2 C:THR175 3.9 0.5 1.0
OQ1 C:KCX203 3.9 0.7 1.0
NE2 C:HIS295 4.0 0.3 1.0
N C:GLU206 4.0 0.9 1.0
CA C:ASP205 4.1 0.1 1.0
CB C:ASP205 4.3 0.1 1.0
NZ C:KCX203 4.4 1.0 1.0
ND2 G:ASN125 4.5 0.4 1.0
CE1 C:HIS295 4.6 0.1 1.0
C C:ASP205 4.6 0.5 1.0
CG C:GLU206 4.7 0.9 1.0
NZ C:LYS177 4.7 0.5 1.0
OG1 C:THR175 4.8 0.1 1.0
CD2 C:HIS295 4.8 0.7 1.0
CB C:GLU206 4.8 0.4 1.0
C4 C:CAP1001 4.8 0.5 1.0
O6 C:CAP1001 4.8 0.9 1.0
CE C:LYS179 4.8 0.8 1.0
CB C:THR175 4.9 0.7 1.0
C1 C:CAP1001 4.9 0.7 1.0

Magnesium binding site 4 out of 8 in 5nv3

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Magnesium binding site 4 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:0.5
occ:1.00
 OQ2 D:KCX203 2.2 0.4 1.0
OE1 D:GLU206 2.4 0.3 1.0
O3 D:CAP1001 2.6 0.8 1.0
O2 D:CAP1001 2.7 0.4 1.0
O7 D:CAP1001 2.8 0.2 1.0
OD2 D:ASP205 2.9 0.1 1.0
CG D:ASP205 3.4 0.9 1.0
CX D:KCX203 3.4 0.5 1.0
CD D:GLU206 3.4 0.4 1.0
C2 D:CAP1001 3.5 0.3 1.0
C D:CAP1001 3.6 0.9 1.0
C3 D:CAP1001 3.6 0.1 1.0
NZ D:LYS179 3.6 0.8 1.0
OD1 D:ASP205 3.7 0.6 1.0
OQ1 D:KCX203 3.9 0.1 1.0
OE2 D:GLU206 3.9 0.2 1.0
CG2 D:THR175 3.9 0.7 1.0
NE2 D:HIS295 4.0 0.4 1.0
N D:GLU206 4.0 0.1 1.0
CA D:ASP205 4.1 0.5 1.0
CB D:ASP205 4.3 0.5 1.0
NZ D:KCX203 4.4 0.1 1.0
ND2 H:ASN125 4.5 0.6 1.0
CE1 D:HIS295 4.6 0.6 1.0
C D:ASP205 4.6 0.5 1.0
NZ D:LYS177 4.6 0.5 1.0
CG D:GLU206 4.7 0.0 1.0
OG1 D:THR175 4.8 0.9 1.0
CD2 D:HIS295 4.8 0.1 1.0
O6 D:CAP1001 4.8 0.7 1.0
CB D:GLU206 4.8 0.1 1.0
C4 D:CAP1001 4.8 0.4 1.0
CE D:LYS179 4.8 0.4 1.0
CB D:THR175 4.9 0.0 1.0
C1 D:CAP1001 4.9 0.9 1.0

Magnesium binding site 5 out of 8 in 5nv3

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Magnesium binding site 5 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:0.1
occ:1.00
 OQ1 E:KCX203 2.2 0.7 1.0
OE1 E:GLU206 2.3 0.8 1.0
O3 E:CAP1001 2.6 1.0 1.0
O2 E:CAP1001 2.7 0.5 1.0
O6 E:CAP1001 2.8 0.7 1.0
OD2 E:ASP205 2.9 0.5 1.0
CG E:ASP205 3.4 1.0 1.0
CX E:KCX203 3.4 0.3 1.0
CD E:GLU206 3.4 0.5 1.0
C2 E:CAP1001 3.5 0.9 1.0
C E:CAP1001 3.6 0.8 1.0
C3 E:CAP1001 3.6 0.2 1.0
NZ E:LYS179 3.7 0.1 1.0
OD1 E:ASP205 3.7 0.4 1.0
OQ2 E:KCX203 3.8 0.2 1.0
OE2 E:GLU206 3.9 0.5 1.0
CG2 E:THR175 3.9 0.4 1.0
NE2 E:HIS295 4.0 0.7 1.0
N E:GLU206 4.0 0.8 1.0
CA E:ASP205 4.2 0.7 1.0
CB E:ASP205 4.3 0.8 1.0
NZ E:KCX203 4.4 0.5 1.0
ND2 A:ASN125 4.5 0.7 1.0
CE1 E:HIS295 4.6 0.4 1.0
C E:ASP205 4.6 0.7 1.0
CG E:GLU206 4.7 0.4 1.0
NZ E:LYS177 4.7 0.4 1.0
OG1 E:THR175 4.8 0.2 1.0
CB E:GLU206 4.8 0.4 1.0
CD2 E:HIS295 4.8 0.4 1.0
C4 E:CAP1001 4.8 0.3 1.0
O7 E:CAP1001 4.8 0.5 1.0
CE E:LYS179 4.8 0.7 1.0
CB E:THR175 4.9 0.2 1.0
C1 E:CAP1001 4.9 0.5 1.0

Magnesium binding site 6 out of 8 in 5nv3

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Magnesium binding site 6 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1002

b:0.6
occ:1.00
 OQ1 F:KCX203 2.2 0.1 1.0
OE1 F:GLU206 2.4 0.7 1.0
O3 F:CAP1001 2.6 0.3 1.0
O6 F:CAP1001 2.8 0.4 1.0
O2 F:CAP1001 2.8 1.0 1.0
OD2 F:ASP205 2.9 0.8 1.0
CG F:ASP205 3.4 0.5 1.0
CX F:KCX203 3.4 0.2 1.0
CD F:GLU206 3.4 0.2 1.0
C2 F:CAP1001 3.5 0.9 1.0
C F:CAP1001 3.5 0.0 1.0
C3 F:CAP1001 3.6 0.8 1.0
NZ F:LYS179 3.7 0.7 1.0
OD1 F:ASP205 3.7 0.1 1.0
OQ2 F:KCX203 3.9 0.7 1.0
OE2 F:GLU206 3.9 0.3 1.0
CG2 F:THR175 3.9 0.2 1.0
NE2 F:HIS295 4.0 0.0 1.0
N F:GLU206 4.0 0.1 1.0
CA F:ASP205 4.1 0.2 1.0
CB F:ASP205 4.3 0.8 1.0
NZ F:KCX203 4.4 0.7 1.0
ND2 B:ASN125 4.5 0.4 1.0
CE1 F:HIS295 4.6 0.7 1.0
C F:ASP205 4.6 0.7 1.0
CG F:GLU206 4.7 0.0 1.0
NZ F:LYS177 4.7 0.5 1.0
O7 F:CAP1001 4.8 0.4 1.0
OG1 F:THR175 4.8 0.3 1.0
CB F:GLU206 4.8 0.9 1.0
CD2 F:HIS295 4.8 0.9 1.0
C4 F:CAP1001 4.8 0.7 1.0
CE F:LYS179 4.9 0.3 1.0
CB F:THR175 4.9 0.9 1.0
C1 F:CAP1001 4.9 0.1 1.0

Magnesium binding site 7 out of 8 in 5nv3

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Magnesium binding site 7 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1002

b:0.2
occ:1.00
 OQ1 G:KCX203 2.2 0.9 1.0
OE1 G:GLU206 2.3 0.9 1.0
O3 G:CAP1001 2.6 0.0 1.0
O2 G:CAP1001 2.7 0.1 1.0
O6 G:CAP1001 2.9 0.3 1.0
OD2 G:ASP205 2.9 0.2 1.0
CG G:ASP205 3.4 0.9 1.0
CX G:KCX203 3.4 0.7 1.0
CD G:GLU206 3.4 0.8 1.0
C2 G:CAP1001 3.5 0.4 1.0
C G:CAP1001 3.6 0.1 1.0
C3 G:CAP1001 3.6 0.8 1.0
NZ G:LYS179 3.7 0.5 1.0
OD1 G:ASP205 3.7 0.4 1.0
OQ2 G:KCX203 3.8 0.1 1.0
OE2 G:GLU206 3.9 0.9 1.0
CG2 G:THR175 3.9 0.5 1.0
NE2 G:HIS295 4.0 0.2 1.0
N G:GLU206 4.0 0.3 1.0
CA G:ASP205 4.1 0.4 1.0
CB G:ASP205 4.3 0.1 1.0
NZ G:KCX203 4.4 0.8 1.0
ND2 C:ASN125 4.5 0.5 1.0
CE1 G:HIS295 4.6 0.4 1.0
C G:ASP205 4.6 0.5 1.0
CG G:GLU206 4.7 0.4 1.0
NZ G:LYS177 4.7 0.7 1.0
OG1 G:THR175 4.8 1.0 1.0
CD2 G:HIS295 4.8 0.2 1.0
CB G:GLU206 4.8 0.6 1.0
C4 G:CAP1001 4.8 0.8 1.0
O7 G:CAP1001 4.8 0.6 1.0
CE G:LYS179 4.9 0.0 1.0
CB G:THR175 4.9 0.9 1.0
C1 G:CAP1001 4.9 0.2 1.0

Magnesium binding site 8 out of 8 in 5nv3

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Magnesium binding site 8 out of 8 in the Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Rubisco From Rhodobacter Sphaeroides in Complex with Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1002

b:0.7
occ:1.00
 OQ1 H:KCX203 2.2 0.6 1.0
OE1 H:GLU206 2.3 0.2 1.0
O3 H:CAP1001 2.6 0.6 1.0
O6 H:CAP1001 2.8 0.8 1.0
O2 H:CAP1001 2.8 0.8 1.0
OD2 H:ASP205 2.9 0.6 1.0
CG H:ASP205 3.4 0.2 1.0
CX H:KCX203 3.4 0.3 1.0
CD H:GLU206 3.4 0.1 1.0
C2 H:CAP1001 3.5 0.1 1.0
C H:CAP1001 3.5 0.4 1.0
C3 H:CAP1001 3.6 0.5 1.0
NZ H:LYS179 3.6 0.1 1.0
OD1 H:ASP205 3.7 0.6 1.0
OQ2 H:KCX203 3.9 0.2 1.0
OE2 H:GLU206 3.9 0.0 1.0
CG2 H:THR175 3.9 0.5 1.0
NE2 H:HIS295 4.0 0.7 1.0
N H:GLU206 4.0 0.0 1.0
CA H:ASP205 4.1 0.5 1.0
CB H:ASP205 4.3 0.8 1.0
NZ H:KCX203 4.4 0.8 1.0
ND2 D:ASN125 4.5 0.1 1.0
CE1 H:HIS295 4.6 0.8 1.0
C H:ASP205 4.6 0.1 1.0
NZ H:LYS177 4.7 0.0 1.0
CG H:GLU206 4.7 0.1 1.0
O7 H:CAP1001 4.8 1.0 1.0
OG1 H:THR175 4.8 0.2 1.0
CD2 H:HIS295 4.8 0.6 1.0
CB H:GLU206 4.8 0.0 1.0
C4 H:CAP1001 4.8 0.7 1.0
CE H:LYS179 4.9 0.4 1.0
CB H:THR175 4.9 0.6 1.0
C1 H:CAP1001 4.9 0.8 1.0

Reference:

J.Y.Bhat, G.Milicic, G.Thieulin-Pardo, A.Bracher, A.Maxwell, S.Ciniawsky, O.Mueller-Cajar, J.R.Engen, F.U.Hartl, P.Wendler, M.Hayer-Hartl. Mechanism of Enzyme Repair By the Aaa(+) Chaperone Rubisco Activase. Mol. Cell V. 67 744 2017.
ISSN: ISSN 1097-4164
PubMed: 28803776
DOI: 10.1016/J.MOLCEL.2017.07.004
Page generated: Sun Sep 29 23:39:53 2024

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