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Calcium in PDB 5cx1: Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant

Enzymatic activity of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant

All present enzymatic activity of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant, PDB code: 5cx1 was solved by C.P.Owens, M.A.Luca, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.68 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 175.502, 144.595, 177.747, 90.00, 114.27, 90.00
R / Rfree (%) 19.8 / 24.5

Other elements in 5cx1:

The structure of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant also contains other interesting chemical elements:

Molybdenum (Mo) 8 atoms
Iron (Fe) 120 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant (pdb code 5cx1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant, PDB code: 5cx1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5cx1

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Calcium binding site 1 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:12.6
occ:1.00
 OD2 B:ASP357 2.3 17.6 1.0
O D:ARG108 2.3 13.1 1.0
O B:HOH778 2.3 10.6 1.0
OE2 D:GLU109 2.3 14.3 1.0
OD2 B:ASP353 2.4 14.7 1.0
O D:HOH951 2.4 9.1 1.0
OD1 B:ASP357 2.5 17.8 1.0
CG B:ASP357 2.8 14.8 1.0
CG B:ASP353 3.3 16.1 1.0
CD D:GLU109 3.4 13.5 1.0
C D:ARG108 3.5 11.8 1.0
OD1 B:ASP353 3.6 15.0 1.0
O B:HOH774 3.8 15.7 1.0
CG D:GLU109 3.9 9.3 1.0
CB D:ARG108 4.1 11.8 1.0
N D:GLU109 4.3 8.6 1.0
O D:PHE107 4.3 9.2 1.0
CB B:ASP357 4.3 13.2 1.0
CD1 C:PHE429 4.4 12.4 1.0
CA D:ARG108 4.4 11.8 1.0
CA D:GLU109 4.4 8.6 1.0
O B:ASP353 4.5 12.7 1.0
OE1 D:GLU109 4.5 16.6 1.0
NZ C:LYS433 4.5 11.3 1.0
CB B:ASP353 4.6 9.4 1.0
CB D:GLU109 4.7 10.3 1.0
O D:HOH965 4.8 11.7 1.0
CE1 C:PHE429 4.8 15.3 1.0
C B:ASP353 4.8 13.3 1.0
CE C:LYS433 4.9 13.3 1.0
CG C:PHE429 4.9 12.6 1.0

Calcium binding site 2 out of 8 in 5cx1

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Calcium binding site 2 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:12.8
occ:1.00
 OD2 D:ASP357 2.3 16.5 1.0
O B:ARG108 2.3 9.6 1.0
OE2 B:GLU109 2.4 12.7 1.0
OD2 D:ASP353 2.4 20.8 1.0
O B:HOH918 2.4 13.0 1.0
OD1 D:ASP353 2.4 29.4 1.0
OD1 D:ASP357 2.4 16.8 1.0
CG D:ASP353 2.8 12.1 1.0
CG D:ASP357 2.8 13.2 1.0
C B:ARG108 3.5 11.1 1.0
CD B:GLU109 3.5 12.2 1.0
CG B:GLU109 4.0 13.1 1.0
O D:HOH706 4.0 12.9 1.0
CB B:ARG108 4.0 11.4 1.0
CB D:ASP353 4.3 15.2 1.0
CB D:ASP357 4.3 10.1 1.0
N B:GLU109 4.4 11.6 1.0
O B:PHE107 4.4 10.2 1.0
CA B:ARG108 4.4 9.5 1.0
O D:ASP353 4.4 14.2 1.0
CD1 A:PHE429 4.4 13.8 1.0
CA B:GLU109 4.4 13.5 1.0
NZ A:LYS433 4.4 10.8 1.0
OE1 B:GLU109 4.5 13.6 1.0
C D:ASP353 4.7 13.4 1.0
CE A:LYS433 4.8 15.8 1.0
CB B:GLU109 4.8 11.3 1.0
O B:HOH977 4.9 12.1 1.0
CG A:PHE429 4.9 11.8 1.0
CE1 A:PHE429 4.9 13.1 1.0

Calcium binding site 3 out of 8 in 5cx1

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Calcium binding site 3 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca601

b:13.3
occ:1.00
 O H:ARG108 2.3 9.3 1.0
OD2 F:ASP353 2.3 12.3 1.0
OD2 F:ASP357 2.3 16.0 1.0
O F:HOH820 2.4 13.3 1.0
OE2 H:GLU109 2.4 12.7 1.0
O F:HOH1018 2.4 12.5 1.0
OD1 F:ASP357 2.4 18.5 1.0
CG F:ASP357 2.8 14.4 1.0
CG F:ASP353 3.3 12.6 1.0
C H:ARG108 3.5 11.4 1.0
CD H:GLU109 3.5 16.3 1.0
OD1 F:ASP353 3.6 13.7 1.0
O F:HOH865 4.0 15.9 1.0
CB H:ARG108 4.0 9.1 1.0
CG H:GLU109 4.1 13.6 1.0
CB F:ASP357 4.3 7.2 1.0
N H:GLU109 4.4 9.5 1.0
CA H:ARG108 4.4 9.8 1.0
CD1 G:PHE429 4.4 13.7 1.0
CA H:GLU109 4.4 10.4 1.0
O H:PHE107 4.4 12.0 1.0
NZ G:LYS433 4.5 13.7 1.0
O F:ASP353 4.5 13.0 1.0
OE1 H:GLU109 4.6 15.0 1.0
CB F:ASP353 4.6 11.2 1.0
C F:ASP353 4.8 10.1 1.0
CE1 G:PHE429 4.9 13.4 1.0
CB H:GLU109 4.9 14.4 1.0
CE G:LYS433 4.9 14.5 1.0
O H:HOH927 4.9 14.3 1.0
CG G:PHE429 5.0 14.5 1.0

Calcium binding site 4 out of 8 in 5cx1

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Calcium binding site 4 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca601

b:14.8
occ:1.00
 O F:ARG108 2.3 12.2 1.0
OD2 H:ASP353 2.3 18.2 1.0
OD2 H:ASP357 2.3 18.7 1.0
OE2 F:GLU109 2.3 14.6 1.0
O H:HOH747 2.4 15.0 1.0
O F:HOH1023 2.4 13.5 1.0
OD1 H:ASP357 2.4 19.6 1.0
CG H:ASP357 2.8 13.6 1.0
CG H:ASP353 3.3 21.3 1.0
CD F:GLU109 3.4 16.3 1.0
C F:ARG108 3.5 14.8 1.0
OD1 H:ASP353 3.5 19.9 1.0
O H:HOH890 3.9 15.9 1.0
CG F:GLU109 3.9 16.3 1.0
CB F:ARG108 4.1 15.6 1.0
NZ E:LYS433 4.3 14.4 1.0
CB H:ASP357 4.3 12.5 1.0
N F:GLU109 4.4 12.8 1.0
CD1 E:PHE429 4.4 12.1 1.0
CA F:GLU109 4.4 12.5 1.0
CA F:ARG108 4.4 12.0 1.0
O F:PHE107 4.5 12.7 1.0
O H:ASP353 4.5 15.6 1.0
OE1 F:GLU109 4.5 18.3 1.0
CB H:ASP353 4.6 13.9 1.0
CE E:LYS433 4.7 12.3 1.0
CB F:GLU109 4.8 14.1 1.0
O F:HOH988 4.8 15.6 1.0
CE1 E:PHE429 4.8 14.2 1.0
C H:ASP353 4.9 16.1 1.0
CG E:PHE429 5.0 12.4 1.0

Calcium binding site 5 out of 8 in 5cx1

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Calcium binding site 5 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca601

b:12.9
occ:1.00
 OD2 J:ASP353 2.3 13.7 1.0
OD2 J:ASP357 2.3 21.4 1.0
O L:ARG108 2.3 13.6 1.0
OE2 L:GLU109 2.4 13.8 1.0
O J:HOH736 2.4 13.6 1.0
O L:HOH933 2.4 14.3 1.0
OD1 J:ASP357 2.4 22.9 1.0
CG J:ASP357 2.8 13.6 1.0
CG J:ASP353 3.3 16.2 1.0
CD L:GLU109 3.4 13.1 1.0
C L:ARG108 3.5 17.2 1.0
OD1 J:ASP353 3.6 18.3 1.0
O J:HOH758 3.7 15.8 1.0
CG L:GLU109 3.9 10.2 1.0
CB L:ARG108 4.0 13.8 1.0
CB J:ASP357 4.3 9.2 1.0
N L:GLU109 4.3 11.0 1.0
O L:PHE107 4.3 10.5 1.0
NZ K:LYS433 4.4 12.9 1.0
CA L:ARG108 4.4 11.5 1.0
CA L:GLU109 4.4 11.1 1.0
CD1 K:PHE429 4.5 13.3 1.0
OE1 L:GLU109 4.5 15.7 1.0
O J:ASP353 4.6 11.8 1.0
CB J:ASP353 4.6 12.2 1.0
O L:HOH1005 4.7 12.4 1.0
CB L:GLU109 4.7 11.7 1.0
O L:HOH1009 4.9 11.6 1.0
C J:ASP353 4.9 12.8 1.0
CE1 K:PHE429 4.9 10.8 1.0
CE K:LYS433 4.9 15.7 1.0
CG K:PHE429 5.0 16.6 1.0

Calcium binding site 6 out of 8 in 5cx1

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Calcium binding site 6 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca601

b:14.4
occ:1.00
 OD2 L:ASP357 2.3 19.8 1.0
O J:ARG108 2.4 12.1 1.0
O L:HOH703 2.4 11.4 1.0
OD2 L:ASP353 2.4 21.8 1.0
OE2 J:GLU109 2.4 14.0 1.0
O L:HOH945 2.4 16.0 1.0
OD1 L:ASP353 2.4 29.6 1.0
OD1 L:ASP357 2.4 19.4 1.0
CG L:ASP357 2.8 16.3 1.0
CG L:ASP353 2.8 18.1 1.0
CD J:GLU109 3.5 15.7 1.0
C J:ARG108 3.5 14.9 1.0
CG J:GLU109 4.0 15.3 1.0
CB J:ARG108 4.1 10.8 1.0
NZ I:LYS433 4.3 12.2 1.0
CB L:ASP357 4.3 13.3 1.0
CB L:ASP353 4.4 14.1 1.0
N J:GLU109 4.4 12.3 1.0
CD1 I:PHE429 4.4 13.9 1.0
O L:ASP353 4.5 14.7 1.0
CA J:GLU109 4.5 10.6 1.0
CA J:ARG108 4.5 12.4 1.0
O J:PHE107 4.5 10.6 1.0
OE1 J:GLU109 4.5 17.6 1.0
O J:HOH1006 4.7 14.7 1.0
C L:ASP353 4.7 11.8 1.0
CE I:LYS433 4.8 13.3 1.0
CB J:GLU109 4.9 11.9 1.0
CE1 I:PHE429 4.9 10.3 1.0
CG I:PHE429 5.0 14.3 1.0
O J:HOH975 5.0 11.5 1.0

Calcium binding site 7 out of 8 in 5cx1

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Calcium binding site 7 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca601

b:11.7
occ:1.00
 OD2 N:ASP353 2.3 9.4 1.0
O P:ARG108 2.3 11.0 1.0
OE2 P:GLU109 2.3 14.4 1.0
OD2 N:ASP357 2.3 19.1 1.0
O N:HOH779 2.4 12.6 1.0
O P:HOH891 2.4 10.6 1.0
OD1 N:ASP357 2.4 19.4 1.0
CG N:ASP357 2.8 12.1 1.0
CG N:ASP353 3.3 11.1 1.0
CD P:GLU109 3.4 9.6 1.0
C P:ARG108 3.5 9.7 1.0
OD1 N:ASP353 3.6 11.6 1.0
CG P:GLU109 3.9 10.5 1.0
O N:HOH861 4.0 10.5 1.0
CB P:ARG108 4.0 7.2 1.0
O P:PHE107 4.3 10.6 1.0
NZ O:LYS433 4.3 10.1 1.0
CB N:ASP357 4.3 11.3 1.0
CA P:ARG108 4.4 8.5 1.0
N P:GLU109 4.4 11.8 1.0
CD1 O:PHE429 4.4 11.1 1.0
CA P:GLU109 4.5 8.4 1.0
OE1 P:GLU109 4.5 8.9 1.0
O N:ASP353 4.5 10.3 1.0
CB N:ASP353 4.6 9.4 1.0
O P:HOH967 4.6 8.7 1.0
CB P:GLU109 4.8 7.5 1.0
CE O:LYS433 4.8 10.6 1.0
C N:ASP353 4.8 10.6 1.0
CE1 O:PHE429 4.8 11.8 1.0
O P:HOH1028 5.0 11.2 1.0

Calcium binding site 8 out of 8 in 5cx1

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Calcium binding site 8 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca601

b:12.1
occ:1.00
 O N:ARG108 2.3 8.2 1.0
OD1 P:ASP353 2.3 11.8 1.0
OD2 P:ASP357 2.3 17.7 1.0
OE2 N:GLU109 2.3 12.6 1.0
O P:HOH786 2.4 10.8 1.0
O N:HOH845 2.4 9.5 1.0
OD1 P:ASP357 2.4 16.5 1.0
CG P:ASP357 2.8 12.8 1.0
CG P:ASP353 3.3 15.4 1.0
C N:ARG108 3.5 8.2 1.0
CD N:GLU109 3.5 12.7 1.0
OD2 P:ASP353 3.6 14.2 1.0
O P:HOH863 4.0 13.4 1.0
CG N:GLU109 4.0 9.1 1.0
CB N:ARG108 4.0 9.6 1.0
NZ M:LYS433 4.3 12.6 1.0
N N:GLU109 4.3 7.5 1.0
O N:PHE107 4.3 8.8 1.0
CB P:ASP357 4.3 10.9 1.0
CA N:ARG108 4.4 7.8 1.0
CA N:GLU109 4.4 8.8 1.0
CD1 M:PHE429 4.4 11.9 1.0
O P:ASP353 4.5 9.8 1.0
OE1 N:GLU109 4.6 12.9 1.0
CB P:ASP353 4.7 12.7 1.0
O N:HOH1032 4.7 12.0 1.0
CB N:GLU109 4.8 8.1 1.0
CE M:LYS433 4.8 12.1 1.0
CE1 M:PHE429 4.9 12.0 1.0
C P:ASP353 4.9 12.8 1.0
CG M:PHE429 5.0 11.7 1.0

Reference:

C.P.Owens, F.E.Katz, C.H.Carter, M.A.Luca, F.A.Tezcan. Evidence For Functionally Relevant Encounter Complexes in Nitrogenase Catalysis. J.Am.Chem.Soc. V. 137 12704 2015.
ISSN: ESSN 1520-5126
PubMed: 26360912
DOI: 10.1021/JACS.5B08310
Page generated: Sun Jul 14 17:23:56 2024

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