Atomistry » Calcium » PDB 4tx8-4uix » 4ueq
Atomistry »
  Calcium »
    PDB 4tx8-4uix »
      4ueq »

Calcium in PDB 4ueq: Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ueq was solved by A.Volbeda, L.Martin, P.-P.Liebgott, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.720, 99.800, 190.800, 90.21, 98.61, 90.11
R / Rfree (%) 13.659 / 18.539

Other elements in 4ueq:

The structure of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Nickel (Ni) 12 atoms
Magnesium (Mg) 10 atoms
Iron (Fe) 72 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4ueq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ueq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4ueq

Go back to Calcium Binding Sites List in 4ueq
Calcium binding site 1 out of 6 in the Structure of the V74C Large Subunit 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 V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ca1554

b:11.3
occ:0.40
 MG Q:MG1553 0.0 11.1 0.6
O Q:HOH2047 2.0 12.0 1.0
O Q:HOH2046 2.0 11.6 1.0
O Q:HOH2278 2.1 9.7 1.0
O Q:LEU495 2.1 10.1 1.0
OE2 Q:GLU53 2.2 12.1 1.0
NE2 Q:HIS549 2.2 9.3 1.0
CE1 Q:HIS549 3.1 10.1 1.0
CD Q:GLU53 3.1 12.6 1.0
CD2 Q:HIS549 3.2 9.9 1.0
C Q:LEU495 3.3 10.4 1.0
OE1 Q:GLU53 3.4 11.3 1.0
N Q:LEU495 3.8 11.7 1.0
OE1 Q:GLN494 4.0 16.8 1.0
CA Q:LEU495 4.1 12.0 1.0
OE2 Q:GLU334 4.1 16.3 1.0
O Q:HOH2286 4.2 14.3 1.0
OE1 Q:GLU334 4.2 12.7 1.0
ND1 Q:HIS549 4.2 9.9 1.0
NZ Q:LYS372 4.3 11.1 1.0
O Q:HOH2318 4.3 8.4 1.0
CB Q:LEU495 4.3 10.4 0.7
CG Q:HIS549 4.3 8.4 1.0
N Q:VAL496 4.4 10.0 1.0
CG Q:GLU53 4.5 12.0 1.0
CD Q:LYS372 4.5 8.1 1.0
CD Q:GLU334 4.6 11.7 1.0
CE Q:LYS372 4.7 9.1 1.0
CA Q:VAL496 4.7 9.3 1.0
C Q:GLN494 4.8 12.1 1.0

Calcium binding site 2 out of 6 in 4ueq

Go back to Calcium Binding Sites List in 4ueq
Calcium binding site 2 out of 6 in the Structure of the V74C Large Subunit 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 V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca1554

b:13.2
occ:0.40
 MG R:MG1553 0.0 12.5 0.6
O R:HOH2249 2.1 11.2 1.0
O R:HOH2040 2.1 14.1 1.0
O R:HOH2041 2.1 12.6 1.0
NE2 R:HIS549 2.2 10.9 1.0
O R:LEU495 2.2 12.1 1.0
OE2 R:GLU53 2.2 13.9 1.0
CE1 R:HIS549 3.0 9.9 1.0
CD R:GLU53 3.1 13.6 1.0
CD2 R:HIS549 3.3 11.1 1.0
C R:LEU495 3.4 10.1 1.0
OE1 R:GLU53 3.4 14.1 1.0
N R:LEU495 3.8 12.0 1.0
CA R:LEU495 4.0 10.2 1.0
OE2 R:GLU334 4.0 12.7 1.0
OE1 R:GLN494 4.1 16.9 1.0
OE1 R:GLU334 4.2 15.7 1.0
O R:HOH2282 4.2 10.0 1.0
ND1 R:HIS549 4.2 11.7 1.0
CB R:LEU495 4.3 9.1 0.7
CB R:LEU495 4.3 10.4 0.3
NZ R:LYS372 4.3 13.9 1.0
O R:HOH2257 4.3 11.2 1.0
CG R:HIS549 4.4 11.4 1.0
N R:VAL496 4.5 9.3 1.0
CG R:GLU53 4.5 15.1 1.0
CD R:GLU334 4.6 11.5 1.0
CD R:LYS372 4.6 15.9 1.0
CA R:VAL496 4.7 9.0 1.0
CE R:LYS372 4.7 13.4 1.0
C R:GLN494 4.8 11.3 1.0

Calcium binding site 3 out of 6 in 4ueq

Go back to Calcium Binding Sites List in 4ueq
Calcium binding site 3 out of 6 in the Structure of the V74C Large Subunit 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 V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca1554

b:16.5
occ:0.40
 MG S:MG1553 0.1 15.6 0.6
O S:HOH2025 2.0 14.3 1.0
O S:HOH2024 2.1 16.0 1.0
O S:LEU495 2.1 15.9 1.0
OE2 S:GLU53 2.1 14.7 1.0
O S:HOH2182 2.1 16.6 1.0
NE2 S:HIS549 2.2 15.8 1.0
CD S:GLU53 3.1 15.3 1.0
CE1 S:HIS549 3.1 17.5 1.0
CD2 S:HIS549 3.2 14.9 1.0
C S:LEU495 3.3 14.3 1.0
OE1 S:GLU53 3.4 16.8 1.0
N S:LEU495 3.6 16.1 1.0
CA S:LEU495 3.9 15.4 1.0
CB S:LEU495 4.1 15.7 0.7
OE1 S:GLN494 4.2 22.3 1.0
OE2 S:GLU334 4.2 23.8 1.0
CB S:LEU495 4.2 16.8 0.3
O S:HOH2201 4.2 15.0 1.0
OE1 S:GLU334 4.3 23.5 1.0
NZ S:LYS372 4.3 17.4 1.0
ND1 S:HIS549 4.3 16.1 1.0
O S:HOH2188 4.3 17.1 1.0
N S:VAL496 4.3 14.5 1.0
CG S:HIS549 4.4 15.3 1.0
CG S:GLU53 4.4 15.8 1.0
CD S:LYS372 4.6 18.4 1.0
CA S:VAL496 4.7 14.9 1.0
CD S:GLU334 4.7 21.9 1.0
C S:GLN494 4.7 18.0 1.0
CE S:LYS372 4.7 16.0 1.0
CA S:GLN494 4.9 17.5 1.0

Calcium binding site 4 out of 6 in 4ueq

Go back to Calcium Binding Sites List in 4ueq
Calcium binding site 4 out of 6 in the Structure of the V74C Large Subunit 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 V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca1554

b:11.3
occ:0.40
 MG T:MG1553 0.0 11.5 0.6
O T:HOH2050 2.0 11.4 1.0
O T:HOH2051 2.1 12.1 1.0
O T:HOH2290 2.1 10.5 1.0
OE2 T:GLU53 2.1 11.5 1.0
O T:LEU495 2.2 10.2 1.0
NE2 T:HIS549 2.2 10.8 1.0
CE1 T:HIS549 3.1 12.7 1.0
CD T:GLU53 3.1 13.2 1.0
CD2 T:HIS549 3.2 11.0 1.0
C T:LEU495 3.3 10.0 1.0
OE1 T:GLU53 3.4 10.3 1.0
N T:LEU495 3.8 11.4 1.0
CA T:LEU495 4.0 12.5 1.0
OE1 T:GLN494 4.0 13.2 1.0
OE2 T:GLU334 4.1 16.4 1.0
OE1 T:GLU334 4.2 13.4 1.0
ND1 T:HIS549 4.2 13.2 1.0
O T:HOH2297 4.2 15.2 1.0
CB T:LEU495 4.3 12.3 0.7
CB T:LEU495 4.3 11.7 0.3
NZ T:LYS372 4.3 11.6 1.0
CG T:HIS549 4.3 11.1 1.0
O T:HOH2331 4.4 8.7 1.0
N T:VAL496 4.4 10.3 1.0
CG T:GLU53 4.5 13.0 1.0
CD T:LYS372 4.6 9.3 1.0
CD T:GLU334 4.6 13.8 1.0
CE T:LYS372 4.7 10.2 1.0
CA T:VAL496 4.7 10.1 1.0
C T:GLN494 4.8 11.4 1.0

Calcium binding site 5 out of 6 in 4ueq

Go back to Calcium Binding Sites List in 4ueq
Calcium binding site 5 out of 6 in the Structure of the V74C Large Subunit 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 5 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Ca1554

b:12.9
occ:0.40
 MG U:MG1553 0.0 12.1 0.6
O U:HOH2049 2.0 11.8 1.0
O U:HOH2048 2.1 13.5 1.0
O U:HOH2255 2.1 11.1 1.0
O U:LEU495 2.2 12.0 1.0
OE2 U:GLU53 2.2 13.9 1.0
NE2 U:HIS549 2.2 11.7 1.0
CE1 U:HIS549 3.1 11.2 1.0
CD U:GLU53 3.1 13.6 1.0
CD2 U:HIS549 3.3 12.8 1.0
C U:LEU495 3.3 11.3 1.0
OE1 U:GLU53 3.5 14.1 1.0
N U:LEU495 3.7 12.2 1.0
CA U:LEU495 4.0 11.7 1.0
OE1 U:GLN494 4.0 14.7 1.0
OE2 U:GLU334 4.1 14.8 1.0
OE1 U:GLU334 4.2 19.3 1.0
NZ U:LYS372 4.2 11.4 1.0
CB U:LEU495 4.3 11.5 0.7
ND1 U:HIS549 4.3 11.6 1.0
O U:HOH2288 4.3 11.1 1.0
CB U:LEU495 4.3 12.1 0.3
O U:HOH2264 4.3 11.9 1.0
CG U:HIS549 4.4 12.0 1.0
N U:VAL496 4.4 11.0 1.0
CG U:GLU53 4.5 13.3 1.0
CD U:LYS372 4.6 10.1 1.0
CD U:GLU334 4.6 14.6 1.0
CE U:LYS372 4.7 10.7 1.0
CA U:VAL496 4.7 11.2 1.0
C U:GLN494 4.7 11.9 1.0
CA U:GLN494 5.0 11.4 1.0

Calcium binding site 6 out of 6 in 4ueq

Go back to Calcium Binding Sites List in 4ueq
Calcium binding site 6 out of 6 in the Structure of the V74C Large Subunit 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 6 of Structure of the V74C Large Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Ca1554

b:15.6
occ:0.40
 MG V:MG1553 0.1 16.1 0.6
O V:HOH2025 2.0 16.0 1.0
O V:HOH2024 2.1 17.4 1.0
O V:HOH2181 2.1 16.5 1.0
OE2 V:GLU53 2.1 15.6 1.0
O V:LEU495 2.1 17.6 1.0
NE2 V:HIS549 2.2 16.2 1.0
CD V:GLU53 3.1 14.7 1.0
CE1 V:HIS549 3.1 18.4 1.0
CD2 V:HIS549 3.3 14.8 1.0
C V:LEU495 3.3 16.8 1.0
OE1 V:GLU53 3.4 16.4 1.0
N V:LEU495 3.7 16.0 1.0
CA V:LEU495 4.0 16.0 1.0
OE1 V:GLN494 4.0 20.6 1.0
OE2 V:GLU334 4.2 20.6 1.0
CB V:LEU495 4.2 14.6 0.7
OE1 V:GLU334 4.2 21.0 1.0
CB V:LEU495 4.2 15.8 0.3
O V:HOH2199 4.3 16.2 1.0
NZ V:LYS372 4.3 16.9 1.0
ND1 V:HIS549 4.3 16.6 1.0
O V:HOH2187 4.4 16.6 1.0
N V:VAL496 4.4 16.2 1.0
CG V:HIS549 4.4 14.8 1.0
CG V:GLU53 4.5 13.4 1.0
CD V:LYS372 4.5 18.1 1.0
CD V:GLU334 4.6 20.4 1.0
C V:GLN494 4.7 17.7 1.0
CA V:VAL496 4.7 16.0 1.0
CE V:LYS372 4.7 18.9 1.0
CA V:GLN494 4.9 17.2 1.0

Reference:

A.Volbeda, L.Martin, P.-P.Liebgott, A.L.De Lacey, J.C.Fontecilla-Camps. [Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation in A Variant with Accrued O2-Tolerance and A Tentative Re-Interpretation of Ni-Si States. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25780984
DOI: 10.1039/C4MT00309H
Page generated: Sun Jul 14 13:42:13 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy