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Chlorine in PDB 5mdk: Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)

Enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)

All present enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3):
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3), PDB code: 5mdk was solved by A.Schmidt, J.Kalms, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.110, 95.567, 119.828, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 15.3

Other elements in 5mdk:

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom
Iron (Fe) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) (pdb code 5mdk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3), PDB code: 5mdk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5mdk

Go back to Chlorine Binding Sites List in 5mdk
Chlorine binding site 1 out of 5 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl702

b:38.0
occ:0.50
 CL L:CL702 0.0 38.0 0.5
CL L:CL702 1.9 62.0 0.5
N L:THR370 2.9 22.5 1.0
O L:HOH1098 3.0 44.9 1.0
O L:THR370 3.7 27.1 1.0
CA L:VAL369 3.7 25.1 1.0
C L:VAL369 3.8 23.1 1.0
CA L:THR370 3.8 22.8 1.0
C L:THR370 3.8 25.0 1.0
CE L:LYS60 3.9 27.4 0.4
CG1 L:VAL369 3.9 29.4 1.0
NZ L:LYS60 4.1 28.1 0.4
CB L:THR370 4.3 21.5 1.0
CB L:VAL369 4.3 27.2 1.0
N L:GLU371 4.6 25.1 1.0
NE2 L:GLN548 4.7 22.9 1.0
O L:GLY368 4.7 24.4 1.0
OG1 L:THR370 4.8 22.3 1.0
O L:HOH901 4.8 36.0 1.0
N L:VAL369 4.8 23.2 1.0
CG2 L:VAL369 4.9 29.7 1.0
O L:HOH1116 4.9 48.5 1.0
O L:VAL369 5.0 24.5 1.0

Chlorine binding site 2 out of 5 in 5mdk

Go back to Chlorine Binding Sites List in 5mdk
Chlorine binding site 2 out of 5 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl702

b:62.0
occ:0.50
 CL L:CL702 0.0 62.0 0.5
CL L:CL702 1.9 38.0 0.5
NZ L:LYS60 3.0 28.1 0.4
CE L:LYS60 3.1 27.4 0.4
O L:HOH1098 3.3 44.9 1.0
NE2 L:GLN548 3.6 22.9 1.0
N L:THR370 3.6 22.5 1.0
O L:HOH830 3.7 33.9 1.0
CB L:THR370 4.0 21.5 1.0
OD1 L:ASN546 4.1 28.9 1.0
OG1 L:THR370 4.2 22.3 1.0
O L:THR370 4.3 27.1 1.0
CA L:THR370 4.3 22.8 1.0
C L:VAL369 4.5 23.1 1.0
CA L:VAL369 4.5 25.1 1.0
CD L:LYS60 4.5 26.8 0.4
O L:GLU56 4.6 23.6 1.0
CG2 L:VAL57 4.6 24.9 1.0
C L:THR370 4.6 25.0 1.0
O L:GLY368 4.8 24.4 1.0
C L:GLU56 4.8 21.1 1.0
CB L:GLU56 4.8 20.0 1.0
N L:VAL57 4.9 20.0 1.0
CA L:VAL57 4.9 21.8 1.0
CD L:GLN548 4.9 22.2 1.0

Chlorine binding site 3 out of 5 in 5mdk

Go back to Chlorine Binding Sites List in 5mdk
Chlorine binding site 3 out of 5 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl703

b:58.9
occ:0.80
 CL L:CL703 0.0 58.9 0.8
CL L:CL703 2.4 42.8 0.2
N L:GLN459 3.4 32.5 1.0
CB L:THR458 4.1 33.3 1.0
C L:GLN459 4.1 35.1 1.0
CA L:GLN459 4.1 37.2 1.0
N L:TYR460 4.1 34.8 1.0
CZ L:TYR460 4.2 34.5 1.0
CE2 L:TYR460 4.3 34.0 1.0
CA L:THR458 4.3 34.0 1.0
CE1 L:TYR460 4.3 35.4 1.0
C L:THR458 4.3 33.3 1.0
CB L:GLN459 4.4 38.5 1.0
CD2 L:TYR460 4.4 30.4 1.0
CD1 L:TYR460 4.5 36.4 1.0
CG L:TYR460 4.5 32.8 1.0
O L:GLN459 4.6 34.1 1.0
CG2 L:THR458 4.6 34.0 1.0
OH L:TYR460 4.7 38.0 1.0
CA L:TYR460 4.8 33.4 1.0

Chlorine binding site 4 out of 5 in 5mdk

Go back to Chlorine Binding Sites List in 5mdk
Chlorine binding site 4 out of 5 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl703

b:42.8
occ:0.20
 CL L:CL703 0.0 42.8 0.2
CL L:CL703 2.4 58.9 0.8
O L:GLN459 3.8 34.1 1.0
C L:GLN459 3.9 35.1 1.0
OE1 L:GLN464 3.9 39.6 1.0
CD1 L:TYR460 4.1 36.4 1.0
N L:TYR460 4.1 34.8 1.0
CA L:TYR460 4.3 33.4 1.0
CE1 L:TYR460 4.3 35.4 1.0
NE2 L:GLN464 4.3 46.2 1.0
CD L:GLN464 4.5 40.8 1.0
CG L:TYR460 4.5 32.8 1.0
CA L:GLN459 4.6 37.2 1.0
N L:GLN459 4.6 32.5 1.0
CB L:GLN459 4.6 38.5 1.0
CZ L:TYR460 4.9 34.5 1.0

Chlorine binding site 5 out of 5 in 5mdk

Go back to Chlorine Binding Sites List in 5mdk
Chlorine binding site 5 out of 5 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl401

b:26.7
occ:1.00
 N S:GLY256 3.2 21.2 1.0
O S:HOH587 3.2 24.4 1.0
N S:CYS120 3.2 19.4 1.0
O S:HOH580 3.3 29.1 1.0
CA S:CYS120 3.5 18.2 1.0
CB S:TRP118 3.7 21.2 1.0
CA S:GLY256 3.9 21.7 1.0
O S:GLU254 4.1 20.6 1.0
CD1 S:PHE257 4.1 19.9 1.0
C S:ASP255 4.2 19.8 1.0
N S:PHE257 4.2 20.5 1.0
N S:GLY119 4.3 20.1 1.0
CA S:ASP255 4.3 20.7 1.0
CE1 S:PHE257 4.4 20.0 1.0
C S:TRP118 4.4 20.6 1.0
C S:GLY119 4.4 19.6 1.0
C S:CYS120 4.5 17.4 1.0
CD1 S:TRP258 4.5 17.7 1.0
CB S:CYS120 4.5 18.1 1.0
CB S:SER114 4.5 18.8 1.0
O S:CYS120 4.5 18.1 1.0
O S:SER114 4.5 19.5 1.0
C S:GLY256 4.6 21.0 1.0
CG S:TRP118 4.6 22.4 1.0
OD1 S:ASP255 4.7 23.0 1.0
CA S:GLY119 4.7 19.0 1.0
CA S:TRP118 4.7 20.2 1.0
O S:TRP118 4.7 22.8 1.0
O S:HOH651 4.8 26.8 1.0
NE1 S:TRP258 4.8 17.6 1.0
O S:HOH677 4.8 40.7 1.0
CD1 S:TRP118 4.9 21.5 1.0
C S:GLU254 4.9 20.4 1.0

Reference:

J.Kalms, A.Schmidt, S.Frielingsdorf, T.Utesch, G.Gotthard, D.Von Stetten, P.Van Der Linden, A.Royant, M.A.Mroginski, P.Carpentier, O.Lenz, P.Scheerer. Tracking the Route of Molecular Oxygen in O2-Tolerant Membrane-Bound [Nife] Hydrogenase. Proc. Natl. Acad. Sci. V. 115 E2229 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29463722
DOI: 10.1073/PNAS.1712267115
Page generated: Sat Jul 12 05:25:40 2025

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