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Calcium in PDB 4kl8: High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air

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

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

Protein crystallography data

The structure of High-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kl8 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 / 1.52
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 (%) 12.2 / 17.1

Other elements in 4kl8:

The structure of High-Resolution 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-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air (pdb code 4kl8). 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-Resolution Structure of Anaerobically Purified Dm. Baculatum [Nifese]-Hydrogenase After Crystallization Under Air, PDB code: 4kl8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4kl8

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Calcium binding site 1 out of 8 in the High-Resolution 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-Resolution 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:9.1
occ:1.00
 O S:GLU152 2.3 7.9 1.0
O S:HOH454 2.4 9.3 1.0
O S:HOH457 2.4 15.4 1.0
O S:HOH455 2.5 11.8 1.0
O S:HOH471 2.5 12.4 1.0
C S:GLU152 3.4 8.5 1.0
CA S:GLU152 4.1 8.4 1.0
OE1 S:GLU152 4.3 8.9 1.0
CB S:GLU152 4.4 7.6 1.0
N S:LYS153 4.4 8.0 1.0
CB S:LYS153 4.5 9.4 1.0
O S:LYS153 4.5 10.4 1.0
C S:LYS153 4.6 9.4 1.0
CA S:LYS153 4.7 9.7 1.0
O S:HOH488 4.8 15.4 0.3

Calcium binding site 2 out of 8 in 4kl8

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Calcium binding site 2 out of 8 in the High-Resolution 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-Resolution 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:22.9
occ:0.60
 O S:HOH633 2.3 31.4 1.0
O S:HOH651 2.5 38.9 1.0
O S:HOH539 2.5 31.6 1.0
O L:HOH903 2.5 26.1 1.0
O L:HOH1098 2.6 22.9 0.5
O S:HOH768 2.6 16.4 0.4
O L:HOH1047 4.2 26.9 0.6
OE2 S:GLU103 4.3 26.3 0.6
O S:HOH516 4.3 15.7 1.0
O L:PRO311 4.4 13.2 1.0
OE1 S:GLU103 4.4 27.7 0.6
O S:HOH763 4.4 34.1 1.0
OE1 S:GLU103 4.5 23.3 0.4
CZ L:PHE291 4.5 11.0 1.0
CD S:ARG87 4.5 12.8 1.0
NH2 S:ARG87 4.6 16.7 1.0
O L:HOH1017 4.7 19.3 0.5
CD S:GLU103 4.8 24.6 0.6
CE1 L:PHE291 4.8 10.8 1.0

Calcium binding site 3 out of 8 in 4kl8

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Calcium binding site 3 out of 8 in the High-Resolution 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-Resolution 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:7.6
occ:1.00
 O L:HOH610 2.3 6.6 1.0
OE1 L:GLU51 2.3 6.7 1.0
O L:HOH611 2.3 11.5 1.0
O L:ILE444 2.3 6.2 1.0
O L:HOH612 2.4 9.2 1.0
NE2 L:HIS498 2.4 6.5 1.0
CD L:GLU51 3.3 5.7 1.0
CE1 L:HIS498 3.3 5.9 1.0
C L:ILE444 3.5 5.9 1.0
CD2 L:HIS498 3.5 6.6 1.0
OE2 L:GLU51 3.5 7.1 1.0
N L:ILE444 3.8 7.5 1.0
CA L:ILE444 4.1 7.1 1.0
OE1 L:GLU285 4.2 9.4 1.0
OE1 L:GLN443 4.3 9.6 1.0
NZ L:LYS321 4.3 9.6 1.0
CB L:ILE444 4.4 5.7 1.0
OE2 L:GLU285 4.4 10.3 1.0
ND1 L:HIS498 4.5 7.3 1.0
O L:HOH627 4.5 8.0 1.0
N L:VAL445 4.6 6.6 1.0
CG L:HIS498 4.6 5.6 1.0
CG L:GLU51 4.6 5.9 1.0
O L:HOH643 4.7 9.0 1.0
CD L:LYS321 4.7 7.9 1.0
CD L:GLU285 4.8 7.6 1.0
CE L:LYS321 4.8 7.9 1.0
C L:GLN443 4.9 6.8 1.0
CA L:VAL445 4.9 5.6 1.0

Calcium binding site 4 out of 8 in 4kl8

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Calcium binding site 4 out of 8 in the High-Resolution 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-Resolution 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:13.3
occ:0.60
 O T:HOH581 2.2 20.4 0.6
O T:HOH549 2.3 17.9 0.6
O T:HOH540 2.4 16.6 0.6
O M:HOH612 2.4 16.3 1.0
O T:HOH530 2.4 19.6 0.6
O T:HOH507 2.5 19.1 1.0
O M:HOH617 2.5 22.6 0.6
OE2 T:GLU103 4.0 26.7 0.6
O T:HOH475 4.2 15.1 1.0
O T:HOH736 4.3 40.8 1.0
O M:PRO311 4.4 11.9 1.0
OE1 T:GLU103 4.4 25.6 0.6
NH2 T:ARG87 4.5 12.8 1.0
O T:HOH754 4.5 25.2 1.0
CZ M:PHE291 4.6 7.9 1.0
CD T:ARG87 4.6 11.8 1.0
CD T:GLU103 4.7 25.5 0.6

Calcium binding site 5 out of 8 in 4kl8

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Calcium binding site 5 out of 8 in the High-Resolution 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-Resolution 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:24.7
occ:0.60
 OD2 T:ASP271 2.3 15.1 1.0
O T:HOH500 2.3 24.0 1.0
O T:HOH747 2.4 48.8 1.0
O T:HOH729 2.4 46.1 1.0
O T:HOH470 2.8 29.9 1.0
O T:GLY275 2.9 13.6 1.0
CG T:ASP271 3.5 13.2 1.0
CA T:GLY275 3.6 9.4 1.0
C T:GLY275 3.6 11.1 1.0
O T:HOH677 3.7 51.2 1.0
O T:HOH622 4.3 77.6 1.0
O T:HOH617 4.4 36.5 1.0
OD1 T:ASP271 4.4 16.4 1.0
CB T:ASP271 4.4 10.3 1.0
NZ T:LYS276 4.4 14.2 1.0
N T:LYS276 4.8 10.1 1.0
O T:HOH731 4.9 33.7 1.0
N T:GLY275 5.0 9.8 1.0
O T:HOH578 5.0 29.6 1.0

Calcium binding site 6 out of 8 in 4kl8

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Calcium binding site 6 out of 8 in the High-Resolution 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-Resolution 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:47.5
occ:0.70
 O T:HOH725 2.3 30.2 1.0
O T:HOH476 2.4 11.5 1.0
O T:HOH733 2.6 34.3 1.0
O T:HOH583 2.9 34.5 1.0
O T:ASP195 3.0 15.6 1.0
OD1 T:ASP196 3.0 17.9 1.0
O T:HOH467 3.2 40.5 1.0
C T:ASP195 3.8 14.4 1.0
CG T:ASP196 3.9 12.8 1.0
CB T:ASP195 4.2 14.9 1.0
OD2 T:ASP196 4.3 14.4 1.0
N T:ASP196 4.4 13.2 1.0
NH2 T:ARG146 4.4 14.8 1.0
CA T:ASP196 4.6 13.4 1.0
CA T:ASP195 4.6 13.5 1.0
O T:HOH609 4.6 25.4 1.0
O T:HOH526 4.6 21.2 1.0
O T:HOH632 4.7 34.0 1.0
CB T:ASP196 4.8 14.1 1.0

Calcium binding site 7 out of 8 in 4kl8

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Calcium binding site 7 out of 8 in the High-Resolution 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-Resolution 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:9.9
occ:1.00
 O M:HOH622 2.3 8.0 1.0
O M:HOH623 2.3 11.7 1.0
OE1 M:GLU51 2.3 8.7 1.0
O M:ILE444 2.3 9.0 1.0
O M:HOH624 2.4 11.9 1.0
NE2 M:HIS498 2.5 8.6 1.0
CD M:GLU51 3.3 7.9 1.0
CE1 M:HIS498 3.3 9.9 1.0
C M:ILE444 3.5 9.3 1.0
OE2 M:GLU51 3.5 10.7 1.0
CD2 M:HIS498 3.5 8.5 1.0
N M:ILE444 3.8 9.9 1.0
CA M:ILE444 4.1 9.4 1.0
OE1 M:GLU285 4.2 11.3 1.0
OE2 M:GLU285 4.3 11.6 1.0
NZ M:LYS321 4.4 10.8 1.0
NE2 M:GLN443 4.4 10.9 1.0
CB M:ILE444 4.4 9.1 1.0
ND1 M:HIS498 4.5 8.0 1.0
O M:HOH639 4.5 9.3 1.0
O M:HOH654 4.6 10.9 1.0
N M:VAL445 4.6 9.7 1.0
CG M:GLU51 4.6 7.7 1.0
CG M:HIS498 4.6 7.7 1.0
CD M:LYS321 4.7 9.9 1.0
CD M:GLU285 4.7 11.2 1.0
CE M:LYS321 4.8 9.9 1.0
C M:GLN443 4.9 10.0 1.0
CA M:VAL445 4.9 10.5 1.0

Calcium binding site 8 out of 8 in 4kl8

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Calcium binding site 8 out of 8 in the High-Resolution 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-Resolution 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:36.9
occ:0.50
 OD1 M:ASP17 2.3 15.8 1.0
O T:HOH594 2.4 40.5 1.0
O M:HOH765 2.5 18.6 1.0
O M:LEU26 3.2 9.7 1.0
N M:LEU26 3.4 8.3 1.0
CG M:ASP17 3.4 15.0 1.0
C M:LEU26 3.5 9.0 1.0
O T:ILE90 3.7 11.5 1.0
C M:HIS25 3.7 8.7 1.0
OD2 M:ASP17 3.8 19.6 1.0
CA M:HIS25 3.9 8.3 1.0
O M:HOH831 3.9 26.7 1.0
CA M:PRO18 4.0 10.3 1.0
CA M:LEU26 4.0 8.6 1.0
CB M:HIS25 4.0 7.1 1.0
O M:HOH720 4.1 10.9 1.0
N M:LYS27 4.2 8.0 1.0
O T:VAL91 4.2 13.3 1.0
CB M:PRO18 4.2 11.1 1.0
C T:VAL91 4.2 11.0 1.0
O M:HIS25 4.5 11.0 1.0
N T:GLY92 4.5 10.6 1.0
ND1 M:HIS25 4.6 11.7 1.0
CB M:ASP17 4.6 10.7 1.0
N M:PRO18 4.6 10.8 1.0
C T:ILE90 4.7 10.7 1.0
CA M:ASP17 4.7 10.3 1.0
CA T:VAL91 4.7 9.4 1.0
CA M:LYS27 4.7 8.6 1.0
CB M:LYS27 4.8 9.3 1.0
CG M:HIS25 4.8 11.2 1.0
CA T:GLY92 4.8 13.0 1.0
O M:HOH611 4.9 19.3 1.0
C M:ASP17 4.9 9.8 1.0
N M:LEU19 5.0 8.1 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 09:09:58 2024

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