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Magnesium in PDB 1xcp: Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound

Enzymatic activity of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound

All present enzymatic activity of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound:
1.18.6.1;

Protein crystallography data

The structure of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound, PDB code: 1xcp was solved by M.S.Jeong, S.B.Jang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 108.950, 91.260, 125.310, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 32.2

Other elements in 1xcp:

The structure of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound (pdb code 1xcp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound, PDB code: 1xcp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1xcp

Go back to Magnesium Binding Sites List in 1xcp
Magnesium binding site 1 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1293

b:19.9
occ:1.00
 OG A:SER16 2.5 39.5 1.0
O1B A:ADP1291 2.5 50.3 1.0
OD1 A:ASP43 2.6 83.8 1.0
OD2 A:ASP39 2.6 0.0 1.0
O2B A:ADP1291 3.0 50.0 1.0
CG A:ASP39 3.1 0.0 1.0
OD1 A:ASP39 3.4 0.0 1.0
PB A:ADP1291 3.5 53.1 1.0
CG A:ASP43 3.5 82.8 1.0
NZ A:LYS15 3.7 40.4 1.0
OD2 A:ASP43 3.7 84.5 1.0
CB A:SER16 3.8 43.4 1.0
O1A A:ADP1291 4.0 51.9 1.0
CB A:ASP39 4.1 98.2 1.0
O3A A:ADP1291 4.2 52.4 1.0
OD1 A:ASP125 4.2 76.5 1.0
OG A:SER44 4.3 71.7 1.0
PA A:ADP1291 4.5 52.4 1.0
N A:SER16 4.6 47.6 1.0
O3B A:ADP1291 4.6 48.9 1.0
CA A:SER16 4.8 46.8 1.0
CB A:ASP43 4.9 80.8 1.0

Magnesium binding site 2 out of 4 in 1xcp

Go back to Magnesium Binding Sites List in 1xcp
Magnesium binding site 2 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1294

b:41.5
occ:1.00
 O3B B:ADP1292 2.4 50.9 1.0
OD2 B:ASP39 2.6 0.0 1.0
OG B:SER16 2.7 37.1 1.0
OD1 B:ASP43 2.9 84.6 1.0
O2B B:ADP1292 2.9 53.9 1.0
CG B:ASP39 3.0 99.0 1.0
OD1 B:ASP39 3.1 97.8 1.0
NZ B:LYS15 3.4 44.5 1.0
PB B:ADP1292 3.5 58.2 1.0
CG B:ASP43 3.8 83.0 1.0
OD2 B:ASP43 3.9 80.4 1.0
CB B:SER16 4.0 43.4 1.0
CB B:ASP39 4.1 97.6 1.0
OD1 B:ASP125 4.2 77.2 1.0
O2A B:ADP1292 4.2 51.6 1.0
O3A B:ADP1292 4.2 54.2 1.0
OG B:SER44 4.5 68.1 1.0
O1B B:ADP1292 4.5 57.2 1.0
PA B:ADP1292 4.6 53.8 1.0
N B:SER16 4.7 45.2 1.0
CE B:LYS15 4.7 41.5 1.0
CA B:SER16 5.0 45.5 1.0
NZ B:LYS41 5.0 94.6 1.0

Magnesium binding site 3 out of 4 in 1xcp

Go back to Magnesium Binding Sites List in 1xcp
Magnesium binding site 3 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2293

b:7.2
occ:1.00
 OG C:SER16 2.3 27.0 1.0
O2B C:ADP2291 2.3 45.5 1.0
OD1 C:ASP39 2.5 89.1 1.0
OD1 C:ASP43 3.0 70.5 1.0
OD1 C:ASP125 3.1 51.4 1.0
CG C:ASP39 3.1 86.8 1.0
O3B C:ADP2291 3.3 41.0 1.0
OD2 C:ASP39 3.4 86.9 1.0
CB C:SER16 3.5 35.0 1.0
PB C:ADP2291 3.5 45.8 1.0
CG C:ASP43 3.8 69.3 1.0
OD2 C:ASP43 4.0 67.8 1.0
CG C:ASP125 4.0 55.5 1.0
OG C:SER44 4.1 61.1 1.0
NZ C:LYS41 4.2 89.0 1.0
N C:SER16 4.2 38.6 1.0
OD2 C:ASP125 4.2 55.2 1.0
CB C:ASP39 4.3 84.5 1.0
O2A C:ADP2291 4.3 43.6 1.0
CA C:SER16 4.3 34.4 1.0
CE C:LYS15 4.4 52.7 1.0
O1B C:ADP2291 4.4 44.7 1.0
NZ C:LYS15 4.5 55.8 1.0
O3A C:ADP2291 4.5 45.8 1.0
PA C:ADP2291 4.7 43.7 1.0
O1A C:ADP2291 5.0 42.1 1.0

Magnesium binding site 4 out of 4 in 1xcp

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2294

b:2.0
occ:1.00
 OG D:SER16 2.3 30.4 1.0
O1B D:ADP2292 2.4 42.0 1.0
OD1 D:ASP43 2.6 72.1 1.0
OD1 D:ASP39 2.7 89.0 1.0
O3B D:ADP2292 3.1 38.9 1.0
CG D:ASP39 3.3 87.2 1.0
CB D:SER16 3.4 35.0 1.0
PB D:ADP2292 3.5 44.2 1.0
CG D:ASP43 3.5 70.6 1.0
OD1 D:ASP125 3.5 54.4 1.0
OD2 D:ASP39 3.7 89.9 1.0
OD2 D:ASP43 3.8 69.1 1.0
NZ D:LYS41 4.0 87.2 1.0
O1A D:ADP2292 4.1 45.4 1.0
OG D:SER44 4.3 65.8 1.0
N D:SER16 4.3 38.4 1.0
CB D:ASP39 4.4 83.7 1.0
CA D:SER16 4.4 36.1 1.0
O3A D:ADP2292 4.4 42.6 1.0
CG D:ASP125 4.4 57.9 1.0
O2B D:ADP2292 4.5 46.5 1.0
PA D:ADP2292 4.6 42.6 1.0
OD2 D:ASP125 4.6 59.6 1.0
CE D:LYS15 4.7 49.4 1.0
NZ D:LYS15 4.7 48.8 1.0
CB D:ASP43 4.8 68.5 1.0
O2A D:ADP2292 4.9 41.5 1.0

Reference:

M.S.Jeong, S.B.Jang. Structural Basis For the Changes in Redox Potential in the Nitrogenase PHE135TRP Fe Protein with Mgadp Bound Mol.Cell V. 18 374 2004.
ISSN: ISSN 1097-2765
PubMed: 15650336
Page generated: Mon Dec 14 07:03:04 2020

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