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Magnesium 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:

Fluorine (F) 6 atoms
Aluminium (Al) 2 atoms
Potassium (K) 1 atom
Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2ynm

Go back to Magnesium Binding Sites List in 2ynm
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg1301

b:26.1
occ:1.00
 F1 A:AF31299 1.9 27.1 1.0
OG A:SER43 2.0 25.5 1.0
O A:HOH2008 2.1 18.6 1.0
O A:HOH2009 2.1 26.5 1.0
O A:HOH2010 2.1 29.7 1.0
O3B A:ADP1300 2.2 20.7 1.0
CB A:SER43 3.0 26.8 1.0
PB A:ADP1300 3.4 25.7 1.0
AL A:AF31299 3.5 32.0 1.0
N A:SER43 3.7 26.7 1.0
O2B A:ADP1300 3.7 31.3 1.0
OD2 A:ASP151 3.8 33.0 1.0
CA A:SER43 3.9 28.0 1.0
OD1 A:ASP70 3.9 33.6 1.0
O A:HOH2016 4.1 29.1 1.0
OD1 A:ASP151 4.2 31.6 1.0
O2A A:ADP1300 4.2 32.8 1.0
OD2 A:ASP66 4.2 27.0 1.0
NZ A:LYS68 4.4 24.4 1.0
CG A:ASP151 4.4 31.5 1.0
O1B A:ADP1300 4.4 21.5 1.0
O3A A:ADP1300 4.5 33.7 1.0
O1A A:ADP1300 4.5 23.6 1.0
F3 A:AF31299 4.5 39.0 1.0
PA A:ADP1300 4.6 28.7 1.0
CB A:LYS42 4.6 16.8 1.0
C A:LYS42 4.7 24.1 1.0
F2 A:AF31299 4.7 17.8 1.0
O A:HOH2019 4.8 32.5 1.0
CG A:ASP70 4.9 35.8 1.0
CE A:LYS42 4.9 16.8 1.0
O A:VAL152 4.9 33.5 1.0
NZ B:LYS37 5.0 25.3 1.0

Magnesium binding site 2 out of 3 in 2ynm

Go back to Magnesium Binding Sites List in 2ynm
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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
B:Mg1297

b:34.2
occ:1.00
 F2 B:AF31298 1.9 29.1 1.0
OG B:SER43 2.0 28.6 1.0
O B:HOH2004 2.0 19.0 1.0
O A:HOH2003 2.1 30.1 1.0
O B:HOH2005 2.1 37.3 1.0
O3B B:ADP1299 2.1 26.4 1.0
CB B:SER43 3.1 27.5 1.0
PB B:ADP1299 3.3 27.0 1.0
O1B B:ADP1299 3.5 29.9 1.0
AL B:AF31298 3.6 44.1 1.0
N B:SER43 3.7 26.2 1.0
CA B:SER43 3.9 29.1 1.0
OD2 B:ASP151 4.0 33.8 1.0
O B:HOH2015 4.1 35.0 1.0
OD1 B:ASP70 4.1 37.8 1.0
O1A B:ADP1299 4.2 20.4 1.0
O2B B:ADP1299 4.3 25.9 1.0
OD1 B:ASP151 4.3 30.5 1.0
OD2 B:ASP66 4.3 22.1 1.0
O3A B:ADP1299 4.4 20.9 1.0
O2A B:ADP1299 4.4 26.8 1.0
F1 B:AF31298 4.5 25.0 1.0
PA B:ADP1299 4.5 24.4 1.0
CG B:ASP151 4.5 32.5 1.0
CB B:LYS42 4.6 23.9 1.0
C B:LYS42 4.7 26.3 1.0
NZ B:LYS68 4.7 24.2 1.0
NZ A:LYS37 4.8 27.2 1.0
F3 B:AF31298 4.8 27.4 1.0
CG B:ASP70 4.8 37.1 1.0
O B:VAL152 4.9 32.2 1.0
CE B:LYS42 4.9 19.0 1.0
OD2 B:ASP70 5.0 37.5 1.0

Magnesium binding site 3 out of 3 in 2ynm

Go back to Magnesium Binding Sites List in 2ynm
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg 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
C:Mg1414

b:24.0
occ:0.94
 MG C:PMR1414 0.0 24.0 0.9
ND C:PMR1414 2.0 26.0 0.9
O C:HOH2019 2.0 14.9 0.9
NB C:PMR1414 2.1 20.4 0.9
NA C:PMR1414 2.1 24.0 0.9
NC C:PMR1414 2.1 18.2 0.9
C4D C:PMR1414 3.0 25.6 0.9
C4A C:PMR1414 3.1 25.4 0.9
C1C C:PMR1414 3.1 14.9 0.9
C4B C:PMR1414 3.1 22.3 0.9
C1B C:PMR1414 3.1 22.1 0.9
C4C C:PMR1414 3.1 18.8 0.9
C1A C:PMR1414 3.1 22.3 0.9
C1D C:PMR1414 3.1 23.3 0.9
CHB C:PMR1414 3.4 23.5 0.9
CHC C:PMR1414 3.4 18.3 0.9
CHD C:PMR1414 3.5 18.5 0.9
CHA C:PMR1414 3.6 23.0 0.9
CE C:MET363 3.7 52.0 1.0
O C:HOH2102 4.2 30.5 0.9
C3D C:PMR1414 4.2 23.3 0.9
SD C:MET363 4.3 49.0 1.0
C3B C:PMR1414 4.4 21.6 0.9
O C:ALA49 4.4 24.5 1.0
C2C C:PMR1414 4.4 20.4 0.9
C2D C:PMR1414 4.4 22.0 0.9
C3A C:PMR1414 4.4 26.3 0.9
C2B C:PMR1414 4.4 21.5 0.9
C3C C:PMR1414 4.4 17.6 0.9
C2A C:PMR1414 4.4 25.1 0.9
CA C:ALA49 4.8 20.8 1.0
CD2 D:LEU41 4.9 30.6 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 Dec 14 07:49:20 2020

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