Atomistry » Calcium » PDB 4uj7-4w9y » 4upe
Atomistry »
  Calcium »
    PDB 4uj7-4w9y »
      4upe »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy