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Calcium in PDB 4ko1: High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

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

All present enzymatic activity of High 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 High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko1 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 / 1.55
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 (%) 14.7 / 18.4

Other elements in 4ko1:

The structure of High 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) 26 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the High X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4ko1). 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 X-Ray Dose Structure of H2-Activated Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4ko1

Go back to Calcium Binding Sites List in 4ko1
Calcium binding site 1 out of 7 in the High 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 High 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:12.3
occ:1.00
 O S:GLU152 2.3 10.8 1.0
O S:HOH456 2.4 15.6 1.0
O S:HOH458 2.4 19.3 1.0
O S:HOH455 2.4 15.8 1.0
O S:HOH472 2.5 20.0 1.0
C S:GLU152 3.4 10.8 1.0
CA S:GLU152 4.1 10.8 1.0
OE1 S:GLU152 4.2 14.3 1.0
CB S:GLU152 4.4 9.8 1.0
N S:LYS153 4.5 10.7 1.0
CB S:LYS153 4.5 12.3 1.0
O S:LYS153 4.6 14.7 1.0
C S:LYS153 4.7 12.6 1.0
CA S:LYS153 4.8 12.9 1.0
O S:HOH489 4.8 20.7 0.3

Calcium binding site 2 out of 7 in 4ko1

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Calcium binding site 2 out of 7 in the High 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 High 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:34.8
occ:0.70
 O S:HOH634 2.3 35.7 1.0
O L:HOH897 2.4 26.9 1.0
O S:HOH652 2.4 50.0 0.7
O L:HOH1085 2.4 37.3 0.7
O S:HOH539 2.5 34.0 1.0
O S:HOH754 2.7 35.0 0.7
OE2 S:GLU103 4.3 34.9 0.7
O S:HOH517 4.3 20.7 1.0
O L:PRO311 4.3 18.7 1.0
OE1 S:GLU103 4.4 36.2 0.7
NH2 S:ARG87 4.5 22.6 1.0
CZ L:PHE291 4.5 15.9 1.0
CD S:ARG87 4.6 15.6 1.0
CD S:GLU103 4.8 33.3 0.7
O S:HOH758 4.8 48.0 1.0
CE1 L:PHE291 4.8 14.6 1.0
O L:HOH1010 4.8 40.0 1.0

Calcium binding site 3 out of 7 in 4ko1

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Calcium binding site 3 out of 7 in the High 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 High 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:12.4
occ:0.80
 O L:HOH610 2.2 18.2 1.0
O L:HOH609 2.3 19.3 0.8
O L:HOH608 2.3 12.2 1.0
OE1 L:GLU51 2.4 12.4 1.0
O L:ILE444 2.4 10.2 1.0
NE2 L:HIS498 2.5 11.0 1.0
CD L:GLU51 3.2 12.2 1.0
CE1 L:HIS498 3.3 11.9 1.0
OE2 L:GLU51 3.5 13.0 1.0
C L:ILE444 3.5 9.3 1.0
CD2 L:HIS498 3.5 9.4 1.0
N L:ILE444 3.9 9.8 1.0
CA L:ILE444 4.1 10.7 1.0
OE1 L:GLU285 4.2 14.8 1.0
OE1 L:GLN443 4.3 15.1 1.0
NZ L:LYS321 4.3 19.8 1.0
CB L:ILE444 4.4 10.0 1.0
OE2 L:GLU285 4.4 19.0 1.0
ND1 L:HIS498 4.5 12.1 1.0
CG L:GLU51 4.6 9.9 1.0
O L:HOH624 4.6 11.5 1.0
N L:VAL445 4.6 8.9 1.0
CG L:HIS498 4.6 9.9 1.0
O L:HOH640 4.7 15.3 1.0
CD L:GLU285 4.7 15.4 1.0
CD L:LYS321 4.9 15.7 1.0
CE L:LYS321 4.9 18.4 1.0
C L:GLN443 4.9 10.8 1.0
CA L:VAL445 4.9 8.8 1.0

Calcium binding site 4 out of 7 in 4ko1

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Calcium binding site 4 out of 7 in the High 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 High 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:20.7
occ:0.60
 O T:HOH556 2.3 25.5 0.6
O T:HOH589 2.3 29.7 0.6
O T:HOH537 2.3 30.3 0.6
O T:HOH547 2.4 25.0 0.6
O M:HOH612 2.4 22.8 1.0
O T:HOH515 2.5 26.7 1.0
O M:HOH617 2.5 29.6 0.6
OE2 T:GLU103 4.0 38.5 0.7
O T:HOH483 4.3 19.1 1.0
OE1 T:GLU103 4.4 35.9 0.7
O M:PRO311 4.4 16.6 1.0
NH2 T:ARG87 4.5 21.8 1.0
CD T:ARG87 4.6 17.5 1.0
CD T:GLU103 4.6 34.5 0.7
CZ M:PHE291 4.6 13.3 1.0
O M:HOH793 4.7 33.1 1.0

Calcium binding site 5 out of 7 in 4ko1

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Calcium binding site 5 out of 7 in the High 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 High 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:29.2
occ:0.60
 O T:HOH508 2.2 29.9 1.0
OD2 T:ASP271 2.3 20.5 1.0
O T:HOH407 2.4 36.6 0.7
O T:HOH728 2.4 46.9 1.0
O T:HOH478 2.6 31.8 1.0
O T:GLY275 2.8 18.4 1.0
C T:GLY275 3.6 15.4 1.0
CG T:ASP271 3.6 19.2 1.0
O T:HOH681 3.6 54.8 1.0
CA T:GLY275 3.6 14.3 1.0
O T:HOH630 4.3 41.6 1.0
NZ T:LYS276 4.4 21.8 1.0
O T:HOH625 4.4 36.5 1.0
CB T:ASP271 4.4 13.5 1.0
OD1 T:ASP271 4.4 21.9 1.0
N T:LYS276 4.8 14.5 1.0
O T:HOH586 4.9 32.0 1.0
O T:HOH729 4.9 44.8 1.0

Calcium binding site 6 out of 7 in 4ko1

Go back to Calcium Binding Sites List in 4ko1
Calcium binding site 6 out of 7 in the High 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 High 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:50.0
occ:0.70
 O T:HOH484 2.3 16.5 1.0
O T:HOH725 2.4 35.5 1.0
O T:HOH731 2.7 34.2 1.0
O T:HOH591 2.7 42.2 1.0
O T:ASP195 2.9 19.0 1.0
OD1 T:ASP196 3.0 21.8 1.0
O T:HOH475 3.7 50.3 1.0
C T:ASP195 3.7 18.3 1.0
CG T:ASP196 3.8 17.4 1.0
CB T:ASP195 4.3 18.9 1.0
OD2 T:ASP196 4.3 18.6 1.0
NH2 T:ARG146 4.3 20.4 1.0
N T:ASP196 4.4 16.6 1.0
CA T:ASP196 4.5 16.5 1.0
CA T:ASP195 4.6 17.5 1.0
O T:HOH640 4.7 36.3 1.0
CB T:ASP196 4.8 17.2 1.0
O T:HOH533 4.8 30.5 1.0
O T:HOH617 4.8 30.6 1.0

Calcium binding site 7 out of 7 in 4ko1

Go back to Calcium Binding Sites List in 4ko1
Calcium binding site 7 out of 7 in the High 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 High 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:13.9
occ:0.80
 O M:HOH624 2.2 28.0 1.0
O M:HOH623 2.2 15.4 1.0
O M:HOH625 2.3 21.2 1.0
O M:ILE444 2.4 13.8 1.0
OE1 M:GLU51 2.4 13.9 1.0
NE2 M:HIS498 2.5 13.2 1.0
CD M:GLU51 3.3 14.4 1.0
CE1 M:HIS498 3.3 15.6 1.0
OE2 M:GLU51 3.5 17.1 1.0
C M:ILE444 3.5 14.1 1.0
CD2 M:HIS498 3.5 13.5 1.0
N M:ILE444 3.9 15.9 1.0
OE1 M:GLU285 4.1 19.9 1.0
CA M:ILE444 4.2 14.5 1.0
OE1 M:GLN443 4.3 22.9 1.0
OE2 M:GLU285 4.3 19.7 1.0
NZ M:LYS321 4.4 20.2 1.0
CB M:ILE444 4.5 14.7 1.0
ND1 M:HIS498 4.5 14.7 1.0
O M:HOH640 4.5 12.9 1.0
N M:VAL445 4.6 13.5 1.0
CG M:HIS498 4.6 13.2 1.0
CG M:GLU51 4.7 12.3 1.0
CD M:GLU285 4.7 17.7 1.0
O M:HOH655 4.7 15.8 1.0
CD M:LYS321 4.7 13.8 1.0
CE M:LYS321 4.8 17.4 1.0
CA M:VAL445 5.0 14.4 1.0
C M:GLN443 5.0 16.0 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 09:12:15 2024

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