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Magnesium in PDB 4lf2: Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium

Enzymatic activity of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium

All present enzymatic activity of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium:
4.1.1.39;

Protein crystallography data

The structure of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium, PDB code: 4lf2 was solved by S.Chan, S.Satagopan, M.R.Sawaya, D.Eisenberg, F.R.Tabita, L.J.Perry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.43 / 2.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.221, 99.777, 100.000, 67.30, 71.28, 86.63
R / Rfree (%) 20.3 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium (pdb code 4lf2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium, PDB code: 4lf2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4lf2

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Magnesium binding site 1 out of 4 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:34.5
occ:1.00
 O B:HOH828 2.2 30.1 1.0
OQ2 A:KCX192 2.4 25.3 1.0
OD1 A:ASP194 2.5 30.8 1.0
OE1 A:GLU195 2.6 24.8 1.0
ND2 B:ASN112 3.3 32.5 1.0
CG A:ASP194 3.4 42.1 1.0
CX A:KCX192 3.4 23.0 1.0
OQ1 A:KCX192 3.5 28.4 1.0
CD A:GLU195 3.6 30.4 1.0
NZ A:LYS167 3.6 61.1 1.0
OD2 A:ASP194 3.7 71.2 1.0
OE2 A:GLU195 3.8 30.1 1.0
CE A:LYS169 4.0 55.1 1.0
NZ A:LYS169 4.0 76.6 1.0
CD1 A:ILE165 4.1 32.6 1.0
NE2 A:HIS288 4.3 19.1 1.0
O A:HOH751 4.4 42.9 1.0
CG B:ASN112 4.5 28.6 1.0
OE2 B:GLU49 4.5 43.1 1.0
O2 A:SO4603 4.6 29.9 1.0
NZ A:KCX192 4.6 26.9 1.0
N A:GLU195 4.7 16.9 1.0
CB A:ASP194 4.7 15.6 1.0
CG2 A:ILE165 4.8 17.7 1.0
CE1 A:HIS288 4.9 22.1 1.0
CA A:ASP194 4.9 21.9 1.0
CE A:LYS167 4.9 43.6 1.0
CG A:GLU195 4.9 29.6 1.0

Magnesium binding site 2 out of 4 in 4lf2

Go back to Magnesium Binding Sites List in 4lf2
Magnesium binding site 2 out of 4 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:62.6
occ:1.00
 O A:HOH938 2.0 54.3 1.0
O A:HOH939 2.0 39.9 1.0
OQ2 B:KCX192 2.7 48.1 1.0
OE1 B:GLU195 3.2 29.0 1.0
OD1 B:ASP194 3.3 52.3 1.0
OQ1 B:KCX192 3.3 32.4 1.0
ND2 A:ASN112 3.4 37.0 1.0
CX B:KCX192 3.5 25.2 1.0
NZ B:LYS167 3.6 38.3 1.0
CD1 B:ILE165 3.7 32.2 1.0
CG B:ASP194 4.0 41.9 1.0
O2 B:SO4603 4.1 56.4 1.0
OD2 B:ASP194 4.2 41.2 1.0
CD B:GLU195 4.2 26.8 1.0
NE2 B:HIS288 4.4 23.6 1.0
OE2 B:GLU195 4.4 22.4 1.0
NZ B:LYS169 4.5 46.7 1.0
CE B:LYS169 4.6 37.2 1.0
CG A:ASN112 4.6 28.9 1.0
OE2 A:GLU49 4.7 63.4 1.0
NZ B:KCX192 4.8 26.5 1.0
CE B:LYS167 4.8 28.2 1.0
OG B:SER369 4.8 26.0 1.0
CG2 B:ILE165 4.9 13.7 1.0
CG1 B:ILE165 4.9 22.8 1.0

Magnesium binding site 3 out of 4 in 4lf2

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Magnesium binding site 3 out of 4 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:52.1
occ:1.00
 O D:HOH945 2.5 48.7 1.0
OD1 C:ASP194 2.8 32.0 1.0
OE1 C:GLU195 2.9 30.7 1.0
OQ2 C:KCX192 3.0 25.4 1.0
ND2 D:ASN112 3.2 30.6 1.0
NZ C:LYS167 3.3 68.0 1.0
CG C:ASP194 3.6 45.0 1.0
NZ C:LYS169 3.6 54.3 1.0
OD2 C:ASP194 3.7 86.4 1.0
CE C:LYS169 3.7 50.5 1.0
CD C:GLU195 3.7 27.3 1.0
OE2 C:GLU195 3.7 44.3 1.0
CX C:KCX192 4.0 52.5 1.0
OQ1 C:KCX192 4.0 36.9 1.0
OE2 D:GLU49 4.2 55.9 1.0
CD1 C:ILE165 4.4 42.3 1.0
CG D:ASN112 4.4 30.7 1.0
O2 C:SO4603 4.5 79.0 1.0
CE C:LYS167 4.7 59.9 1.0
NE2 C:HIS288 4.7 24.4 1.0
CB C:ASP194 5.0 28.2 1.0

Magnesium binding site 4 out of 4 in 4lf2

Go back to Magnesium Binding Sites List in 4lf2
Magnesium binding site 4 out of 4 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with Sulfate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:44.9
occ:1.00
 O D:HOH944 1.8 43.2 1.0
O C:HOH953 2.4 40.1 1.0
OD1 D:ASP194 2.4 23.4 1.0
OQ2 D:KCX192 2.4 18.6 1.0
OE1 D:GLU195 2.5 26.4 1.0
ND2 C:ASN112 3.3 32.8 1.0
CG D:ASP194 3.4 28.6 1.0
CD D:GLU195 3.4 24.0 1.0
CX D:KCX192 3.5 27.9 1.0
OQ1 D:KCX192 3.6 24.3 1.0
OE2 D:GLU195 3.6 21.2 1.0
OD2 D:ASP194 3.7 51.7 1.0
NZ D:LYS167 3.7 33.6 1.0
CE D:LYS169 4.0 39.6 1.0
NZ D:LYS169 4.0 63.3 1.0
NE2 D:HIS288 4.2 14.7 1.0
CD1 D:ILE165 4.3 27.5 1.0
O D:HOH802 4.4 41.3 1.0
CG C:ASN112 4.5 21.9 1.0
OE2 C:GLU49 4.6 37.5 1.0
N D:GLU195 4.6 13.4 1.0
NZ D:KCX192 4.7 28.9 1.0
CB D:ASP194 4.7 15.1 1.0
O2 D:SO4603 4.7 31.3 1.0
CE1 D:HIS288 4.8 14.3 1.0
CG D:GLU195 4.8 32.1 1.0
CA D:ASP194 4.8 17.1 1.0
CG2 D:ILE165 4.9 15.5 1.0

Reference:

S.Chan, S.Satagopan, M.R.Sawaya, D.Eisenberg, F.R.Tabita, L.J.Perry. Structure-Function Studies with the Unique Hexameric Form II Rubisco From Rhodopseudomonas Palustris J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
Page generated: Sat Aug 17 04:54:22 2024

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