Atomistry » Fluorine » PDB 2y1x-2z5z » 2ynm
Atomistry »
  Fluorine »
    PDB 2y1x-2z5z »
      2ynm »

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: Mon Jul 14 15:02:14 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy