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Calcium in PDB 4kn9: High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

Enzymatic activity of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

All present enzymatic activity of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air:
1.12.99.6;

Protein crystallography data

The structure of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kn9 was solved by A.Volbeda, C.Cavazza, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.260, 108.730, 136.500, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 16.8

Other elements in 4kn9:

The structure of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air also contains other interesting chemical elements:

Nickel (Ni) 6 atoms
Iron (Fe) 26 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4kn9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kn9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4kn9

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Calcium binding site 1 out of 7 in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca304

b:12.8
occ:1.00
 O S:GLU152 2.3 12.1 1.0
O S:HOH456 2.4 16.3 1.0
O S:HOH455 2.4 16.6 1.0
O S:HOH458 2.4 18.9 1.0
O S:HOH472 2.5 21.4 1.0
C S:GLU152 3.4 11.0 1.0
CA S:GLU152 4.1 11.1 1.0
OE1 S:GLU152 4.2 15.8 1.0
CB S:GLU152 4.4 10.7 1.0
N S:LYS153 4.5 11.3 1.0
CB S:LYS153 4.5 13.2 1.0
O S:LYS153 4.6 15.5 1.0
C S:LYS153 4.7 13.5 1.0
CA S:LYS153 4.7 14.0 1.0
O S:HOH489 4.9 19.7 0.3

Calcium binding site 2 out of 7 in 4kn9

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Calcium binding site 2 out of 7 in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca308

b:33.3
occ:0.70
 O S:HOH651 2.3 42.9 0.7
O S:HOH633 2.4 36.8 1.0
O L:HOH899 2.4 25.8 1.0
O L:HOH1091 2.4 37.4 0.7
O S:HOH539 2.5 35.4 1.0
O S:HOH753 2.6 33.5 0.7
OE2 S:GLU103 4.3 35.4 0.7
O S:HOH516 4.3 22.9 1.0
O L:PRO311 4.4 19.9 1.0
OE1 S:GLU103 4.4 35.6 0.7
NH2 S:ARG87 4.5 23.4 1.0
CZ L:PHE291 4.5 17.4 1.0
CD S:ARG87 4.6 17.1 1.0
O S:HOH755 4.8 47.0 1.0
CD S:GLU103 4.8 34.5 0.7
CE1 L:PHE291 4.8 15.7 1.0
O L:HOH1013 4.8 42.4 1.0

Calcium binding site 3 out of 7 in 4kn9

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Calcium binding site 3 out of 7 in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca503

b:13.1
occ:0.80
 O L:HOH609 2.2 20.9 1.0
O L:HOH610 2.2 19.7 1.0
O L:HOH608 2.3 13.5 1.0
O L:ILE444 2.4 10.9 1.0
OE1 L:GLU51 2.4 12.8 1.0
NE2 L:HIS498 2.5 11.6 1.0
CD L:GLU51 3.3 12.9 1.0
CE1 L:HIS498 3.3 12.3 1.0
OE2 L:GLU51 3.5 14.4 1.0
C L:ILE444 3.5 9.7 1.0
CD2 L:HIS498 3.5 10.7 1.0
N L:ILE444 3.9 10.2 1.0
CA L:ILE444 4.1 11.1 1.0
OE1 L:GLU285 4.2 16.0 1.0
OE1 L:GLN443 4.3 15.4 1.0
NZ L:LYS321 4.3 21.8 1.0
CB L:ILE444 4.4 11.2 1.0
OE2 L:GLU285 4.4 19.9 1.0
ND1 L:HIS498 4.5 12.6 1.0
CG L:GLU51 4.6 11.1 1.0
N L:VAL445 4.6 9.2 1.0
O L:HOH625 4.6 12.5 1.0
CG L:HIS498 4.6 9.6 1.0
CD L:GLU285 4.7 16.2 1.0
O L:HOH641 4.7 16.1 1.0
CD L:LYS321 4.8 16.1 1.0
CE L:LYS321 4.9 18.3 1.0
C L:GLN443 4.9 11.3 1.0
CA L:VAL445 4.9 9.2 1.0

Calcium binding site 4 out of 7 in 4kn9

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Calcium binding site 4 out of 7 in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca304

b:20.6
occ:0.60
 O T:HOH582 2.3 27.2 0.6
O T:HOH549 2.3 26.9 0.6
O T:HOH540 2.4 23.7 0.6
O T:HOH530 2.4 30.9 0.6
O T:HOH506 2.5 27.7 1.0
O M:HOH609 2.5 22.8 1.0
O M:HOH612 2.5 31.0 0.6
OE2 T:GLU103 4.0 39.5 0.7
O T:HOH474 4.3 19.9 1.0
O M:PRO311 4.4 17.1 1.0
OE1 T:GLU103 4.4 36.6 0.7
NH2 T:ARG87 4.5 22.4 1.0
CD T:ARG87 4.6 17.4 1.0
CZ M:PHE291 4.6 13.5 1.0
CD T:GLU103 4.7 34.7 0.7
O M:HOH786 4.7 33.1 1.0

Calcium binding site 5 out of 7 in 4kn9

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Calcium binding site 5 out of 7 in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca305

b:29.2
occ:0.60
 O T:HOH499 2.3 30.8 1.0
OD2 T:ASP271 2.3 21.5 1.0
O T:HOH735 2.4 39.0 0.7
O T:HOH724 2.5 44.7 1.0
O T:HOH469 2.6 32.2 1.0
O T:GLY275 2.8 19.5 1.0
C T:GLY275 3.6 15.7 1.0
CG T:ASP271 3.6 20.0 1.0
O T:HOH675 3.6 55.6 1.0
CA T:GLY275 3.6 15.4 1.0
O T:HOH623 4.4 41.1 1.0
NZ T:LYS276 4.4 22.6 1.0
O T:HOH618 4.4 37.0 1.0
CB T:ASP271 4.4 14.5 1.0
OD1 T:ASP271 4.4 22.5 1.0
N T:LYS276 4.8 14.7 1.0
O T:HOH725 4.9 46.3 1.0
O T:HOH579 5.0 32.4 1.0

Calcium binding site 6 out of 7 in 4kn9

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Calcium binding site 6 out of 7 in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca306

b:82.2
occ:1.00
 O T:HOH475 2.3 15.9 1.0
O T:HOH721 2.4 36.5 1.0
O T:HOH727 2.7 32.2 1.0
O T:HOH584 2.8 45.0 1.0
O T:ASP195 2.9 19.7 1.0
OD1 T:ASP196 3.0 22.3 1.0
O T:HOH466 3.6 46.1 1.0
C T:ASP195 3.7 18.8 1.0
CG T:ASP196 3.8 18.1 1.0
CB T:ASP195 4.3 19.8 1.0
OD2 T:ASP196 4.3 18.6 1.0
NH2 T:ARG146 4.3 20.5 1.0
N T:ASP196 4.4 16.6 1.0
CA T:ASP196 4.5 17.8 1.0
CA T:ASP195 4.6 17.8 1.0
O T:HOH633 4.6 35.4 1.0
O T:HOH610 4.8 30.8 1.0
O T:HOH526 4.8 30.9 1.0
CB T:ASP196 4.8 18.3 1.0

Calcium binding site 7 out of 7 in 4kn9

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Calcium binding site 7 out of 7 in the High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of High-Resolution Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca503

b:14.4
occ:0.80
 O M:HOH618 2.2 28.9 1.0
O M:HOH617 2.3 16.2 1.0
O M:HOH619 2.3 20.5 1.0
O M:ILE444 2.4 14.7 1.0
OE1 M:GLU51 2.4 14.8 1.0
NE2 M:HIS498 2.5 13.6 1.0
CD M:GLU51 3.3 15.1 1.0
CE1 M:HIS498 3.3 15.8 1.0
OE2 M:GLU51 3.5 18.8 1.0
C M:ILE444 3.5 14.9 1.0
CD2 M:HIS498 3.5 13.4 1.0
N M:ILE444 3.9 16.5 1.0
OE1 M:GLU285 4.1 19.7 1.0
CA M:ILE444 4.2 15.2 1.0
OE1 M:GLN443 4.3 23.1 1.0
OE2 M:GLU285 4.3 20.2 1.0
NZ M:LYS321 4.4 20.3 1.0
CB M:ILE444 4.5 15.2 1.0
ND1 M:HIS498 4.5 14.7 1.0
O M:HOH634 4.5 12.9 1.0
N M:VAL445 4.6 14.2 1.0
CG M:HIS498 4.6 14.1 1.0
CG M:GLU51 4.7 12.4 1.0
CD M:GLU285 4.7 18.9 1.0
O M:HOH648 4.7 16.6 1.0
CD M:LYS321 4.7 14.7 1.0
CE M:LYS321 4.8 17.7 1.0
CA M:VAL445 4.9 15.2 1.0
C M:GLN443 5.0 17.0 1.0

Reference:

A.Volbeda, P.Amara, M.Iannello, A.L.De Lacey, C.Cavazza, J.C.Fontecilla-Camps. Structural Foundations For the O2 Resistance of Desulfomicrobium Baculatum [Nifese]-Hydrogenase. Chem.Commun.(Camb.) V. 49 7061 2013.
ISSN: ISSN 1359-7345
PubMed: 23811828
DOI: 10.1039/C3CC43619E
Page generated: Sun Jul 14 09:10:54 2024

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