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Magnesium in PDB 9hbn: A. Vinelandii Nitrogenase Mofe Protein ANC1B

Protein crystallography data

The structure of A. Vinelandii Nitrogenase Mofe Protein ANC1B, PDB code: 9hbn was solved by F.Detemple, B.Kacar, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.83 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.083, 128.984, 209.445, 90, 90, 90
R / Rfree (%) 20.6 / 26.9

Other elements in 9hbn:

The structure of A. Vinelandii Nitrogenase Mofe Protein ANC1B also contains other interesting chemical elements:

Iron (Fe) 30 atoms
Molybdenum (Mo) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A. Vinelandii Nitrogenase Mofe Protein ANC1B (pdb code 9hbn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the A. Vinelandii Nitrogenase Mofe Protein ANC1B, PDB code: 9hbn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 9hbn

Go back to Magnesium Binding Sites List in 9hbn
Magnesium binding site 1 out of 5 in the A. Vinelandii Nitrogenase Mofe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A. Vinelandii Nitrogenase Mofe Protein ANC1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:30.6
occ:1.00
 O B:HOH703 2.2 25.4 1.0
O B:HOH760 2.2 9.6 1.0
OG1 B:THR360 2.4 19.5 1.0
O B:HOH721 2.8 16.3 1.0
OD1 C:ASP445 3.0 25.9 1.0
O C:HOH677 3.0 27.2 1.0
NZ C:LYS428 3.2 28.7 1.0
CG2 B:THR360 3.3 20.7 1.0
CB B:THR360 3.4 20.1 1.0
CG C:ASP445 3.7 24.6 1.0
O C:HOH605 3.9 28.1 1.0
CD2 C:TYR446 4.0 21.7 1.0
O C:HOH620 4.1 37.0 1.0
O C:ASP445 4.1 21.1 1.0
CE2 C:TYR446 4.1 21.1 1.0
O B:ASP357 4.2 18.4 1.0
OD2 C:ASP445 4.3 24.3 1.0
CB C:ASP445 4.4 23.6 1.0
O C:HOH617 4.5 32.5 1.0
MG C:MG503 4.5 26.6 1.0
CE C:LYS428 4.6 27.3 1.0
O B:ARG523 4.6 21.5 1.0
CA B:THR360 4.6 19.4 1.0
NE1 B:TRP361 4.6 18.6 1.0
CD1 B:TRP361 4.7 18.0 1.0
N B:THR360 4.7 18.5 1.0
C C:ASP445 4.8 21.4 1.0
CA C:ASP445 4.8 22.4 1.0

Magnesium binding site 2 out of 5 in 9hbn

Go back to Magnesium Binding Sites List in 9hbn
Magnesium binding site 2 out of 5 in the A. Vinelandii Nitrogenase Mofe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A. Vinelandii Nitrogenase Mofe Protein ANC1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:24.6
occ:1.00
 O B:HOH746 1.8 31.5 1.0
OE2 D:GLU109 2.0 18.4 1.0
OD2 B:ASP353 2.0 18.6 1.0
O D:LYS108 2.1 18.1 1.0
OD2 B:ASP357 2.1 17.8 1.0
O D:HOH745 2.1 17.0 1.0
CG B:ASP353 3.0 19.0 1.0
CG B:ASP357 3.0 18.1 1.0
CD D:GLU109 3.1 19.3 1.0
OD1 B:ASP357 3.3 18.0 1.0
OD1 B:ASP353 3.3 18.6 1.0
C D:LYS108 3.3 18.1 1.0
CG D:GLU109 3.8 18.9 1.0
O D:HOH830 4.0 51.5 1.0
CB D:LYS108 4.1 18.2 1.0
OE1 D:GLU109 4.2 19.7 1.0
O D:PHE107 4.2 16.2 1.0
N D:GLU109 4.2 18.3 1.0
CA D:GLU109 4.2 18.8 1.0
NZ C:LYS433 4.3 25.8 1.0
CA D:LYS108 4.3 17.9 1.0
O D:HOH887 4.3 21.2 1.0
CB B:ASP353 4.3 18.9 1.0
O B:ASP353 4.4 16.7 1.0
CB B:ASP357 4.5 17.7 1.0
O D:HOH826 4.6 17.1 1.0
CB D:GLU109 4.7 18.8 1.0
CD1 C:TYR429 4.7 21.0 1.0
C B:ASP353 4.7 17.9 1.0
CE C:LYS433 4.8 24.9 1.0
O D:HOH765 5.0 14.3 1.0

Magnesium binding site 3 out of 5 in 9hbn

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Magnesium binding site 3 out of 5 in the A. Vinelandii Nitrogenase Mofe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A. Vinelandii Nitrogenase Mofe Protein ANC1B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:32.5
occ:1.00
 O D:HOH881 2.1 30.8 1.0
O D:HOH760 2.2 24.0 1.0
O B:HOH701 2.2 28.5 1.0
O B:HOH878 2.5 30.7 1.0
NH1 B:ARG16 2.8 33.9 1.0
O D:HOH733 3.2 26.2 1.0
CD B:ARG16 3.2 27.8 1.0
O B:PHE15 3.3 21.1 1.0
O D:HOH919 3.6 36.5 1.0
CZ B:ARG16 3.7 32.0 1.0
O D:THR514 3.7 25.4 1.0
CE2 D:TYR517 3.8 18.9 1.0
NE B:ARG16 3.8 30.1 1.0
C B:PHE15 3.9 21.5 1.0
CG B:LYS21 4.1 28.4 1.0
CD1 B:LEU24 4.2 22.3 1.0
CA B:ARG16 4.3 24.3 1.0
N B:ARG16 4.4 23.5 1.0
CD2 D:TYR517 4.5 19.0 1.0
CG B:ARG16 4.5 26.2 1.0
CB B:PHE15 4.6 20.9 1.0
OH D:TYR517 4.6 18.7 1.0
CZ D:TYR517 4.6 18.6 1.0
O B:HOH876 4.7 21.6 1.0
C D:THR514 4.8 22.8 1.0
CA B:PHE15 4.8 21.1 1.0
NH2 B:ARG16 4.9 33.4 1.0
CD1 A:ILE101 4.9 22.4 0.5
CD1 A:ILE101 4.9 21.3 0.5

Magnesium binding site 4 out of 5 in 9hbn

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Magnesium binding site 4 out of 5 in the A. Vinelandii Nitrogenase Mofe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A. Vinelandii Nitrogenase Mofe Protein ANC1B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:26.6
occ:1.00
 O C:HOH617 2.1 32.5 1.0
NZ C:LYS428 2.3 28.7 1.0
NE2 C:GLN432 2.4 22.1 1.0
CE C:LYS428 2.5 27.3 1.0
O C:HOH677 2.7 27.2 1.0
O C:HOH604 2.9 5.6 1.0
O C:PHE438 3.0 18.5 1.0
CD C:LYS428 3.1 26.2 1.0
OD2 C:ASP445 3.1 24.3 1.0
CD C:GLN432 3.7 22.8 1.0
CG C:LYS428 3.7 24.6 1.0
OD1 C:ASP445 3.8 25.9 1.0
CG C:ASP445 3.8 24.6 1.0
C C:PHE438 4.0 18.7 1.0
O B:HOH703 4.1 25.4 1.0
OE1 C:GLN432 4.3 22.6 1.0
CD1 C:PHE438 4.4 18.4 1.0
CB C:PHE438 4.5 18.4 1.0
MG B:MG603 4.5 30.6 1.0
CE1 B:HIS359 4.6 18.9 1.0
CG C:GLN432 4.7 23.3 1.0
CA C:PHE438 4.8 18.7 1.0
N C:ARG439 4.8 19.1 1.0
CG2 B:THR360 4.9 20.7 1.0
CG C:PHE438 4.9 18.4 1.0
O B:THR356 4.9 21.1 1.0
CA C:ARG439 5.0 19.4 1.0

Magnesium binding site 5 out of 5 in 9hbn

Go back to Magnesium Binding Sites List in 9hbn
Magnesium binding site 5 out of 5 in the A. Vinelandii Nitrogenase Mofe Protein ANC1B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A. Vinelandii Nitrogenase Mofe Protein ANC1B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:17.7
occ:1.00
 O B:LYS108 2.0 16.6 1.0
OD2 D:ASP357 2.1 16.9 1.0
O B:HOH815 2.1 14.9 1.0
OD2 D:ASP353 2.2 17.0 1.0
O D:HOH753 2.2 19.3 1.0
OE2 B:GLU109 2.3 19.1 1.0
CG D:ASP357 3.1 16.9 1.0
CG D:ASP353 3.2 16.5 1.0
C B:LYS108 3.2 16.7 1.0
CD B:GLU109 3.3 19.1 1.0
OD1 D:ASP357 3.5 17.1 1.0
OD1 D:ASP353 3.5 16.8 1.0
O D:HOH732 3.7 22.1 1.0
CG B:GLU109 3.7 18.4 1.0
O B:PHE107 4.1 15.5 1.0
N B:GLU109 4.1 16.6 1.0
CB B:LYS108 4.2 17.4 1.0
CA B:LYS108 4.3 16.6 1.0
CA B:GLU109 4.3 17.2 1.0
NZ A:LYS433 4.4 21.4 1.0
CB D:ASP357 4.4 16.5 1.0
OE1 B:GLU109 4.4 19.6 1.0
CB D:ASP353 4.5 15.9 1.0
O D:ASP353 4.5 15.2 1.0
O B:HOH786 4.5 13.2 1.0
CD1 A:TYR429 4.6 18.6 1.0
CB B:GLU109 4.6 18.0 1.0
O B:HOH774 4.8 21.4 1.0
C D:ASP353 4.8 15.6 1.0
CE A:LYS433 5.0 21.3 1.0

Reference:

B.Cuevas-Zuviria, F.Detemple, K.Amritkar, A.K.Garcia, L.C.Seefeldt, O.Einsle, B.Kacar. Structural Evolution of Nitrogenase Enzymes Over Geologic Time Elife 2025.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.105613.3
Page generated: Sat Dec 13 19:41:58 2025

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