Atomistry » Magnesium » PDB 2ynj-2z4w » 2ynm
Atomistry »
  Magnesium »
    PDB 2ynj-2z4w »
      2ynm »

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: Wed Aug 14 07:38:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy