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Fluorine in PDB 2ynm: Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A

Enzymatic activity of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A

All present enzymatic activity of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A:
1.3.7.7;

Protein crystallography data

The structure of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A, PDB code: 2ynm was solved by J.Krausze, C.Lange, D.W.Heinz, J.Moser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.510 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 308.400, 74.110, 74.230, 90.00, 91.24, 90.00
R / Rfree (%) 19.89 / 23.31

Other elements in 2ynm:

The structure of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Aluminium (Al) 2 atoms
Potassium (K) 1 atom
Iron (Fe) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A (pdb code 2ynm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A, PDB code: 2ynm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2ynm

Go back to Fluorine Binding Sites List in 2ynm
Fluorine binding site 1 out of 6 in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1299

b:27.1
occ:1.00
 F1 A:AF31299 0.0 27.1 1.0
AL A:AF31299 1.8 32.0 1.0
MG A:MG1301 1.9 26.1 1.0
O A:HOH2009 2.7 26.5 1.0
O A:HOH2008 2.7 18.6 1.0
O A:HOH2010 2.9 29.7 1.0
O3B A:ADP1300 2.9 20.7 1.0
O A:HOH2019 3.0 32.5 1.0
O2B A:ADP1300 3.0 31.3 1.0
F3 A:AF31299 3.1 39.0 1.0
F2 A:AF31299 3.1 17.8 1.0
OD2 A:ASP66 3.2 27.0 1.0
PB A:ADP1300 3.4 25.7 1.0
NZ A:LYS68 3.5 24.4 1.0
OG A:SER43 3.8 25.5 1.0
CA A:LEU153 4.2 28.2 1.0
O1B A:ADP1300 4.2 21.5 1.0
CE A:LYS42 4.2 16.8 1.0
O A:HOH2006 4.4 35.1 1.0
CG A:ASP66 4.4 27.9 1.0
NZ B:LYS37 4.5 25.3 1.0
OD1 A:ASP70 4.5 33.6 1.0
NZ A:LYS42 4.5 17.2 1.0
O A:VAL152 4.6 33.5 1.0
CE A:LYS68 4.7 23.8 1.0
CB A:LEU153 4.7 27.8 1.0
O2A A:ADP1300 4.7 32.8 1.0
O3A A:ADP1300 4.8 33.7 1.0
O A:HOH2016 4.8 29.1 1.0
N A:GLY154 4.8 32.3 1.0
C A:LEU153 4.9 31.1 1.0
CB A:SER43 4.9 26.8 1.0
N A:LEU153 4.9 26.1 1.0

Fluorine binding site 2 out of 6 in 2ynm

Go back to Fluorine Binding Sites List in 2ynm
Fluorine binding site 2 out of 6 in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1299

b:17.8
occ:1.00
 F2 A:AF31299 0.0 17.8 1.0
AL A:AF31299 1.8 32.0 1.0
O A:HOH2006 2.5 35.1 1.0
NZ A:LYS42 2.8 17.2 1.0
O2B A:ADP1300 3.0 31.3 1.0
O A:HOH2019 3.1 32.5 1.0
F1 A:AF31299 3.1 27.1 1.0
F3 A:AF31299 3.1 39.0 1.0
N A:GLY154 3.1 32.3 1.0
N A:GLY39 3.2 24.8 1.0
CA A:GLY38 3.2 22.0 1.0
CE A:LYS42 3.3 16.8 1.0
CA A:GLY154 3.5 31.9 1.0
O1B A:ADP1300 3.6 21.5 1.0
PB A:ADP1300 3.7 25.7 1.0
C A:GLY38 3.7 21.8 1.0
C A:LEU153 3.9 31.1 1.0
O A:HOH2047 4.0 24.6 1.0
N A:GLY38 4.3 22.1 1.0
CA A:LEU153 4.3 28.2 1.0
OD2 B:ASP155 4.3 24.8 1.0
O3B A:ADP1300 4.3 20.7 1.0
O A:LYS37 4.3 20.8 1.0
CA A:GLY39 4.4 25.2 1.0
MG A:MG1301 4.7 26.1 1.0
C A:LYS37 4.7 20.9 1.0
OD1 B:ASP155 4.7 28.4 1.0
CB A:LEU153 4.8 27.8 1.0
CD A:LYS42 4.8 25.2 1.0
O B:HOH2003 4.8 25.3 1.0
O A:HOH2008 4.8 18.6 1.0
O A:LEU153 4.8 35.3 1.0
C A:GLY154 4.9 30.5 1.0
O A:GLY38 5.0 21.2 1.0
CG B:ASP155 5.0 28.1 1.0

Fluorine binding site 3 out of 6 in 2ynm

Go back to Fluorine Binding Sites List in 2ynm
Fluorine binding site 3 out of 6 in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1299

b:39.0
occ:1.00
 F3 A:AF31299 0.0 39.0 1.0
AL A:AF31299 1.8 32.0 1.0
O A:HOH2006 2.1 35.1 1.0
NZ B:LYS37 2.7 25.3 1.0
O2B A:ADP1300 2.8 31.3 1.0
O B:HOH2003 2.9 25.3 1.0
NZ A:LYS68 2.9 24.4 1.0
O A:HOH2019 2.9 32.5 1.0
F1 A:AF31299 3.1 27.1 1.0
F2 A:AF31299 3.1 17.8 1.0
CE A:LYS68 3.1 23.8 1.0
CE B:LYS37 3.3 17.7 1.0
CD B:LYS37 3.5 18.4 1.0
O A:HOH2010 4.0 29.7 1.0
OD1 B:ASP155 4.1 28.4 1.0
O A:HOH2022 4.2 28.9 1.0
PB A:ADP1300 4.2 25.7 1.0
N A:GLY39 4.3 24.8 1.0
OD2 A:ASP66 4.4 27.0 1.0
CD A:LYS68 4.5 23.2 1.0
MG A:MG1301 4.5 26.1 1.0
N B:GLY38 4.5 22.1 1.0
O3B A:ADP1300 4.7 20.7 1.0
O2A A:ADP1300 4.7 32.8 1.0
CA A:GLY39 4.7 25.2 1.0
CG B:LYS37 4.8 22.4 1.0
O A:HOH2047 5.0 24.6 1.0
CA B:GLY38 5.0 21.7 1.0

Fluorine binding site 4 out of 6 in 2ynm

Go back to Fluorine Binding Sites List in 2ynm
Fluorine binding site 4 out of 6 in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1298

b:25.0
occ:1.00
 F1 B:AF31298 0.0 25.0 1.0
AL B:AF31298 1.8 44.1 1.0
O1B B:ADP1299 2.7 29.9 1.0
O A:HOH2046 2.7 32.9 1.0
O A:HOH2005 2.8 29.0 1.0
NZ A:LYS37 2.9 27.2 1.0
F2 B:AF31298 3.1 29.1 1.0
F3 B:AF31298 3.1 27.4 1.0
NZ B:LYS68 3.3 24.2 1.0
CE A:LYS37 3.3 26.0 1.0
CD A:LYS37 3.6 26.3 1.0
CE B:LYS68 3.6 22.8 1.0
O A:HOH2003 4.0 30.1 1.0
OD1 A:ASP155 4.1 33.3 1.0
PB B:ADP1299 4.1 27.0 1.0
N B:GLY39 4.2 24.7 1.0
O A:HOH2004 4.4 27.2 1.0
N A:GLY38 4.5 22.1 1.0
OD2 B:ASP66 4.5 22.1 1.0
MG B:MG1297 4.5 34.2 1.0
CA B:GLY39 4.6 26.5 1.0
CG A:LYS37 4.6 26.1 1.0
O3B B:ADP1299 4.7 26.4 1.0
O2B B:ADP1299 4.8 25.9 1.0
O1A B:ADP1299 4.8 20.4 1.0
CA A:GLY38 4.9 22.0 1.0
O A:HOH2047 4.9 24.6 1.0

Fluorine binding site 5 out of 6 in 2ynm

Go back to Fluorine Binding Sites List in 2ynm
Fluorine binding site 5 out of 6 in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1298

b:29.1
occ:1.00
 F2 B:AF31298 0.0 29.1 1.0
AL B:AF31298 1.8 44.1 1.0
MG B:MG1297 1.9 34.2 1.0
O B:HOH2004 2.7 19.0 1.0
O B:HOH2005 2.8 37.3 1.0
O3B B:ADP1299 2.8 26.4 1.0
O1B B:ADP1299 2.8 29.9 1.0
O A:HOH2003 2.9 30.1 1.0
F1 B:AF31298 3.1 25.0 1.0
F3 B:AF31298 3.1 27.4 1.0
PB B:ADP1299 3.1 27.0 1.0
O A:HOH2046 3.3 32.9 1.0
OD2 B:ASP66 3.5 22.1 1.0
O2B B:ADP1299 3.8 25.9 1.0
OG B:SER43 3.9 28.6 1.0
CE B:LYS42 4.0 19.0 1.0
NZ B:LYS68 4.1 24.2 1.0
CA B:LEU153 4.1 29.9 1.0
NZ B:LYS42 4.4 20.3 1.0
NZ A:LYS37 4.4 27.2 1.0
O B:VAL152 4.4 32.2 1.0
O3A B:ADP1299 4.6 20.9 1.0
N B:GLY154 4.6 30.0 1.0
C B:LEU153 4.7 27.8 1.0
CG B:ASP66 4.7 23.4 1.0
CB B:LEU153 4.8 30.6 1.0
O1A B:ADP1299 4.8 20.4 1.0
CB B:LYS42 4.9 23.9 1.0
OD1 B:ASP70 4.9 37.8 1.0
N B:LEU153 4.9 29.5 1.0
O B:HOH2015 4.9 35.0 1.0
CB B:SER43 5.0 27.5 1.0
C B:VAL152 5.0 31.3 1.0

Fluorine binding site 6 out of 6 in 2ynm

Go back to Fluorine Binding Sites List in 2ynm
Fluorine binding site 6 out of 6 in the Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the ADPXALF3-Stabilized Transition State of the Nitrogenase-Like Dark-Operative Protochlorophyllide Oxidoreductase Complex From Prochlorococcus Marinus with Its Substrate Protochlorophyllide A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1298

b:27.4
occ:1.00
 F3 B:AF31298 0.0 27.4 1.0
AL B:AF31298 1.8 44.1 1.0
NZ B:LYS42 2.5 20.3 1.0
N B:GLY39 3.0 24.7 1.0
O1B B:ADP1299 3.1 29.9 1.0
F2 B:AF31298 3.1 29.1 1.0
N B:GLY154 3.1 30.0 1.0
F1 B:AF31298 3.1 25.0 1.0
CA B:GLY38 3.2 21.7 1.0
CE B:LYS42 3.2 19.0 1.0
CA B:GLY154 3.3 29.1 1.0
O2B B:ADP1299 3.3 25.9 1.0
O A:HOH2046 3.5 32.9 1.0
C B:GLY38 3.6 23.2 1.0
PB B:ADP1299 3.6 27.0 1.0
C B:LEU153 3.9 27.8 1.0
O A:HOH2047 4.0 24.6 1.0
CA B:GLY39 4.1 26.5 1.0
O B:LYS37 4.2 27.6 1.0
N B:GLY38 4.2 22.1 1.0
O3B B:ADP1299 4.4 26.4 1.0
CA B:LEU153 4.4 29.9 1.0
OD2 A:ASP155 4.5 31.7 1.0
C B:LYS37 4.6 23.4 1.0
CD B:LYS42 4.7 20.8 1.0
O B:LEU153 4.7 23.8 1.0
C B:GLY154 4.7 31.4 1.0
O B:GLY38 4.8 24.1 1.0
MG B:MG1297 4.8 34.2 1.0
O A:HOH2005 4.8 29.0 1.0
OD1 A:ASP155 4.8 33.3 1.0
O3A B:ADP1299 5.0 20.9 1.0
O B:GLY36 5.0 21.8 1.0

Reference:

J.Moser, C.Lange, J.Krausze, J.Rebelein, W.Schubert, M.W.Ribbe, D.W.Heinz, D.Jahn. Structure of Adp-Aluminium Fluoride-Stabilized Protochlorophyllide Oxidoreductase Complex. Proc.Natl.Acad.Sci.Usa V. 110 2094 2013.
ISSN: ISSN 0027-8424
PubMed: 23341615
DOI: 10.1073/PNAS.1218303110
Page generated: Wed Jul 31 16:54:37 2024

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