Atomistry » Iron » PDB 2yeq-2z4g » 2ynm
Atomistry »
  Iron »
    PDB 2yeq-2z4g »
      2ynm »

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

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 8 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 1 out of 8 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 Iron with other atoms in the Fe 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:Fe1302

b:18.9
occ:1.00
 FE1 A:SF41302 0.0 18.9 1.0
S2 A:SF41302 2.3 22.0 1.0
S3 A:SF41302 2.3 21.9 1.0
S4 A:SF41302 2.3 21.1 1.0
SG A:CYS158 2.3 23.1 1.0
FE4 A:SF41302 2.7 18.3 1.0
FE2 A:SF41302 2.7 19.7 1.0
FE3 A:SF41302 2.7 17.5 1.0
CB A:CYS158 3.0 20.3 1.0
O A:HOH2051 3.9 21.2 1.0
S1 A:SF41302 3.9 21.9 1.0
CG2 A:VAL157 4.3 28.2 1.0
CA A:CYS158 4.4 26.1 1.0
CA A:GLY126 4.4 25.3 1.0
N A:GLY126 4.5 15.8 1.0
SG A:CYS124 4.5 26.2 1.0
O A:VAL157 4.6 22.2 1.0
N A:CYS158 4.6 28.1 1.0
C A:VAL157 4.7 27.0 1.0
CG2 B:VAL157 4.8 15.0 1.0
SG B:CYS124 4.8 20.7 1.0
CE2 A:PHE161 5.0 25.5 1.0

Iron binding site 2 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 2 out of 8 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 Iron with other atoms in the Fe 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:Fe1302

b:19.7
occ:1.00
 FE2 A:SF41302 0.0 19.7 1.0
S3 A:SF41302 2.3 21.9 1.0
S1 A:SF41302 2.3 21.9 1.0
S4 A:SF41302 2.3 21.1 1.0
SG B:CYS124 2.3 20.7 1.0
FE4 A:SF41302 2.7 18.3 1.0
FE3 A:SF41302 2.7 17.5 1.0
FE1 A:SF41302 2.7 18.9 1.0
CB B:CYS124 3.5 14.7 1.0
S2 A:SF41302 3.9 22.0 1.0
CA B:CYS124 3.9 18.7 1.0
CG1 C:VAL107 4.2 20.2 1.0
N B:GLY126 4.3 15.0 1.0
O A:HOH2089 4.4 25.3 1.0
C B:CYS124 4.4 20.7 1.0
CA B:GLY126 4.5 21.8 1.0
CB A:CYS158 4.6 20.3 1.0
SG B:CYS158 4.6 19.8 1.0
O C:VAL107 4.7 28.6 1.0
N B:TYR127 4.7 23.7 1.0
N B:GLY125 4.7 17.8 1.0
SG A:CYS124 4.8 26.2 1.0
SG A:CYS158 4.8 23.1 1.0

Iron binding site 3 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 3 out of 8 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 Iron with other atoms in the Fe 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:Fe1302

b:17.5
occ:1.00
 FE3 A:SF41302 0.0 17.5 1.0
S2 A:SF41302 2.3 22.0 1.0
S4 A:SF41302 2.3 21.1 1.0
S1 A:SF41302 2.3 21.9 1.0
SG B:CYS158 2.4 19.8 1.0
FE2 A:SF41302 2.7 19.7 1.0
FE1 A:SF41302 2.7 18.9 1.0
FE4 A:SF41302 2.7 18.3 1.0
CB B:CYS158 3.0 15.7 1.0
O A:HOH2089 3.8 25.3 1.0
S3 A:SF41302 3.9 21.9 1.0
CG2 B:VAL157 4.0 15.0 1.0
CA B:GLY126 4.2 21.8 1.0
CA B:CYS158 4.4 22.2 1.0
N B:GLY126 4.4 15.0 1.0
N B:CYS158 4.6 22.7 1.0
CE2 B:PHE161 4.6 18.1 1.0
SG B:CYS124 4.6 20.7 1.0
O B:VAL157 4.7 19.6 1.0
C B:VAL157 4.7 22.5 1.0
SG A:CYS124 4.8 26.2 1.0
CG2 A:VAL157 5.0 28.2 1.0
SG A:CYS158 5.0 23.1 1.0
CD2 B:PHE161 5.0 18.5 1.0

Iron binding site 4 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 4 out of 8 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 Iron with other atoms in the Fe 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
A:Fe1302

b:18.3
occ:1.00
 FE4 A:SF41302 0.0 18.3 1.0
SG A:CYS124 2.3 26.2 1.0
S1 A:SF41302 2.3 21.9 1.0
S3 A:SF41302 2.3 21.9 1.0
S2 A:SF41302 2.3 22.0 1.0
FE2 A:SF41302 2.7 19.7 1.0
FE1 A:SF41302 2.7 18.9 1.0
FE3 A:SF41302 2.7 17.5 1.0
CB A:CYS124 3.4 24.2 1.0
CA A:CYS124 3.8 21.6 1.0
S4 A:SF41302 3.9 21.1 1.0
C A:CYS124 4.3 21.8 1.0
N A:GLY126 4.4 15.8 1.0
O D:LEU99 4.5 33.7 1.0
CB B:CYS158 4.5 15.7 1.0
N A:GLY125 4.6 19.7 1.0
SG A:CYS158 4.7 23.1 1.0
O A:HOH2051 4.7 21.2 1.0
SG B:CYS158 4.8 19.8 1.0
CG2 C:ILE108 4.8 22.6 1.0
CA A:GLY126 4.8 25.3 1.0
SG B:CYS124 4.9 20.7 1.0
O A:CYS124 4.9 24.1 1.0
N A:TYR127 4.9 23.2 1.0
CG1 C:VAL107 5.0 20.2 1.0

Iron binding site 5 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 5 out of 8 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 Iron with other atoms in the Fe 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
C:Fe1413

b:23.6
occ:1.00
 FE1 C:SF41413 0.0 23.6 1.0
S4 C:SF41413 2.3 25.5 1.0
S2 C:SF41413 2.3 22.8 1.0
S3 C:SF41413 2.3 19.5 1.0
SG C:CYS17 2.3 25.4 1.0
FE3 C:SF41413 2.7 23.0 1.0
FE2 C:SF41413 2.7 20.8 1.0
FE4 C:SF41413 2.7 20.9 1.0
CB C:CYS17 3.2 23.6 1.0
CD1 C:LEU19 3.9 28.0 1.0
S1 C:SF41413 3.9 26.6 1.0
CG C:LEU19 4.2 25.6 1.0
N C:GLY136 4.2 26.9 1.0
CD2 C:LEU45 4.3 23.1 1.0
OD1 D:ASP36 4.3 23.9 0.5
O C:HOH2008 4.5 18.9 1.0
CA C:CYS17 4.7 23.2 1.0
SG C:CYS103 4.7 23.0 1.0
CA C:GLY136 4.7 23.8 1.0
CB C:LEU19 4.8 21.2 1.0
O C:GLY134 4.8 25.1 1.0
SG C:CYS42 4.8 19.6 1.0
OD1 D:ASP36 5.0 23.0 0.5

Iron binding site 6 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 6 out of 8 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 Iron with other atoms in the Fe 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
C:Fe1413

b:20.8
occ:1.00
 FE2 C:SF41413 0.0 20.8 1.0
S3 C:SF41413 2.3 19.5 1.0
SG C:CYS103 2.3 23.0 1.0
S1 C:SF41413 2.3 26.6 1.0
S4 C:SF41413 2.3 25.5 1.0
FE3 C:SF41413 2.7 23.0 1.0
FE4 C:SF41413 2.7 20.9 1.0
FE1 C:SF41413 2.7 23.6 1.0
CB C:CYS103 3.2 21.2 1.0
N C:CYS103 3.8 21.3 1.0
N C:GLY136 3.8 26.9 1.0
S2 C:SF41413 3.9 22.8 1.0
CG D:PRO33 4.0 22.2 1.0
OD1 D:ASP36 4.0 23.9 0.5
CA C:CYS103 4.1 20.4 1.0
CA C:GLY136 4.4 23.8 1.0
OG1 D:THR96 4.5 23.1 1.0
CB D:PRO33 4.6 21.4 1.0
CD C:PRO104 4.7 19.5 1.0
SG C:CYS42 4.8 19.6 1.0
SG C:CYS17 4.8 25.4 1.0
C C:SER135 4.8 29.9 1.0
CA C:SER135 4.8 27.7 1.0
CB C:CYS17 4.9 23.6 1.0
O D:GLN34 4.9 28.9 1.0
OD1 D:ASP36 4.9 23.0 0.5
C C:SER102 4.9 22.6 1.0
O C:HOH2100 5.0 17.8 1.0

Iron binding site 7 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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:Fe1413

b:23.0
occ:1.00
 FE3 C:SF41413 0.0 23.0 1.0
OD1 D:ASP36 2.0 23.9 0.5
S2 C:SF41413 2.3 22.8 1.0
S4 C:SF41413 2.3 25.5 1.0
S1 C:SF41413 2.3 26.6 1.0
OD1 D:ASP36 2.5 23.0 0.5
FE2 C:SF41413 2.7 20.8 1.0
FE1 C:SF41413 2.7 23.6 1.0
FE4 C:SF41413 2.7 20.9 1.0
CG D:ASP36 3.1 24.4 0.5
CG D:ASP36 3.3 24.6 0.5
OD2 D:ASP36 3.7 25.4 0.5
OD2 D:ASP36 3.7 25.2 0.5
S3 C:SF41413 3.9 19.5 1.0
CG2 C:THR41 4.0 17.8 1.0
CB D:ASP36 4.3 26.1 0.5
CA D:ASP36 4.3 27.3 0.5
N D:ASP36 4.3 26.4 1.0
CA D:ASP36 4.3 27.4 0.5
CB D:ASP36 4.4 26.4 0.5
O C:HOH2100 4.4 17.8 1.0
CG D:PRO33 4.5 22.2 1.0
C D:GLY35 4.6 27.0 1.0
SG C:CYS17 4.7 25.4 1.0
CB C:THR41 4.8 18.6 1.0
SG C:CYS103 4.8 23.0 1.0
SG C:CYS42 4.8 19.6 1.0
O D:GLY35 4.8 26.5 1.0

Iron binding site 8 out of 8 in 2ynm

Go back to Iron Binding Sites List in 2ynm
Iron binding site 8 out of 8 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 Iron with other atoms in the Fe binding site number 8 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:Fe1413

b:20.9
occ:1.00
 FE4 C:SF41413 0.0 20.9 1.0
S1 C:SF41413 2.3 26.6 1.0
S2 C:SF41413 2.3 22.8 1.0
S3 C:SF41413 2.3 19.5 1.0
SG C:CYS42 2.3 19.6 1.0
FE2 C:SF41413 2.7 20.8 1.0
FE3 C:SF41413 2.7 23.0 1.0
FE1 C:SF41413 2.7 23.6 1.0
CB C:CYS42 3.5 24.4 1.0
CA C:CYS42 3.8 21.4 1.0
CD1 C:LEU19 3.9 28.0 1.0
S4 C:SF41413 3.9 25.5 1.0
N C:CYS42 4.0 20.0 1.0
CB C:SER102 4.3 21.9 1.0
CD C:PRO104 4.6 19.5 1.0
N C:CYS103 4.6 21.3 1.0
OD1 D:ASP36 4.7 23.9 0.5
C C:THR41 4.7 20.6 1.0
SG C:CYS103 4.8 23.0 1.0
SG C:CYS17 4.9 25.4 1.0
CG2 C:THR41 4.9 17.8 1.0
CB C:THR41 4.9 18.6 1.0
CG C:LEU19 4.9 25.6 1.0
OD1 D:ASP36 4.9 23.0 0.5
OG C:SER39 5.0 22.1 1.0
CB C:CYS103 5.0 21.2 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: Sun Aug 4 05:40:35 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy