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Chlorine in PDB 5mac: Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate

Enzymatic activity of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate

All present enzymatic activity of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate:
4.1.1.39;

Protein crystallography data

The structure of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate, PDB code: 5mac was solved by L.H.Gunn, K.Valegard, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.37 / 2.60
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 273.760, 273.760, 96.740, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 22.5

Other elements in 5mac:

The structure of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate (pdb code 5mac). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate, PDB code: 5mac:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5mac

Go back to Chlorine Binding Sites List in 5mac
Chlorine binding site 1 out of 5 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:49.9
occ:1.00
 N A:LEU22 3.3 58.4 1.0
CB A:LEU22 3.7 56.4 1.0
CG A:LEU22 3.7 58.6 1.0
CA A:LEU22 4.1 57.6 1.0
CG1 A:VAL20 4.1 53.4 1.0
CA A:ASP21 4.2 57.7 1.0
CD1 A:LEU22 4.2 58.4 1.0
C A:ASP21 4.2 62.1 1.0
CG1 A:VAL9 4.3 64.0 1.0
CD A:LYS23 4.3 93.7 1.0
O A:VAL20 4.5 56.2 1.0
CG2 A:VAL9 4.5 63.2 1.0
N A:LYS23 4.6 62.8 1.0
N A:ASP21 4.6 56.3 1.0
CE A:MET1 4.6 99.5 1.0
C A:VAL20 4.6 56.6 1.0
C A:LEU22 4.8 64.2 1.0
OD1 A:ASP21 4.9 63.3 1.0
CG A:LYS23 5.0 79.3 1.0

Chlorine binding site 2 out of 5 in 5mac

Go back to Chlorine Binding Sites List in 5mac
Chlorine binding site 2 out of 5 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:48.4
occ:1.00
 N B:LEU22 3.3 55.3 1.0
CB B:LEU22 3.9 51.9 1.0
CA B:ASP21 4.0 59.0 1.0
CA B:LEU22 4.1 53.5 1.0
C B:ASP21 4.2 60.9 1.0
CG B:LEU22 4.3 53.5 1.0
N B:ASP21 4.4 60.0 1.0
CE B:MET1 4.5 77.3 1.0
CG1 B:VAL20 4.5 59.2 1.0
CG2 B:VAL9 4.6 57.0 1.0
CG1 B:VAL9 4.6 56.6 1.0
N B:LYS23 4.6 57.7 1.0
CD1 B:LEU22 4.6 52.1 1.0
O B:VAL20 4.7 63.5 1.0
C B:VAL20 4.7 63.1 1.0
C B:LEU22 4.7 60.6 1.0
CG B:LYS23 4.8 57.8 1.0
OD1 B:ASP21 4.8 66.9 1.0

Chlorine binding site 3 out of 5 in 5mac

Go back to Chlorine Binding Sites List in 5mac
Chlorine binding site 3 out of 5 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:49.5
occ:1.00
 N C:LEU22 3.4 61.2 1.0
CB C:LEU22 4.0 59.5 1.0
CA C:ASP21 4.0 60.5 1.0
CG C:LEU22 4.1 62.4 1.0
C C:ASP21 4.2 65.4 1.0
CA C:LEU22 4.2 60.2 1.0
CG2 C:VAL9 4.3 68.4 1.0
CG1 C:VAL20 4.3 62.1 1.0
O C:VAL20 4.4 62.1 1.0
CD1 C:LEU22 4.4 62.4 1.0
N C:ASP21 4.4 60.5 1.0
C C:VAL20 4.6 63.2 1.0
N C:LYS23 4.6 61.0 1.0
CG1 C:VAL9 4.7 68.3 1.0
OD1 C:ASP21 4.7 64.4 1.0
C C:LEU22 4.9 64.9 1.0
CG C:LYS23 4.9 76.0 1.0

Chlorine binding site 4 out of 5 in 5mac

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Chlorine binding site 4 out of 5 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:61.7
occ:1.00
 N D:LEU22 3.5 62.6 1.0
CB D:LEU22 3.9 60.8 1.0
CG D:LEU22 4.0 65.2 1.0
CG1 D:VAL20 4.1 62.8 1.0
CA D:ASP21 4.2 63.1 1.0
CA D:LEU22 4.2 61.4 1.0
CG2 D:VAL9 4.3 66.4 1.0
C D:ASP21 4.3 66.8 1.0
CE D:LYS23 4.4 0.8 1.0
CD1 D:LEU22 4.4 65.2 1.0
O D:VAL20 4.5 62.3 1.0
CG1 D:VAL9 4.5 65.6 1.0
N D:ASP21 4.5 62.1 1.0
C D:VAL20 4.6 63.5 1.0
NZ D:LYS23 4.6 0.4 1.0
N D:LYS23 4.7 60.5 1.0
CD D:LYS23 4.7 92.0 1.0
CE D:MET1 4.9 91.7 1.0
OD1 D:ASP21 4.9 70.7 1.0
C D:LEU22 5.0 64.1 1.0
CG D:LYS23 5.0 76.6 1.0
CB D:VAL20 5.0 62.6 1.0

Chlorine binding site 5 out of 5 in 5mac

Go back to Chlorine Binding Sites List in 5mac
Chlorine binding site 5 out of 5 in the Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Decameric Methanococcoides Burtonii Rubisco Complexed with 2-Carboxyarabinitol Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl504

b:63.0
occ:1.00
 N E:LEU22 3.3 75.3 1.0
CB E:LEU22 3.9 74.8 1.0
CD2 E:LEU22 3.9 83.2 1.0
CA E:ASP21 4.0 73.0 1.0
CG1 E:VAL20 4.1 76.3 1.0
CA E:LEU22 4.1 74.9 1.0
C E:ASP21 4.2 78.1 1.0
N E:ASP21 4.4 73.0 1.0
CG E:LEU22 4.4 80.2 1.0
CG1 E:VAL9 4.4 85.1 1.0
CG2 E:VAL9 4.4 85.3 1.0
O E:VAL20 4.6 77.3 1.0
N E:LYS23 4.6 76.9 1.0
C E:VAL20 4.6 76.8 1.0
C E:LEU22 4.9 80.2 1.0
OD1 E:ASP21 4.9 77.2 1.0
CD E:LYS23 4.9 0.1 1.0

Reference:

L.H.Gunn, K.Valegard, I.Andersson. A Unique Structural Domain in Methanococcoides Burtonii Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Acts As A Small Subunit Mimic. J. Biol. Chem. V. 292 6838 2017.
ISSN: ESSN 1083-351X
PubMed: 28154188
DOI: 10.1074/JBC.M116.767145
Page generated: Fri Jul 26 12:32:09 2024

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