Atomistry » Calcium » PDB 4ko2-4l19 » 4ko3
Atomistry »
  Calcium »
    PDB 4ko2-4l19 »
      4ko3 »

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

Go back to Calcium Binding Sites List in 4ko3
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

Go back to Calcium Binding Sites List in 4ko3
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

Go back to Calcium Binding Sites List in 4ko3
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

Go back to Calcium Binding Sites List in 4ko3
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

Go back to Calcium Binding Sites List in 4ko3
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

Go back to Calcium Binding Sites List in 4ko3
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

Go back to Calcium Binding Sites List in 4ko3
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

Go back to Calcium Binding Sites List in 4ko3
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: Sat Dec 12 04:55:27 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy