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Calcium in PDB 4ko3: Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

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

All present enzymatic activity of Low 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 Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko3 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 / 1.70
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 (%) 16.4 / 20.1

Other elements in 4ko3:

The structure of Low 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 Low X-Ray Dose Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4ko3). 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 Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4ko3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4ko3

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Calcium binding site 1 out of 8 in the Low 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 Low 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:10.1
occ:1.00
 O S:GLU152 2.3 9.5 1.0
O S:HOH457 2.5 15.9 1.0
O S:HOH454 2.5 10.8 1.0
O S:HOH455 2.5 11.1 1.0
O S:HOH471 2.5 13.0 1.0
C S:GLU152 3.4 8.7 1.0
CA S:GLU152 4.1 8.9 1.0
OE1 S:GLU152 4.3 9.2 1.0
CB S:GLU152 4.4 8.6 1.0
N S:LYS153 4.4 8.7 1.0
CB S:LYS153 4.5 10.6 1.0
O S:LYS153 4.5 10.7 1.0
C S:LYS153 4.6 10.7 1.0
CA S:LYS153 4.7 10.1 1.0
O S:HOH488 4.9 13.3 0.3

Calcium binding site 2 out of 8 in 4ko3

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Calcium binding site 2 out of 8 in the Low 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 Low 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:25.7
occ:0.60
 O S:HOH634 2.3 33.4 1.0
O S:HOH652 2.4 42.0 1.0
O S:HOH539 2.4 32.6 1.0
O L:HOH901 2.5 25.3 1.0
O L:HOH1095 2.6 27.6 0.5
O S:HOH767 2.6 16.8 0.4
O L:HOH1045 4.2 25.1 0.6
OE2 S:GLU103 4.3 25.8 0.6
O S:HOH516 4.3 17.1 1.0
OE1 S:GLU103 4.3 28.2 0.6
O L:PRO311 4.4 13.5 1.0
O S:HOH762 4.4 37.0 1.0
OE1 S:GLU103 4.5 23.5 0.4
CZ L:PHE291 4.5 12.5 1.0
CD S:ARG87 4.5 12.3 1.0
NH2 S:ARG87 4.6 18.5 1.0
O L:HOH1015 4.7 18.0 0.5
CD S:GLU103 4.8 25.5 0.6
CE1 L:PHE291 4.8 12.0 1.0

Calcium binding site 3 out of 8 in 4ko3

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Calcium binding site 3 out of 8 in the Low 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 Low 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:8.3
occ:1.00
 O L:HOH609 2.3 6.5 1.0
OE1 L:GLU51 2.3 7.7 1.0
O L:HOH610 2.3 12.1 1.0
O L:ILE444 2.3 7.1 1.0
O L:HOH611 2.4 8.9 1.0
NE2 L:HIS498 2.4 8.2 1.0
CD L:GLU51 3.3 6.9 1.0
CE1 L:HIS498 3.3 5.4 1.0
C L:ILE444 3.5 7.4 1.0
CD2 L:HIS498 3.5 6.7 1.0
OE2 L:GLU51 3.5 7.9 1.0
N L:ILE444 3.8 7.8 1.0
CA L:ILE444 4.1 7.8 1.0
OE1 L:GLU285 4.2 9.5 1.0
OE1 L:GLN443 4.3 10.1 1.0
NZ L:LYS321 4.3 9.3 1.0
CB L:ILE444 4.3 6.5 1.0
OE2 L:GLU285 4.4 11.1 1.0
O L:HOH626 4.5 8.3 1.0
ND1 L:HIS498 4.5 8.0 1.0
N L:VAL445 4.6 7.1 1.0
CG L:HIS498 4.6 7.4 1.0
CG L:GLU51 4.6 6.4 1.0
O L:HOH642 4.7 8.7 1.0
CD L:LYS321 4.7 8.6 1.0
CD L:GLU285 4.8 8.5 1.0
CE L:LYS321 4.8 8.8 1.0
C L:GLN443 4.9 8.0 1.0
CA L:VAL445 4.9 6.8 1.0

Calcium binding site 4 out of 8 in 4ko3

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Calcium binding site 4 out of 8 in the Low 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 Low 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:15.8
occ:0.60
 O T:HOH580 2.3 22.5 0.6
O T:HOH547 2.3 20.4 0.6
O T:HOH538 2.4 16.3 0.6
O M:HOH615 2.4 15.8 1.0
O T:HOH528 2.4 19.4 0.6
O M:HOH620 2.4 23.7 0.6
O T:HOH506 2.5 20.9 1.0
OE2 T:GLU103 4.0 28.2 0.6
O T:HOH474 4.3 17.0 1.0
O T:HOH735 4.3 39.7 1.0
O M:PRO311 4.4 13.1 1.0
OE1 T:GLU103 4.4 24.5 0.6
NH2 T:ARG87 4.5 15.2 1.0
O T:HOH754 4.5 27.0 1.0
CD T:ARG87 4.6 11.8 1.0
CZ M:PHE291 4.6 9.6 1.0
CD T:GLU103 4.7 26.3 0.6

Calcium binding site 5 out of 8 in 4ko3

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Calcium binding site 5 out of 8 in the Low 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 Low 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:26.7
occ:0.60
 O T:HOH499 2.3 26.7 1.0
O T:HOH746 2.3 49.3 1.0
OD2 T:ASP271 2.3 15.4 1.0
O T:HOH728 2.5 46.5 1.0
O T:HOH469 2.8 27.3 1.0
O T:GLY275 2.9 14.3 1.0
CA T:GLY275 3.6 10.8 1.0
C T:GLY275 3.6 11.9 1.0
CG T:ASP271 3.6 14.3 1.0
O T:HOH676 3.7 57.1 1.0
O T:HOH621 4.2 66.6 1.0
OD1 T:ASP271 4.4 18.1 1.0
CB T:ASP271 4.4 10.8 1.0
O T:HOH616 4.4 40.1 1.0
NZ T:LYS276 4.4 14.8 1.0
N T:LYS276 4.8 11.4 1.0
O T:HOH730 4.9 37.5 1.0
O T:HOH577 4.9 27.2 1.0
N T:GLY275 5.0 10.8 1.0

Calcium binding site 6 out of 8 in 4ko3

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Calcium binding site 6 out of 8 in the Low 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 Low 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:46.3
occ:0.70
 O T:HOH724 2.3 32.3 1.0
O T:HOH475 2.4 14.4 1.0
O T:HOH732 2.6 32.1 1.0
O T:HOH582 2.9 38.7 1.0
O T:ASP195 3.0 16.4 1.0
OD1 T:ASP196 3.1 19.4 1.0
O T:HOH466 3.2 39.4 1.0
C T:ASP195 3.8 15.2 1.0
CG T:ASP196 3.9 15.6 1.0
CB T:ASP195 4.2 15.4 1.0
OD2 T:ASP196 4.3 15.8 1.0
N T:ASP196 4.4 14.7 1.0
NH2 T:ARG146 4.5 16.4 1.0
CA T:ASP196 4.6 14.1 1.0
O T:HOH608 4.6 27.7 1.0
CA T:ASP195 4.6 14.6 1.0
O T:HOH524 4.6 23.1 1.0
O T:HOH631 4.8 34.9 1.0
CB T:ASP196 4.9 15.0 1.0

Calcium binding site 7 out of 8 in 4ko3

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Calcium binding site 7 out of 8 in the Low 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 Low 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 9.3 1.0
O M:HOH626 2.3 13.0 1.0
OE1 M:GLU51 2.3 9.2 1.0
O M:ILE444 2.3 10.6 1.0
O M:HOH627 2.4 10.6 1.0
NE2 M:HIS498 2.4 8.5 1.0
CD M:GLU51 3.3 8.9 1.0
CE1 M:HIS498 3.3 10.3 1.0
C M:ILE444 3.5 10.3 1.0
CD2 M:HIS498 3.5 10.9 1.0
OE2 M:GLU51 3.5 11.1 1.0
N M:ILE444 3.8 10.5 1.0
CA M:ILE444 4.1 10.4 1.0
OE1 M:GLU285 4.1 12.1 1.0
OE2 M:GLU285 4.3 11.3 1.0
NZ M:LYS321 4.3 11.1 1.0
NE2 M:GLN443 4.4 12.0 1.0
CB M:ILE444 4.4 10.5 1.0
O M:HOH642 4.5 9.4 1.0
ND1 M:HIS498 4.5 9.1 1.0
O M:HOH657 4.6 11.7 1.0
N M:VAL445 4.6 10.4 1.0
CG M:HIS498 4.6 8.4 1.0
CG M:GLU51 4.6 8.5 1.0
CD M:LYS321 4.7 10.5 1.0
CD M:GLU285 4.7 12.4 1.0
CE M:LYS321 4.8 11.4 1.0
C M:GLN443 4.9 10.7 1.0
CA M:VAL445 4.9 11.3 1.0

Calcium binding site 8 out of 8 in 4ko3

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Calcium binding site 8 out of 8 in the Low 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 Low 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:37.2
occ:0.50
 OD1 M:ASP17 2.4 14.5 1.0
O T:HOH593 2.4 39.4 1.0
O M:HOH767 2.5 18.5 1.0
O M:LEU26 3.2 10.3 1.0
N M:LEU26 3.3 9.5 1.0
CG M:ASP17 3.4 14.9 1.0
C M:LEU26 3.5 9.9 1.0
C M:HIS25 3.7 9.3 1.0
O T:ILE90 3.7 11.4 1.0
CA M:HIS25 3.9 9.4 1.0
OD2 M:ASP17 3.9 18.5 1.0
CB M:HIS25 3.9 8.8 1.0
O M:HOH832 4.0 25.5 1.0
CA M:LEU26 4.0 9.7 1.0
CA M:PRO18 4.0 10.8 1.0
O M:HOH722 4.1 12.2 1.0
O T:VAL91 4.2 13.0 1.0
N M:LYS27 4.2 9.2 1.0
C T:VAL91 4.2 11.8 1.0
CB M:PRO18 4.3 10.8 1.0
O M:HIS25 4.4 11.3 1.0
ND1 M:HIS25 4.5 12.9 1.0
N T:GLY92 4.5 11.7 1.0
CB M:ASP17 4.6 11.9 1.0
N M:PRO18 4.6 11.7 1.0
C T:ILE90 4.6 11.3 1.0
CA T:VAL91 4.7 10.7 1.0
CG M:HIS25 4.7 11.6 1.0
CA M:ASP17 4.7 11.2 1.0
CA M:LYS27 4.8 9.7 1.0
CB M:LYS27 4.8 9.4 1.0
CA T:GLY92 4.8 13.5 1.0
O M:HOH614 4.8 20.3 1.0
C M:ASP17 4.9 10.7 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 09:15:24 2024

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