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Calcium in PDB 4upe: Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4upe was solved by A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.Delacey, P.P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.430, 98.960, 184.950, 90.00, 91.19, 90.00
R / Rfree (%) 15.09 / 18.977

Other elements in 4upe:

The structure of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Nickel (Ni) 3 atoms
Iron (Fe) 36 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4upe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4upe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4upe

Go back to Calcium Binding Sites List in 4upe
Calcium binding site 1 out of 4 in the Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ca1552

b:14.0
occ:0.90
 O Q:HOH2004 2.1 11.2 1.0
O Q:HOH2003 2.2 11.9 1.0
O Q:LEU495 2.2 10.8 1.0
O Q:HOH2002 2.2 9.6 1.0
NE2 Q:HIS549 2.3 11.9 1.0
OE2 Q:GLU53 2.3 11.9 1.0
CE1 Q:HIS549 3.2 10.7 1.0
CD Q:GLU53 3.2 11.4 1.0
CD2 Q:HIS549 3.3 10.4 1.0
C Q:LEU495 3.4 12.1 1.0
OE1 Q:GLU53 3.5 11.9 1.0
N Q:LEU495 3.8 12.1 1.0
CA Q:LEU495 4.0 12.5 1.0
OE2 Q:GLU334 4.0 13.1 1.0
OE1 Q:GLN494 4.1 16.6 1.0
OE1 Q:GLU334 4.1 12.9 1.0
NZ Q:LYS372 4.3 11.8 1.0
O Q:HOH2036 4.3 11.2 1.0
CB Q:LEU495 4.3 14.2 1.0
O Q:HOH2042 4.3 10.7 1.0
ND1 Q:HIS549 4.4 11.0 1.0
N Q:VAL496 4.4 11.2 1.0
CG Q:HIS549 4.5 10.9 1.0
CD Q:GLU334 4.5 12.7 1.0
CG Q:GLU53 4.6 11.4 1.0
CD Q:LYS372 4.6 12.8 1.0
CE Q:LYS372 4.6 13.5 1.0
CA Q:VAL496 4.7 11.0 1.0
C Q:GLN494 4.8 12.5 1.0

Calcium binding site 2 out of 4 in 4upe

Go back to Calcium Binding Sites List in 4upe
Calcium binding site 2 out of 4 in the Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca1552

b:15.1
occ:0.90
 O R:HOH2002 2.1 12.1 1.0
O R:HOH2003 2.2 11.8 1.0
OE2 R:GLU53 2.2 16.4 1.0
O R:HOH2004 2.2 14.0 1.0
NE2 R:HIS549 2.2 11.6 1.0
O R:LEU495 2.2 14.4 1.0
CD R:GLU53 3.1 15.5 1.0
CE1 R:HIS549 3.1 11.0 1.0
CD2 R:HIS549 3.2 11.1 1.0
OE1 R:GLU53 3.3 16.8 1.0
C R:LEU495 3.4 12.6 1.0
N R:LEU495 3.8 13.3 1.0
CA R:LEU495 4.0 13.2 1.0
OE2 R:GLU334 4.1 12.0 1.0
OE1 R:GLN494 4.1 13.6 1.0
O R:HOH2045 4.2 13.7 1.0
OE1 R:GLU334 4.2 13.3 1.0
NZ R:LYS372 4.2 11.8 1.0
O R:HOH2039 4.2 11.8 1.0
CB R:LEU495 4.3 12.7 1.0
ND1 R:HIS549 4.3 11.9 1.0
CG R:HIS549 4.4 11.0 1.0
N R:VAL496 4.5 12.3 1.0
CG R:GLU53 4.5 13.1 1.0
CD R:LYS372 4.5 12.7 1.0
CD R:GLU334 4.6 12.8 1.0
CE R:LYS372 4.6 12.9 1.0
CA R:VAL496 4.7 11.6 1.0
C R:GLN494 4.8 13.8 1.0

Calcium binding site 3 out of 4 in 4upe

Go back to Calcium Binding Sites List in 4upe
Calcium binding site 3 out of 4 in the Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca1564

b:24.6
occ:0.40
 O R:HOH2113 2.1 16.8 1.0
O R:HOH2343 2.1 17.2 1.0
O R:HOH2212 2.6 26.2 1.0
OD1 R:ASN181 2.6 15.8 1.0
CG R:ASN181 3.8 15.0 1.0
N R:ASN181 3.9 15.8 1.0
O R:HOH2331 4.0 42.0 1.0
CA R:ASN181 4.1 16.0 1.0
O B:HOH2125 4.4 27.8 1.0
CD1 R:LEU185 4.5 13.8 1.0
CB R:ASN181 4.6 16.2 1.0
O2 R:GOL1562 4.7 18.9 1.0
ND2 R:ASN181 4.8 14.9 1.0
CG2 R:THR180 4.9 15.8 1.0
OE1 B:GLN62 4.9 26.1 0.5
NE2 B:GLN62 5.0 23.0 0.5

Calcium binding site 4 out of 4 in 4upe

Go back to Calcium Binding Sites List in 4upe
Calcium binding site 4 out of 4 in the Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Unready Ni-A State of the S499C Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca1552

b:15.0
occ:0.90
 O S:HOH2003 2.1 16.1 1.0
O S:HOH2004 2.1 13.0 1.0
O S:HOH2002 2.1 13.8 1.0
NE2 S:HIS549 2.2 15.4 1.0
OE2 S:GLU53 2.2 13.4 1.0
O S:LEU495 2.3 13.9 1.0
CD S:GLU53 3.2 13.3 1.0
CD2 S:HIS549 3.2 15.5 1.0
CE1 S:HIS549 3.2 14.9 1.0
OE1 S:GLU53 3.4 13.2 1.0
C S:LEU495 3.4 14.1 1.0
N S:LEU495 3.8 12.1 1.0
OE2 S:GLU334 4.0 16.1 1.0
CA S:LEU495 4.1 13.0 1.0
OE1 S:GLN494 4.1 18.2 1.0
NZ S:LYS372 4.2 16.1 1.0
O S:HOH2036 4.2 13.4 1.0
OE1 S:GLU334 4.2 15.8 1.0
O S:HOH2042 4.3 18.4 1.0
CB S:LEU495 4.3 13.8 1.0
ND1 S:HIS549 4.3 13.0 1.0
CG S:HIS549 4.3 13.7 1.0
CG S:GLU53 4.5 12.6 1.0
N S:VAL496 4.5 14.1 1.0
CD S:GLU334 4.6 15.8 1.0
CD S:LYS372 4.6 16.7 1.0
CE S:LYS372 4.7 16.2 1.0
C S:GLN494 4.8 14.1 1.0
CA S:VAL496 4.8 14.5 1.0

Reference:

A.Volbeda, L.Martin, E.Barbier, O.Gutierrez-Sanz, A.L.De Lacey, P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps. Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9
Page generated: Sun Jul 14 13:47:04 2024

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