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Calcium in PDB 4ko2: Low X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

Enzymatic activity of Low X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

All present enzymatic activity of Low X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air:
1.12.99.6; 1.18.99.1;

Protein crystallography data

The structure of Low X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko2 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 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.230, 108.910, 136.340, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.4

Other elements in 4ko2:

The structure of Low X-Ray Dose 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) 28 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Low X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4ko2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Low X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4ko2

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Calcium binding site 1 out of 8 in the Low X-Ray Dose 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 Low X-Ray Dose 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:11.8
occ:1.00
 O S:GLU152 2.3 10.2 1.0
O S:HOH456 2.4 14.5 1.0
O S:HOH458 2.4 18.3 1.0
O S:HOH455 2.4 15.0 1.0
O S:HOH472 2.5 18.9 1.0
C S:GLU152 3.4 10.3 1.0
CA S:GLU152 4.1 10.5 1.0
OE1 S:GLU152 4.3 13.6 1.0
CB S:GLU152 4.4 9.2 1.0
N S:LYS153 4.5 10.4 1.0
CB S:LYS153 4.5 13.0 1.0
O S:LYS153 4.6 13.4 1.0
C S:LYS153 4.7 12.2 1.0
CA S:LYS153 4.7 12.1 1.0
O S:HOH489 4.9 19.4 0.3

Calcium binding site 2 out of 8 in 4ko2

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Calcium binding site 2 out of 8 in the Low X-Ray Dose 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 Low X-Ray Dose 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:Ca307

b:35.2
occ:0.70
 O S:HOH634 2.3 36.1 1.0
O L:HOH897 2.4 27.0 1.0
O S:HOH652 2.4 45.8 0.7
O L:HOH1085 2.4 35.0 0.7
O S:HOH539 2.5 31.6 1.0
O S:HOH755 2.7 33.9 0.7
OE2 S:GLU103 4.3 33.4 0.7
O S:HOH517 4.3 19.1 1.0
O L:PRO311 4.3 18.1 1.0
OE1 S:GLU103 4.4 34.1 0.7
NH2 S:ARG87 4.5 21.2 1.0
CZ L:PHE291 4.5 14.9 1.0
CD S:ARG87 4.6 14.8 1.0
O S:HOH759 4.7 47.7 1.0
CD S:GLU103 4.8 32.7 0.7
O L:HOH1010 4.8 40.0 1.0
CE1 L:PHE291 4.8 14.4 1.0

Calcium binding site 3 out of 8 in 4ko2

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Calcium binding site 3 out of 8 in the Low X-Ray Dose 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 Low X-Ray Dose 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:28.2
occ:0.50
 O S:HOH708 2.2 47.3 1.0
O S:HOH574 2.5 39.6 1.0
OD2 S:ASP39 2.9 27.0 1.0
OD1 S:ASP39 3.1 25.7 1.0
CG S:ASP39 3.4 20.1 1.0
O M:HOH979 4.3 40.5 1.0
O M:HOH799 4.4 24.3 1.0
OE2 S:GLU35 4.6 17.1 1.0
CB S:LEU38 4.6 11.6 1.0
CG S:GLU35 4.7 13.3 1.0
O M:HOH801 4.9 35.0 1.0
O M:HOH765 4.9 24.3 1.0
CB S:ASP39 4.9 15.4 1.0
CD1 S:LEU38 4.9 13.4 1.0
O S:HOH742 5.0 31.3 0.8

Calcium binding site 4 out of 8 in 4ko2

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Calcium binding site 4 out of 8 in the Low X-Ray Dose 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 Low X-Ray Dose 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:11.6
occ:0.80
 O L:HOH610 2.2 17.2 1.0
O L:HOH609 2.3 17.3 0.8
O L:HOH608 2.3 10.8 1.0
OE1 L:GLU51 2.4 11.4 1.0
O L:ILE444 2.4 9.8 1.0
NE2 L:HIS498 2.5 10.3 1.0
CD L:GLU51 3.3 11.6 1.0
CE1 L:HIS498 3.3 12.5 1.0
OE2 L:GLU51 3.5 12.0 1.0
C L:ILE444 3.5 9.2 1.0
CD2 L:HIS498 3.5 9.0 1.0
N L:ILE444 3.9 9.4 1.0
CA L:ILE444 4.1 9.6 1.0
OE1 L:GLU285 4.2 14.0 1.0
OE1 L:GLN443 4.3 14.3 1.0
NZ L:LYS321 4.4 18.5 1.0
CB L:ILE444 4.4 10.0 1.0
OE2 L:GLU285 4.4 18.4 1.0
ND1 L:HIS498 4.5 11.9 1.0
O L:HOH624 4.6 10.6 1.0
CG L:GLU51 4.6 9.3 1.0
CG L:HIS498 4.6 9.1 1.0
N L:VAL445 4.6 8.4 1.0
O L:HOH639 4.7 14.0 1.0
CD L:GLU285 4.8 14.5 1.0
CD L:LYS321 4.8 14.8 1.0
CE L:LYS321 4.9 17.8 1.0
C L:GLN443 4.9 10.6 1.0
CA L:VAL445 4.9 8.4 1.0

Calcium binding site 5 out of 8 in 4ko2

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Calcium binding site 5 out of 8 in the Low X-Ray Dose 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 Low X-Ray Dose 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:20.9
occ:0.60
 O T:HOH545 2.3 24.6 0.6
O T:HOH578 2.3 27.7 0.6
O T:HOH526 2.3 29.1 0.6
O T:HOH536 2.4 23.9 0.6
O M:HOH612 2.4 22.8 1.0
O M:HOH618 2.5 28.0 0.6
O T:HOH505 2.5 27.4 1.0
OE2 T:GLU103 4.0 38.0 0.7
O T:HOH473 4.3 19.8 1.0
OE1 T:GLU103 4.4 34.3 0.7
O M:PRO311 4.4 15.9 1.0
NH2 T:ARG87 4.5 20.9 1.0
CD T:ARG87 4.6 16.6 1.0
CD T:GLU103 4.6 33.5 0.7
CZ M:PHE291 4.6 12.1 1.0
O M:HOH793 4.7 31.9 1.0

Calcium binding site 6 out of 8 in 4ko2

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Calcium binding site 6 out of 8 in the Low X-Ray Dose 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 Low X-Ray Dose 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:28.9
occ:0.60
 O T:HOH498 2.2 30.5 1.0
OD2 T:ASP271 2.3 18.7 1.0
O T:HOH718 2.4 44.0 1.0
O T:HOH729 2.4 32.3 0.7
O T:HOH468 2.6 32.4 1.0
O T:GLY275 2.8 18.1 1.0
C T:GLY275 3.6 15.3 1.0
CG T:ASP271 3.6 18.2 1.0
O T:HOH670 3.6 56.8 1.0
CA T:GLY275 3.6 13.7 1.0
O T:HOH619 4.2 40.4 1.0
O T:HOH614 4.4 39.0 1.0
NZ T:LYS276 4.4 21.0 1.0
CB T:ASP271 4.4 12.8 1.0
OD1 T:ASP271 4.4 20.6 1.0
N T:LYS276 4.8 14.0 1.0
O T:HOH575 4.9 35.3 1.0
O T:HOH719 4.9 44.7 1.0

Calcium binding site 7 out of 8 in 4ko2

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Calcium binding site 7 out of 8 in the Low X-Ray Dose 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 Low X-Ray Dose 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:52.0
occ:0.70
 O T:HOH474 2.3 15.2 1.0
O T:HOH715 2.4 36.3 1.0
O T:HOH721 2.7 30.8 1.0
O T:HOH580 2.7 45.6 1.0
O T:ASP195 2.9 18.6 1.0
OD1 T:ASP196 3.0 21.7 1.0
O T:HOH732 3.4 30.4 0.5
O T:HOH465 3.7 46.5 1.0
C T:ASP195 3.8 17.8 1.0
CG T:ASP196 3.8 17.9 1.0
OD2 T:ASP196 4.3 17.6 1.0
CB T:ASP195 4.3 17.8 1.0
NH2 T:ARG146 4.3 19.8 1.0
N T:ASP196 4.4 15.6 1.0
CA T:ASP196 4.5 15.8 1.0
CA T:ASP195 4.6 17.1 1.0
O T:HOH629 4.7 36.9 1.0
CB T:ASP196 4.8 16.4 1.0
O T:HOH522 4.8 30.0 1.0
O T:HOH606 4.8 30.5 1.0

Calcium binding site 8 out of 8 in 4ko2

Go back to Calcium Binding Sites List in 4ko2
Calcium binding site 8 out of 8 in the Low X-Ray Dose 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 8 of Low X-Ray Dose 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:13.5
occ:0.80
 O M:HOH624 2.2 27.3 1.0
O M:HOH623 2.2 14.5 1.0
O M:HOH625 2.3 21.0 1.0
O M:ILE444 2.4 13.2 1.0
OE1 M:GLU51 2.4 13.2 1.0
NE2 M:HIS498 2.5 13.2 1.0
CD M:GLU51 3.3 14.3 1.0
CE1 M:HIS498 3.3 15.1 1.0
OE2 M:GLU51 3.5 16.7 1.0
CD2 M:HIS498 3.5 14.0 1.0
C M:ILE444 3.5 13.8 1.0
N M:ILE444 3.9 15.1 1.0
OE1 M:GLU285 4.1 18.6 1.0
CA M:ILE444 4.2 14.7 1.0
OE1 M:GLN443 4.3 21.0 1.0
OE2 M:GLU285 4.3 17.7 1.0
NZ M:LYS321 4.4 18.7 1.0
CB M:ILE444 4.5 14.5 1.0
ND1 M:HIS498 4.5 14.2 1.0
O M:HOH640 4.5 12.6 1.0
CG M:HIS498 4.6 13.2 1.0
N M:VAL445 4.6 12.8 1.0
CG M:GLU51 4.7 11.7 1.0
CD M:GLU285 4.7 17.2 1.0
CD M:LYS321 4.7 13.1 1.0
O M:HOH655 4.7 15.9 1.0
CE M:LYS321 4.8 16.4 1.0
CA M:VAL445 5.0 14.1 1.0
C M:GLN443 5.0 15.5 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: ESSN 1364-548X
PubMed: 23811828
DOI: 10.1039/C3CC43619E
Page generated: Sun Jul 14 09:15:24 2024

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