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Calcium in PDB 4ko4: High X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

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

All present enzymatic activity of High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko4 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.200, 108.720, 136.620, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.2

Other elements in 4ko4:

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

Nickel (Ni) 6 atoms
Iron (Fe) 28 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the High X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4ko4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the High X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4ko4

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Calcium binding site 1 out of 8 in the High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca304

b:7.7
occ:1.00
 O S:GLU152 2.3 9.8 1.0
O S:HOH457 2.4 12.7 1.0
O S:HOH454 2.5 7.5 1.0
O S:HOH455 2.5 8.5 1.0
O S:HOH471 2.5 10.2 1.0
C S:GLU152 3.4 10.5 1.0
CA S:GLU152 4.1 10.1 1.0
OE1 S:GLU152 4.3 11.0 1.0
CB S:GLU152 4.4 8.3 1.0
N S:LYS153 4.4 10.1 1.0
CB S:LYS153 4.5 11.5 1.0
O S:LYS153 4.5 12.0 1.0
C S:LYS153 4.6 11.6 1.0
CA S:LYS153 4.7 11.7 1.0
O S:HOH488 4.8 7.0 0.3

Calcium binding site 2 out of 8 in 4ko4

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Calcium binding site 2 out of 8 in the High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca308

b:23.5
occ:0.60
 O S:HOH633 2.3 29.1 1.0
O S:HOH651 2.4 36.9 1.0
O L:HOH900 2.5 23.7 1.0
O S:HOH539 2.5 29.3 1.0
O S:HOH772 2.5 14.3 0.4
O L:HOH1093 2.7 19.4 0.5
O L:HOH1044 4.1 24.1 0.6
OE2 S:GLU103 4.3 27.5 0.6
O S:HOH516 4.3 13.8 1.0
OE1 S:GLU103 4.4 28.0 0.6
O L:PRO311 4.4 14.5 1.0
O S:HOH766 4.4 33.1 1.0
OE1 S:GLU103 4.5 26.4 0.4
CZ L:PHE291 4.5 10.7 1.0
CD S:ARG87 4.6 14.2 1.0
NH2 S:ARG87 4.6 19.2 1.0
O L:HOH1014 4.7 16.2 0.5
CD S:GLU103 4.8 25.5 0.6
CE1 L:PHE291 4.9 12.4 1.0

Calcium binding site 3 out of 8 in 4ko4

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Calcium binding site 3 out of 8 in the High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca503

b:8.7
occ:1.00
 O L:HOH608 2.3 6.8 1.0
O L:HOH609 2.3 11.3 1.0
OE1 L:GLU51 2.3 7.5 1.0
O L:ILE444 2.3 6.4 1.0
O L:HOH610 2.4 9.1 1.0
NE2 L:HIS498 2.4 7.1 1.0
CD L:GLU51 3.3 6.6 1.0
CE1 L:HIS498 3.3 6.3 1.0
C L:ILE444 3.5 6.5 1.0
CD2 L:HIS498 3.5 6.5 1.0
OE2 L:GLU51 3.5 7.5 1.0
N L:ILE444 3.8 7.5 1.0
CA L:ILE444 4.1 7.2 1.0
OE1 L:GLU285 4.2 10.1 1.0
OE1 L:GLN443 4.3 10.8 1.0
NZ L:LYS321 4.3 10.7 1.0
CB L:ILE444 4.4 6.2 1.0
OE2 L:GLU285 4.4 11.4 1.0
ND1 L:HIS498 4.5 7.5 1.0
O L:HOH625 4.5 6.3 1.0
N L:VAL445 4.6 7.2 1.0
CG L:HIS498 4.6 6.4 1.0
CG L:GLU51 4.6 6.7 1.0
O L:HOH640 4.7 7.4 1.0
CD L:LYS321 4.7 9.9 1.0
CD L:GLU285 4.8 10.0 1.0
CE L:LYS321 4.8 9.5 1.0
C L:GLN443 4.9 8.0 1.0
CA L:VAL445 4.9 6.4 1.0

Calcium binding site 4 out of 8 in 4ko4

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Calcium binding site 4 out of 8 in the High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca304

b:12.8
occ:0.60
 O T:HOH579 2.2 18.2 0.6
O T:HOH547 2.3 14.8 0.6
O T:HOH538 2.3 14.3 0.6
O M:HOH614 2.4 13.9 1.0
O M:HOH618 2.4 17.1 0.6
O T:HOH506 2.5 16.8 1.0
O M:HOH620 2.5 19.1 0.6
OE2 T:GLU103 4.1 28.4 0.6
O T:HOH474 4.2 13.1 1.0
O M:HOH1104 4.3 38.5 1.0
O M:PRO311 4.4 13.1 1.0
OE1 T:GLU103 4.4 26.9 0.6
NH2 T:ARG87 4.5 15.5 1.0
O T:HOH750 4.5 24.4 1.0
CZ M:PHE291 4.6 9.8 1.0
CD T:ARG87 4.6 14.9 1.0
CD T:GLU103 4.7 26.5 0.6

Calcium binding site 5 out of 8 in 4ko4

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Calcium binding site 5 out of 8 in the High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca305

b:24.9
occ:0.60
 O T:HOH499 2.3 21.3 1.0
O T:HOH746 2.3 50.9 1.0
OD2 T:ASP271 2.3 17.0 1.0
O T:HOH727 2.4 38.1 1.0
O T:HOH469 2.7 27.2 1.0
O T:GLY275 2.9 15.6 1.0
CA T:GLY275 3.6 12.3 1.0
CG T:ASP271 3.6 15.9 1.0
C T:GLY275 3.6 13.5 1.0
O T:HOH675 3.7 48.0 1.0
O T:HOH620 4.3 58.7 1.0
O T:HOH615 4.4 32.1 1.0
OD1 T:ASP271 4.4 17.7 1.0
CB T:ASP271 4.4 11.9 1.0
NZ T:LYS276 4.4 16.4 1.0
N T:LYS276 4.8 12.3 1.0
O T:HOH729 4.9 32.2 1.0
O T:HOH576 4.9 26.2 1.0
N T:GLY275 5.0 11.5 1.0

Calcium binding site 6 out of 8 in 4ko4

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Calcium binding site 6 out of 8 in the High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca306

b:47.0
occ:0.70
 O T:HOH723 2.3 27.8 1.0
O T:HOH475 2.4 9.2 1.0
O T:HOH731 2.6 28.2 1.0
O T:HOH581 2.8 33.4 1.0
O T:ASP195 3.0 16.8 1.0
OD1 T:ASP196 3.1 19.6 1.0
O T:HOH466 3.2 39.9 1.0
C T:ASP195 3.8 16.1 1.0
CG T:ASP196 3.9 15.7 1.0
CB T:ASP195 4.2 17.8 1.0
OD2 T:ASP196 4.3 16.7 1.0
N T:ASP196 4.4 14.8 1.0
NH2 T:ARG146 4.5 16.4 1.0
CA T:ASP196 4.6 14.7 1.0
O T:HOH607 4.6 22.8 1.0
CA T:ASP195 4.6 15.5 1.0
O T:HOH525 4.6 19.8 1.0
O T:HOH630 4.8 34.3 1.0
CB T:ASP196 4.8 15.7 1.0

Calcium binding site 7 out of 8 in 4ko4

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Calcium binding site 7 out of 8 in the High X-Ray Dose Structure of 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca503

b:10.9
occ:1.00
 O M:HOH625 2.3 8.0 1.0
O M:HOH626 2.3 13.6 1.0
O M:ILE444 2.3 9.3 1.0
OE1 M:GLU51 2.3 9.3 1.0
O M:HOH627 2.4 12.4 1.0
NE2 M:HIS498 2.5 9.4 1.0
CD M:GLU51 3.3 9.3 1.0
CE1 M:HIS498 3.3 9.3 1.0
C M:ILE444 3.5 10.1 1.0
CD2 M:HIS498 3.5 9.2 1.0
OE2 M:GLU51 3.5 10.9 1.0
N M:ILE444 3.8 10.8 1.0
CA M:ILE444 4.1 10.3 1.0
OE1 M:GLU285 4.1 12.7 1.0
OE2 M:GLU285 4.3 13.3 1.0
NZ M:LYS321 4.3 12.3 1.0
NE2 M:GLN443 4.4 11.3 1.0
CB M:ILE444 4.4 9.9 1.0
ND1 M:HIS498 4.5 8.5 1.0
O M:HOH642 4.5 6.7 1.0
O M:HOH657 4.6 8.9 1.0
N M:VAL445 4.6 10.5 1.0
CD M:LYS321 4.6 10.2 1.0
CG M:GLU51 4.6 9.0 1.0
CG M:HIS498 4.6 7.8 1.0
CD M:GLU285 4.7 12.7 1.0
CE M:LYS321 4.8 10.6 1.0
C M:GLN443 4.9 11.1 1.0
CA M:VAL445 4.9 10.8 1.0

Calcium binding site 8 out of 8 in 4ko4

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Calcium binding site 8 out of 8 in the High X-Ray Dose Structure of 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 High X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca507

b:35.3
occ:0.50
 OD1 M:ASP17 2.3 17.9 1.0
O T:HOH592 2.4 35.0 1.0
O M:HOH768 2.5 17.4 1.0
O M:LEU26 3.3 9.8 1.0
CG M:ASP17 3.4 16.8 1.0
N M:LEU26 3.4 8.8 1.0
C M:LEU26 3.6 10.0 1.0
O T:ILE90 3.7 12.4 1.0
C M:HIS25 3.8 9.2 1.0
OD2 M:ASP17 3.8 22.0 1.0
O M:HOH834 3.9 26.5 1.0
CA M:HIS25 4.0 8.6 1.0
CA M:PRO18 4.0 10.9 1.0
CB M:HIS25 4.0 6.7 1.0
CA M:LEU26 4.1 9.0 1.0
O M:HOH723 4.2 9.6 1.0
O T:VAL91 4.2 13.7 1.0
N M:LYS27 4.2 8.7 1.0
C T:VAL91 4.2 12.4 1.0
CB M:PRO18 4.3 11.2 1.0
O M:HIS25 4.5 11.1 1.0
N T:GLY92 4.5 12.3 1.0
ND1 M:HIS25 4.5 11.7 1.0
CB M:ASP17 4.6 12.6 1.0
N M:PRO18 4.6 12.2 1.0
C T:ILE90 4.6 11.4 1.0
CA T:VAL91 4.7 11.2 1.0
CA M:ASP17 4.7 12.1 1.0
CG M:HIS25 4.8 11.3 1.0
CA M:LYS27 4.8 9.8 1.0
CB M:LYS27 4.8 10.0 1.0
CA T:GLY92 4.8 14.5 1.0
O M:HOH613 4.9 18.2 1.0
C M:ASP17 4.9 11.5 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: ISSN 1359-7345
PubMed: 23811828
DOI: 10.1039/C3CC43619E
Page generated: Sat Dec 12 04:55:28 2020

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