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Calcium in PDB 8rhp: Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii)

Enzymatic activity of Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii)

All present enzymatic activity of Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii):
1.18.6.1;

Other elements in 8rhp:

The structure of Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii) also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Iron (Fe) 72 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii) (pdb code 8rhp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii), PDB code: 8rhp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8rhp

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Calcium binding site 1 out of 4 in the Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:91.5
occ:0.49
 OD1 B:ASP353 2.2 103.9 1.0
OD2 B:ASP357 2.3 102.0 1.0
OE2 C:GLU109 2.3 101.5 1.0
OD2 B:ASP353 2.4 103.0 1.0
O C:ARG108 2.4 94.1 1.0
CG B:ASP353 2.6 102.7 1.0
CD C:GLU109 2.8 102.5 1.0
OE1 C:GLU109 2.8 102.5 1.0
CG B:ASP357 3.1 97.4 1.0
OD1 B:ASP357 3.2 98.8 1.0
C C:ARG108 3.6 93.9 1.0
NZ D:LYS433 3.7 114.2 1.0
CD1 D:PHE429 4.0 110.6 1.0
CB B:ASP353 4.1 91.0 1.0
CG C:GLU109 4.1 101.6 1.0
O B:ASP353 4.2 99.7 1.0
CA C:GLU109 4.3 100.6 1.0
N C:GLU109 4.4 100.9 1.0
CB C:ARG108 4.5 92.9 1.0
CB B:ASP357 4.5 86.8 1.0
C B:ASP353 4.6 89.9 1.0
CE1 D:PHE429 4.6 107.4 1.0
CB C:GLU109 4.7 100.5 1.0
CE D:LYS433 4.7 114.7 1.0
CA C:ARG108 4.7 92.7 1.0
CG D:PHE429 4.7 111.1 1.0
CA B:ASP353 4.8 82.5 1.0
CB D:PHE429 4.8 106.4 1.0

Calcium binding site 2 out of 4 in 8rhp

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Calcium binding site 2 out of 4 in the Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:144.5
occ:1.00
 OD2 C:ASP357 2.3 105.4 1.0
OE2 B:GLU109 2.4 124.4 1.0
O B:ARG108 2.4 119.3 1.0
OD2 C:ASP353 2.5 117.3 1.0
CD B:GLU109 2.6 124.5 1.0
OE1 B:GLU109 2.6 122.8 1.0
OD1 C:ASP353 2.8 118.2 1.0
CG C:ASP353 2.9 117.7 1.0
CG C:ASP357 3.3 105.4 1.0
OD1 C:ASP357 3.5 105.6 1.0
C B:ARG108 3.6 109.5 1.0
CG B:GLU109 3.7 122.0 1.0
NZ A:LYS433 4.2 101.0 1.0
CA B:GLU109 4.2 117.2 1.0
CB C:ASP353 4.3 116.5 1.0
N B:GLU109 4.3 114.9 1.0
CB B:GLU109 4.5 116.7 1.0
O C:ASP353 4.5 116.6 1.0
CB B:ARG108 4.5 107.8 1.0
CD1 A:PHE429 4.5 91.9 1.0
CB C:ASP357 4.6 104.7 1.0
CA B:ARG108 4.7 106.6 1.0
O B:PHE107 4.8 92.5 1.0
C C:ASP353 4.8 115.9 1.0
CE A:LYS433 4.9 96.0 1.0

Calcium binding site 3 out of 4 in 8rhp

Go back to Calcium Binding Sites List in 8rhp
Calcium binding site 3 out of 4 in the Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca602

b:94.2
occ:0.55
 OD1 I:ASP353 2.2 106.8 1.0
OD2 I:ASP357 2.3 104.4 1.0
OE2 J:GLU109 2.3 103.8 1.0
OD2 I:ASP353 2.4 106.4 1.0
O J:ARG108 2.4 95.3 1.0
CG I:ASP353 2.6 105.5 1.0
CD J:GLU109 2.8 104.8 1.0
OE1 J:GLU109 2.8 104.8 1.0
CG I:ASP357 3.1 99.1 1.0
OD1 I:ASP357 3.2 101.3 1.0
C J:ARG108 3.6 95.1 1.0
NZ K:LYS433 3.7 117.2 1.0
CD1 K:PHE429 4.0 112.4 1.0
CG J:GLU109 4.1 103.9 1.0
CB I:ASP353 4.1 90.9 1.0
O I:ASP353 4.2 102.2 1.0
CA J:GLU109 4.3 102.9 1.0
N J:GLU109 4.4 103.2 1.0
CB J:ARG108 4.5 94.1 1.0
CB I:ASP357 4.5 85.0 1.0
C I:ASP353 4.6 90.1 1.0
CE1 K:PHE429 4.6 109.3 1.0
CB J:GLU109 4.7 102.9 1.0
CA J:ARG108 4.7 93.8 1.0
CE K:LYS433 4.7 117.8 1.0
CG K:PHE429 4.7 113.0 1.0
CA I:ASP353 4.8 80.3 1.0
CB K:PHE429 4.8 109.1 1.0

Calcium binding site 4 out of 4 in 8rhp

Go back to Calcium Binding Sites List in 8rhp
Calcium binding site 4 out of 4 in the Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca601

b:144.4
occ:1.00
 OD2 J:ASP357 2.3 108.9 1.0
OE2 I:GLU109 2.4 123.9 1.0
O I:ARG108 2.4 121.3 1.0
OD2 J:ASP353 2.5 122.4 1.0
CD I:GLU109 2.6 124.7 1.0
OE1 I:GLU109 2.6 122.5 1.0
OD1 J:ASP353 2.8 123.2 1.0
CG J:ASP353 2.9 122.7 1.0
CG J:ASP357 3.2 108.9 1.0
OD1 J:ASP357 3.5 109.1 1.0
C I:ARG108 3.6 108.9 1.0
CG I:GLU109 3.7 121.7 1.0
NZ H:LYS433 4.2 102.9 1.0
CA I:GLU109 4.2 114.8 1.0
CB J:ASP353 4.3 121.5 1.0
N I:GLU109 4.3 111.8 1.0
CB I:GLU109 4.5 114.4 1.0
O J:ASP353 4.5 121.6 1.0
CD1 H:PHE429 4.5 92.6 1.0
CB I:ARG108 4.5 107.2 1.0
CB J:ASP357 4.6 108.2 1.0
CA I:ARG108 4.7 105.7 1.0
C J:ASP353 4.8 120.9 1.0
O I:PHE107 4.8 96.9 1.0
CE H:LYS433 4.9 97.6 1.0

Reference:

P.Franke, L.Zhang, O.Einsle. Cryo-Em Structure of the Molybdenum Nitrogenase Complexed with Iron Protein (Nifh) and Shethna Protein II (Fesii) To Be Published.
Page generated: Sat Feb 8 16:10:13 2025

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