Chlorine in PDB 6fpw: Structure of Fully Reduced Hydrogenase (Hyd-1)

Enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1)

All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1):
1.12.99.6;

Protein crystallography data

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1), PDB code: 6fpw was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.46 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.835, 97.729, 182.911, 90.00, 90.00, 90.00
R / Rfree (%) 11.4 / 14.4

Other elements in 6fpw:

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Fully Reduced Hydrogenase (Hyd-1) (pdb code 6fpw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Fully Reduced Hydrogenase (Hyd-1), PDB code: 6fpw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6fpw

Go back to Chlorine Binding Sites List in 6fpw
Chlorine binding site 1 out of 6 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:15.4
occ:1.00
H S:GLY256 2.1 11.7 1.0
H S:CYS120 2.3 9.4 1.0
O S:HOH589 3.0 14.5 1.0
HB2 S:TRP118 3.0 14.2 1.0
N S:GLY256 3.1 11.4 1.0
N S:CYS120 3.1 9.7 1.0
HA S:CYS120 3.2 9.2 1.0
O S:HOH654 3.2 25.6 1.0
HB3 S:TRP118 3.3 14.5 1.0
HA2 S:GLY256 3.3 12.3 1.0
HG21 S:THR114 3.4 11.0 1.0
HG23 S:THR114 3.5 11.1 1.0
HA S:ASN255 3.5 11.3 1.0
CB S:TRP118 3.6 14.7 1.0
H S:PHE257 3.7 11.3 1.0
CA S:CYS120 3.7 9.3 1.0
HG22 S:THR114 3.7 10.7 1.0
HD1 S:TRP258 3.7 9.8 1.0
CG2 S:THR114 3.7 11.2 1.0
CA S:GLY256 3.7 12.0 1.0
HD1 S:PHE257 4.0 10.0 1.0
N S:GLY119 4.1 10.8 1.0
C S:TRP118 4.1 11.4 1.0
HA3 S:GLY119 4.1 10.2 1.0
C S:ASN255 4.2 12.2 1.0
C S:GLY119 4.2 10.0 1.0
CA S:ASN255 4.3 11.2 1.0
O S:TRP118 4.3 14.0 1.0
OD1 S:ASN255 4.3 16.2 1.0
O S:GLU254 4.3 11.8 1.0
H S:GLY119 4.3 10.5 1.0
O S:CYS120 4.3 10.2 1.0
N S:PHE257 4.3 11.5 1.0
CA S:GLY119 4.3 10.2 1.0
C S:CYS120 4.5 8.8 1.0
C S:GLY256 4.5 12.0 1.0
O S:HOH640 4.5 27.5 1.0
HB3 S:ALA123 4.5 11.8 1.0
CD1 S:TRP258 4.5 10.1 1.0
HA3 S:GLY256 4.5 11.8 1.0
CA S:TRP118 4.6 10.6 1.0
H S:TRP258 4.6 9.3 1.0
HD1 S:TRP118 4.6 17.4 1.0
CG S:TRP118 4.6 16.4 1.0
CD1 S:PHE257 4.7 10.1 1.0
HE1 S:PHE257 4.7 11.3 1.0
HB2 S:CYS120 4.8 9.5 1.0
HE1 S:TRP258 4.8 9.1 1.0
CB S:CYS120 4.9 9.7 1.0
O S:THR114 4.9 9.1 1.0
CD1 S:TRP118 4.9 17.9 1.0
O S:HOH626 4.9 30.1 1.0

Chlorine binding site 2 out of 6 in 6fpw

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Chlorine binding site 2 out of 6 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl406

b:18.9
occ:1.00
H S:HIS13 2.3 10.4 1.0
HZ3 S:LYS98 2.3 22.2 1.0
HB S:ILE12 2.9 12.1 1.0
HA S:ILE12 2.9 10.4 1.0
O S:HOH555 3.0 27.8 1.0
O S:HOH585 3.1 20.9 1.0
HE2 S:TYR44 3.2 12.6 1.0
NZ S:LYS98 3.2 21.6 1.0
O S:HOH533 3.3 24.8 0.5
N S:HIS13 3.3 10.8 1.0
HE2 S:LYS98 3.3 20.4 1.0
HD3 S:LYS98 3.4 20.4 1.0
HG21 S:ILE12 3.4 13.1 1.0
CB S:ILE12 3.5 12.0 1.0
CA S:ILE12 3.6 10.0 1.0
OD2 S:ASP46 3.6 25.1 1.0
HB2 S:HIS13 3.6 12.1 1.0
HZ2 S:LYS98 3.6 21.3 1.0
HE1 S:PHE95 3.7 13.0 1.0
CE S:LYS98 3.7 20.2 1.0
HZ1 S:LYS98 3.9 21.2 1.0
CG2 S:ILE12 3.9 13.3 1.0
O S:HIS13 3.9 12.4 1.0
HD2 S:HIS13 3.9 13.8 1.0
C S:ILE12 3.9 10.0 1.0
O S:HOH603 3.9 29.6 1.0
CD S:LYS98 4.0 19.7 1.0
HG22 S:ILE12 4.1 13.4 1.0
CE2 S:TYR44 4.1 13.6 1.0
HH S:TYR44 4.2 16.9 0.0
HE1 L:HIS30 4.2 17.2 1.0
CG S:ASP46 4.2 21.8 1.0
CA S:HIS13 4.2 10.2 1.0
CB S:HIS13 4.3 12.3 1.0
HB2 S:ASP46 4.4 18.7 1.0
C S:HIS13 4.5 10.1 1.0
OH S:TYR44 4.5 17.2 1.0
CE1 S:PHE95 4.5 13.8 1.0
HD1 S:PHE95 4.6 12.2 1.0
HD2 S:LYS98 4.6 19.1 1.0
HE3 S:LYS98 4.6 20.7 1.0
CD2 S:HIS13 4.7 14.7 1.0
OD1 S:ASP46 4.7 22.5 1.0
H S:ASP46 4.7 15.3 1.0
O S:TRP11 4.7 13.2 1.0
HG23 S:ILE12 4.8 13.3 1.0
CZ S:TYR44 4.8 15.5 1.0
CG1 S:ILE12 4.9 12.8 1.0
N S:ILE12 4.9 10.3 1.0
HG2 S:LYS98 4.9 17.3 1.0
CG S:HIS13 4.9 13.0 1.0
CB S:ASP46 4.9 18.5 1.0
HG S:SER90 5.0 25.5 0.0
HD11 S:ILE12 5.0 14.5 1.0
CD1 S:PHE95 5.0 12.1 1.0
HD2 S:TYR44 5.0 12.4 1.0

Chlorine binding site 3 out of 6 in 6fpw

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Chlorine binding site 3 out of 6 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl407

b:16.4
occ:1.00
H S:ASP154 2.4 9.4 1.0
H S:ASP237 2.4 10.8 1.0
H S:ASN236 2.6 9.0 1.0
HB2 S:PRO153 2.8 9.4 1.0
O S:HOH579 3.0 14.0 1.0
HD2 S:PRO153 3.1 9.6 1.0
HB2 S:ASP154 3.1 12.1 1.0
O S:HOH565 3.2 28.1 1.0
N S:ASN236 3.3 8.8 1.0
HG23 S:ILE152 3.3 10.1 1.0
N S:ASP154 3.3 9.6 1.0
HG2 S:PRO153 3.3 9.4 1.0
HA S:ASN236 3.4 9.1 1.0
N S:ASP237 3.4 10.9 1.0
CG S:ASP154 3.5 14.1 1.0
CB S:PRO153 3.6 9.2 1.0
HG21 S:ILE152 3.6 10.5 1.0
OD2 S:ASP154 3.6 16.9 1.0
CD S:PRO153 3.7 9.5 1.0
HA S:TRP235 3.7 8.9 1.0
CB S:ASP154 3.7 11.5 1.0
CG S:PRO153 3.7 9.3 1.0
CA S:ASN236 3.8 9.3 1.0
CG2 S:ILE152 3.9 10.5 1.0
N S:PRO153 3.9 8.5 1.0
HA S:ASP237 4.0 12.0 1.0
OD1 S:ASP154 4.0 17.4 1.0
C S:TRP235 4.1 8.8 1.0
CA S:PRO153 4.1 9.0 1.0
CA S:ASP154 4.1 10.5 1.0
C S:ASN236 4.2 10.5 1.0
HG22 S:ILE152 4.2 10.2 1.0
C S:PRO153 4.2 8.3 1.0
O S:HOH509 4.2 18.6 1.0
H S:GLY238 4.3 12.4 1.0
HB3 S:PRO153 4.3 9.3 1.0
CA S:ASP237 4.4 11.8 1.0
CA S:TRP235 4.4 9.1 1.0
O S:ARG234 4.5 10.8 1.0
HD3 S:PRO153 4.6 9.4 1.0
HB3 S:ASP154 4.6 10.7 1.0
HG3 S:PRO153 4.7 9.4 1.0
HA S:ASP154 4.7 10.4 1.0
HA S:SER27 4.7 11.2 1.0
H S:ALA28 4.7 12.2 1.0
C S:ILE152 4.8 8.1 1.0
H S:VAL155 5.0 9.3 1.0

Chlorine binding site 4 out of 6 in 6fpw

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Chlorine binding site 4 out of 6 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:17.0
occ:1.00
H T:GLY256 2.1 12.3 1.0
H T:CYS120 2.3 10.0 1.0
O T:HOH610 3.0 16.9 1.0
HB2 T:TRP118 3.1 15.1 1.0
N T:GLY256 3.1 12.3 1.0
O T:HOH660 3.2 29.2 1.0
HA T:CYS120 3.2 9.7 1.0
N T:CYS120 3.2 10.2 1.0
HB3 T:TRP118 3.3 14.8 1.0
HA2 T:GLY256 3.4 12.3 1.0
HG21 T:THR114 3.4 10.6 1.0
HA T:ASN255 3.5 12.2 1.0
HG23 T:THR114 3.5 10.7 1.0
CB T:TRP118 3.6 15.1 1.0
H T:PHE257 3.6 11.6 1.0
CA T:CYS120 3.7 9.9 1.0
HD1 T:TRP258 3.7 9.5 1.0
HG22 T:THR114 3.7 10.0 1.0
CA T:GLY256 3.8 12.2 1.0
CG2 T:THR114 3.8 10.6 1.0
HD1 T:PHE257 4.0 10.8 1.0
N T:GLY119 4.1 10.8 1.0
C T:TRP118 4.1 11.9 1.0
C T:ASN255 4.1 11.9 1.0
HA3 T:GLY119 4.1 10.1 1.0
C T:GLY119 4.2 10.5 1.0
CA T:ASN255 4.2 12.1 1.0
O T:TRP118 4.3 15.0 1.0
OD1 T:ASN255 4.3 17.9 1.0
N T:PHE257 4.3 11.6 1.0
O T:GLU254 4.3 12.4 1.0
H T:GLY119 4.3 10.4 1.0
CA T:GLY119 4.3 9.8 1.0
O T:CYS120 4.4 10.2 1.0
C T:GLY256 4.5 11.8 1.0
C T:CYS120 4.5 9.6 1.0
O T:HOH647 4.5 30.6 1.0
CA T:TRP118 4.5 12.5 1.0
CD1 T:TRP258 4.6 9.7 1.0
H T:TRP258 4.6 10.4 1.0
HB3 T:ALA123 4.6 11.9 1.0
HA3 T:GLY256 4.6 12.1 1.0
CG T:TRP118 4.6 16.4 1.0
HD1 T:TRP118 4.7 17.6 1.0
CD1 T:PHE257 4.7 11.3 1.0
HE1 T:PHE257 4.8 10.1 1.0
HB2 T:CYS120 4.8 10.2 1.0
CB T:CYS120 4.9 10.2 1.0
HE1 T:TRP258 4.9 9.7 1.0
O T:THR114 4.9 9.9 1.0
O T:HOH633 4.9 32.2 1.0
CD1 T:TRP118 5.0 18.6 1.0

Chlorine binding site 5 out of 6 in 6fpw

Go back to Chlorine Binding Sites List in 6fpw
Chlorine binding site 5 out of 6 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl406

b:20.1
occ:1.00
HZ3 T:LYS98 2.3 20.1 1.0
H T:HIS13 2.3 10.5 1.0
HB T:ILE12 2.9 12.8 1.0
HA T:ILE12 2.9 11.6 1.0
O T:HOH572 3.0 35.0 1.0
O T:HOH607 3.1 21.1 1.0
NZ T:LYS98 3.2 20.6 1.0
HE2 T:TYR44 3.2 13.8 1.0
N T:HIS13 3.3 11.5 1.0
HE2 T:LYS98 3.3 20.1 1.0
HD3 T:LYS98 3.3 20.8 1.0
HG21 T:ILE12 3.4 14.4 1.0
CB T:ILE12 3.5 12.6 1.0
CA T:ILE12 3.6 11.4 1.0
HZ2 T:LYS98 3.6 20.6 1.0
OD2 T:ASP46 3.6 24.3 1.0
HE1 T:PHE95 3.6 14.9 1.0
CE T:LYS98 3.7 20.1 1.0
HB2 T:HIS13 3.8 13.3 1.0
HZ1 T:LYS98 3.9 20.7 1.0
CG2 T:ILE12 3.9 14.4 1.0
O T:HIS13 3.9 12.6 1.0
HD2 T:HIS13 3.9 14.9 1.0
C T:ILE12 4.0 12.1 1.0
CD T:LYS98 4.0 20.6 1.0
O T:HOH629 4.0 32.2 1.0
HG22 T:ILE12 4.1 14.1 1.0
CE2 T:TYR44 4.1 14.1 1.0
CG T:ASP46 4.2 23.9 1.0
HE1 M:HIS30 4.2 18.9 1.0
CA T:HIS13 4.2 12.6 1.0
CB T:HIS13 4.4 13.5 1.0
C T:HIS13 4.5 10.8 1.0
HB2 T:ASP46 4.5 20.1 1.0
CE1 T:PHE95 4.5 15.5 1.0
HD1 T:PHE95 4.5 14.2 1.0
OH T:TYR44 4.5 17.0 1.0
HD2 T:LYS98 4.6 20.6 1.0
HE3 T:LYS98 4.6 20.2 1.0
OD1 T:ASP46 4.7 24.5 1.0
CD2 T:HIS13 4.7 15.6 1.0
H T:ASP46 4.7 15.7 1.0
HG23 T:ILE12 4.8 14.4 1.0
O T:TRP11 4.8 13.7 1.0
HG T:SER90 4.9 36.2 0.0
CZ T:TYR44 4.9 14.5 1.0
CG1 T:ILE12 4.9 13.3 1.0
HG2 T:LYS98 4.9 18.2 1.0
N T:ILE12 4.9 11.6 1.0
HH T:TYR44 4.9 16.6 0.0
CD1 T:PHE95 5.0 14.4 1.0
CB T:ASP46 5.0 19.8 1.0
CG T:HIS13 5.0 13.2 1.0
HD11 T:ILE12 5.0 14.4 1.0

Chlorine binding site 6 out of 6 in 6fpw

Go back to Chlorine Binding Sites List in 6fpw
Chlorine binding site 6 out of 6 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl407

b:15.7
occ:1.00
H T:ASP237 2.4 11.7 1.0
H T:ASP154 2.5 9.6 1.0
H T:ASN236 2.5 9.4 1.0
HB2 T:PRO153 2.7 9.5 1.0
HD2 T:PRO153 3.0 9.2 1.0
O T:HOH582 3.0 13.8 1.0
HB2 T:ASP154 3.2 12.3 1.0
N T:ASN236 3.2 9.8 1.0
HG23 T:ILE152 3.3 11.6 1.0
N T:ASP154 3.4 10.2 1.0
HA T:ASN236 3.4 10.2 1.0
N T:ASP237 3.4 11.9 1.0
HG2 T:PRO153 3.4 10.2 1.0
O T:HOH532 3.5 35.3 1.0
CG T:ASP154 3.5 14.5 1.0
CB T:PRO153 3.5 9.3 1.0
HG21 T:ILE152 3.6 11.7 1.0
OD2 T:ASP154 3.6 17.2 1.0
CD T:PRO153 3.6 9.4 1.0
CB T:ASP154 3.7 12.4 1.0
HA T:TRP235 3.7 9.4 1.0
CG T:PRO153 3.7 10.4 1.0
CA T:ASN236 3.8 10.0 1.0
CG2 T:ILE152 3.8 12.0 1.0
N T:PRO153 4.0 9.1 1.0
OD1 T:ASP154 4.0 18.3 1.0
HA T:ASP237 4.0 12.0 1.0
C T:ASN236 4.1 11.7 1.0
CA T:PRO153 4.1 8.8 1.0
C T:TRP235 4.1 9.3 1.0
CA T:ASP154 4.1 11.0 1.0
C T:PRO153 4.2 9.5 1.0
HG22 T:ILE152 4.2 11.7 1.0
O T:HOH505 4.2 18.5 1.0
HB3 T:PRO153 4.3 9.4 1.0
H T:GLY238 4.3 11.4 1.0
CA T:ASP237 4.4 11.6 1.0
CA T:TRP235 4.4 9.3 1.0
HD3 T:PRO153 4.5 9.5 1.0
O T:ARG234 4.5 11.3 1.0
HB3 T:ASP154 4.6 12.1 1.0
H T:ALA28 4.7 12.4 1.0
HA T:ASP154 4.7 11.1 1.0
HG3 T:PRO153 4.7 10.0 1.0
HA T:SER27 4.7 11.6 1.0
C T:ILE152 4.8 8.6 1.0
H T:VAL155 5.0 10.3 1.0

Reference:

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798
Page generated: Sat Dec 12 12:59:41 2020

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