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Magnesium in PDB 4lf1: Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp

Enzymatic activity of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp

All present enzymatic activity of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp:
4.1.1.39;

Protein crystallography data

The structure of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp, PDB code: 4lf1 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) 71.29 / 2.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.033, 100.720, 100.690, 66.51, 108.32, 95.41
R / Rfree (%) 26.3 / 31.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp (pdb code 4lf1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp, PDB code: 4lf1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4lf1

Go back to Magnesium Binding Sites List in 4lf1
Magnesium binding site 1 out of 6 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp


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 2-Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:12.7
occ:1.00
 OD1 A:ASP194 1.9 18.3 1.0
OE1 A:GLU195 2.0 16.9 1.0
OQ2 A:KCX192 2.0 22.5 1.0
O6 A:CAP800 2.2 18.7 1.0
O2 A:CAP800 2.3 10.9 1.0
O3 A:CAP800 2.3 6.6 1.0
C2 A:CAP800 2.9 12.1 1.0
C A:CAP800 2.9 13.0 1.0
CG A:ASP194 3.0 11.2 1.0
CD A:GLU195 3.1 13.0 1.0
CX A:KCX192 3.2 11.2 1.0
C3 A:CAP800 3.2 12.1 1.0
OE2 A:GLU195 3.6 10.1 1.0
OQ1 A:KCX192 3.6 25.3 1.0
OD2 A:ASP194 3.6 11.9 1.0
N A:GLU195 3.7 11.2 1.0
NZ A:LYS169 3.8 16.1 1.0
NZ A:LYS167 3.9 8.2 1.0
ND2 B:ASN112 3.9 16.8 1.0
CA A:ASP194 4.0 11.7 1.0
CB A:ASP194 4.1 9.5 1.0
NE2 A:HIS288 4.1 11.0 1.0
O7 A:CAP800 4.2 20.2 1.0
NZ A:KCX192 4.2 17.5 1.0
CG A:GLU195 4.3 17.2 1.0
C A:ASP194 4.3 10.8 1.0
C1 A:CAP800 4.4 13.4 1.0
CG2 A:ILE165 4.4 8.8 1.0
C4 A:CAP800 4.4 15.7 1.0
CE A:LYS169 4.4 13.9 1.0
CB A:GLU195 4.4 17.9 1.0
CE1 A:HIS288 4.6 14.0 1.0
CA A:GLU195 4.7 10.4 1.0
O1 A:CAP800 4.8 10.8 1.0

Magnesium binding site 2 out of 6 in 4lf1

Go back to Magnesium Binding Sites List in 4lf1
Magnesium binding site 2 out of 6 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp


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 2-Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:33.3
occ:1.00
 OE1 B:GLU195 1.8 17.2 1.0
O6 B:CAP800 2.0 21.2 1.0
OQ2 B:KCX192 2.0 22.3 1.0
OD1 B:ASP194 2.1 18.3 1.0
O3 B:CAP800 2.4 15.7 1.0
O2 B:CAP800 2.7 4.3 1.0
C B:CAP800 2.9 13.8 1.0
CD B:GLU195 2.9 13.1 1.0
C2 B:CAP800 3.1 13.6 1.0
CX B:KCX192 3.2 11.0 1.0
CG B:ASP194 3.2 11.4 1.0
C3 B:CAP800 3.3 13.4 1.0
OE2 B:GLU195 3.4 9.4 1.0
ND2 A:ASN112 3.5 3.0 1.0
OQ1 B:KCX192 3.6 25.0 1.0
N B:GLU195 3.7 11.3 1.0
OD2 B:ASP194 3.9 12.1 1.0
NE2 B:HIS288 3.9 10.8 1.0
O7 B:CAP800 4.0 11.9 1.0
CA B:ASP194 4.1 11.5 1.0
CG B:GLU195 4.2 17.2 1.0
NZ B:LYS169 4.2 17.3 1.0
NZ B:KCX192 4.3 17.7 1.0
CB B:ASP194 4.3 9.4 1.0
CB B:GLU195 4.3 18.0 1.0
NZ B:LYS167 4.3 9.7 1.0
CE1 B:HIS288 4.4 14.2 1.0
C4 B:CAP800 4.4 14.0 1.0
C B:ASP194 4.4 10.9 1.0
CG2 B:ILE165 4.6 9.0 1.0
C1 B:CAP800 4.6 2.0 1.0
CG A:ASN112 4.6 17.9 1.0
CA B:GLU195 4.6 10.8 1.0
CE B:LYS169 4.7 11.3 1.0
C5 B:CAP800 4.8 22.8 1.0
CD2 B:HIS288 4.9 13.7 1.0
O1 B:CAP800 4.9 7.7 1.0
OD1 A:ASN112 5.0 19.4 1.0

Magnesium binding site 3 out of 6 in 4lf1

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Magnesium binding site 3 out of 6 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp


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 2-Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg801

b:33.4
occ:1.00
 OD1 C:ASP194 1.8 18.3 1.0
OQ2 C:KCX192 2.2 22.5 1.0
OE1 C:GLU195 2.4 17.1 1.0
O2 C:CAP800 2.5 7.8 1.0
O6 C:CAP800 2.5 13.2 1.0
O3 C:CAP800 2.6 13.6 1.0
CG C:ASP194 2.8 11.5 1.0
C2 C:CAP800 3.2 10.7 1.0
C C:CAP800 3.2 2.0 1.0
CX C:KCX192 3.3 10.9 1.0
CD C:GLU195 3.4 13.0 1.0
C3 C:CAP800 3.4 17.6 1.0
OD2 C:ASP194 3.4 11.9 1.0
NZ C:LYS167 3.5 7.8 1.0
OQ1 C:KCX192 3.7 25.1 1.0
OE2 C:GLU195 3.7 10.0 1.0
NZ C:LYS169 3.9 17.6 1.0
N C:GLU195 3.9 11.2 1.0
ND2 D:ASN112 3.9 9.9 1.0
CG2 C:ILE165 4.0 9.1 1.0
CB C:ASP194 4.0 9.4 1.0
CA C:ASP194 4.0 11.6 1.0
CE C:LYS169 4.3 12.7 1.0
NZ C:KCX192 4.4 17.5 1.0
O7 C:CAP800 4.4 5.2 1.0
NE2 C:HIS288 4.4 10.9 1.0
C C:ASP194 4.5 10.8 1.0
CG C:GLU195 4.7 17.3 1.0
C1 C:CAP800 4.7 2.0 1.0
C4 C:CAP800 4.8 17.1 1.0
CE C:LYS167 4.8 12.6 1.0
CB C:GLU195 4.8 18.0 1.0
O1 C:CAP800 4.9 16.2 1.0
O C:HOH966 5.0 14.5 1.0
CE1 C:HIS288 5.0 14.2 1.0

Magnesium binding site 4 out of 6 in 4lf1

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Magnesium binding site 4 out of 6 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp


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 2-Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg801

b:14.0
occ:1.00
 OD1 D:ASP194 1.8 18.3 1.0
OQ2 D:KCX192 2.2 22.6 1.0
OE1 D:GLU195 2.3 17.0 1.0
O2 D:CAP800 2.3 15.7 1.0
O6 D:CAP800 2.4 34.9 1.0
O3 D:CAP800 2.5 4.1 1.0
CG D:ASP194 2.9 11.2 1.0
C2 D:CAP800 3.1 16.1 1.0
C D:CAP800 3.1 14.2 1.0
NZ D:LYS169 3.2 17.4 1.0
CD D:GLU195 3.3 12.9 1.0
CX D:KCX192 3.3 11.2 1.0
C3 D:CAP800 3.3 15.6 1.0
OD2 D:ASP194 3.4 11.9 1.0
NZ D:LYS167 3.5 7.3 1.0
OE2 D:GLU195 3.7 10.2 1.0
OQ1 D:KCX192 3.7 25.3 1.0
ND2 C:ASN112 3.7 20.4 1.0
N D:GLU195 3.9 10.9 1.0
CB D:ASP194 4.0 9.5 1.0
CA D:ASP194 4.0 11.7 1.0
O7 D:CAP800 4.3 22.0 1.0
CG2 D:ILE165 4.3 8.8 1.0
NZ D:KCX192 4.4 17.5 1.0
C D:ASP194 4.4 10.8 1.0
NE2 D:HIS288 4.5 10.9 1.0
CE D:LYS169 4.5 12.0 1.0
C1 D:CAP800 4.5 17.8 1.0
CG D:GLU195 4.5 17.3 1.0
C4 D:CAP800 4.6 24.2 1.0
CB D:GLU195 4.7 17.8 1.0
O1 D:CAP800 4.8 17.1 1.0
CA D:GLU195 4.9 10.6 1.0
CE1 D:HIS288 4.9 14.1 1.0
CE D:LYS167 4.9 9.3 1.0

Magnesium binding site 5 out of 6 in 4lf1

Go back to Magnesium Binding Sites List in 4lf1
Magnesium binding site 5 out of 6 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg801

b:21.8
occ:1.00
 OD1 E:ASP194 1.9 18.4 1.0
OQ2 E:KCX192 2.1 22.5 1.0
OE1 E:GLU195 2.2 16.8 1.0
O3 E:CAP800 2.4 2.2 1.0
O6 E:CAP800 2.4 14.6 1.0
O2 E:CAP800 2.5 2.0 1.0
CG E:ASP194 3.0 11.4 1.0
C E:CAP800 3.1 4.5 1.0
C2 E:CAP800 3.1 5.2 1.0
CX E:KCX192 3.2 11.1 1.0
CD E:GLU195 3.2 13.0 1.0
C3 E:CAP800 3.3 7.4 1.0
OD2 E:ASP194 3.6 11.9 1.0
OQ1 E:KCX192 3.6 25.1 1.0
OE2 E:GLU195 3.7 10.0 1.0
NZ E:LYS169 3.8 14.8 1.0
N E:GLU195 3.8 11.1 1.0
ND2 F:ASN112 3.9 6.8 1.0
NZ E:LYS167 4.0 7.7 1.0
CA E:ASP194 4.0 11.5 1.0
CB E:ASP194 4.1 9.4 1.0
NE2 E:HIS288 4.2 10.9 1.0
NZ E:KCX192 4.3 17.6 1.0
CG2 E:ILE165 4.3 9.0 1.0
O7 E:CAP800 4.3 11.7 1.0
C E:ASP194 4.4 10.7 1.0
CG E:GLU195 4.5 17.3 1.0
CE E:LYS169 4.5 14.3 1.0
C1 E:CAP800 4.6 2.0 1.0
C4 E:CAP800 4.6 2.0 1.0
CB E:GLU195 4.7 17.8 1.0
CE1 E:HIS288 4.8 14.2 1.0
O1 E:CAP800 4.8 13.2 1.0
CA E:GLU195 4.9 10.7 1.0

Magnesium binding site 6 out of 6 in 4lf1

Go back to Magnesium Binding Sites List in 4lf1
Magnesium binding site 6 out of 6 in the Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Hexameric Form II Rubisco From Rhodopseudomonas Palustris, Activated and Complexed with 2-Cabp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg801

b:11.1
occ:1.00
 OQ2 F:KCX192 1.9 22.5 1.0
O6 F:CAP800 2.0 14.7 1.0
OD1 F:ASP194 2.0 18.1 1.0
O3 F:CAP800 2.2 21.8 1.0
OE1 F:GLU195 2.3 16.9 1.0
O2 F:CAP800 2.4 23.5 1.0
C F:CAP800 2.8 20.6 1.0
C2 F:CAP800 3.0 22.8 1.0
CX F:KCX192 3.0 11.2 1.0
CG F:ASP194 3.1 11.3 1.0
C3 F:CAP800 3.1 12.9 1.0
CD F:GLU195 3.4 12.9 1.0
OQ1 F:KCX192 3.4 25.2 1.0
OD2 F:ASP194 3.7 11.9 1.0
NZ F:LYS167 3.8 6.7 1.0
OE2 F:GLU195 3.8 9.8 1.0
N F:GLU195 3.9 11.2 1.0
O7 F:CAP800 4.0 29.9 1.0
CA F:ASP194 4.0 11.4 1.0
ND2 E:ASN112 4.0 5.0 1.0
NE2 F:HIS288 4.1 11.0 1.0
NZ F:KCX192 4.1 17.6 1.0
CB F:ASP194 4.1 9.4 1.0
CG2 F:ILE165 4.3 9.0 1.0
C4 F:CAP800 4.4 10.9 1.0
C1 F:CAP800 4.5 14.7 1.0
C F:ASP194 4.5 10.8 1.0
CE F:LYS169 4.6 14.9 1.0
CG F:GLU195 4.6 17.4 1.0
CB F:GLU195 4.7 17.8 1.0
CE1 F:HIS288 4.7 14.2 1.0
O1 F:CAP800 4.8 16.6 1.0
NZ F:LYS169 4.8 18.4 1.0
CA F:GLU195 4.9 10.7 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 04:54:05 2024

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