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Chlorine in PDB 4gd3: Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B

Enzymatic activity of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B

All present enzymatic activity of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B:
1.12.99.6;

Protein crystallography data

The structure of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B, PDB code: 4gd3 was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.000, 165.300, 212.800, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.6

Other elements in 4gd3:

The structure of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Magnesium (Mg) 4 atoms
Iron (Fe) 54 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B (pdb code 4gd3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B, PDB code: 4gd3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 4gd3

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Chlorine binding site 1 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl404

b:90.0
occ:1.00
 N S:CYS120 3.0 80.2 1.0
N S:GLY256 3.2 84.4 1.0
CB S:TRP118 3.4 83.3 1.0
C S:TRP118 3.6 83.0 1.0
CA S:GLY256 3.7 86.9 1.0
N S:GLY119 3.7 82.2 1.0
CA S:CYS120 3.7 79.8 1.0
O S:TRP118 3.8 83.4 1.0
C S:GLY119 3.8 82.1 1.0
CG2 S:THR114 3.9 73.2 1.0
CA S:GLY119 3.9 82.8 1.0
OD1 S:ASN255 3.9 92.9 1.0
O S:CYS120 4.1 83.3 1.0
CA S:TRP118 4.2 83.5 1.0
C S:ASN255 4.3 83.0 1.0
C S:CYS120 4.4 81.5 1.0
CA S:ASN255 4.5 82.0 1.0
CG S:TRP118 4.6 83.7 1.0
C S:GLY256 4.7 86.6 1.0
O S:THR114 4.7 79.7 1.0
N S:PHE257 4.8 84.9 1.0
O S:GLU254 4.8 81.4 1.0
CD1 S:TRP258 4.9 81.9 1.0
O S:GLY119 4.9 82.6 1.0

Chlorine binding site 2 out of 10 in 4gd3

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Chlorine binding site 2 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:92.8
occ:1.00
 ND1 S:HIS29 3.1 82.4 1.0
OD1 S:ASP237 3.5 94.6 1.0
OD2 S:ASP237 3.5 0.9 1.0
CD1 M:LEU259 3.6 63.3 0.5
CE1 S:HIS29 3.7 83.3 1.0
CG S:ASP237 3.9 95.8 1.0
CG S:HIS29 4.2 78.6 1.0
CB S:ALA28 4.3 81.2 1.0
O S:ALA28 4.3 83.4 1.0
OG M:SER262 4.4 70.1 0.6
NZ M:LYS218 4.5 73.5 1.0
CB S:HIS29 4.6 76.1 1.0
CG M:LEU259 4.7 60.9 0.5
C S:ALA28 4.7 80.6 1.0
NH1 M:ARG266 4.7 85.9 1.0
CD2 M:LEU259 4.8 59.0 0.5
NE2 S:HIS29 4.9 82.5 1.0

Chlorine binding site 3 out of 10 in 4gd3

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Chlorine binding site 3 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl604

b:0.2
occ:1.00
 NE L:ARG266 3.2 94.2 1.0
NH2 L:ARG266 3.3 95.3 1.0
CE1 L:PHE212 3.6 90.7 1.0
CD1 L:PHE212 3.7 90.2 1.0
CZ L:ARG266 3.7 94.9 1.0
CD L:ARG266 4.3 93.8 1.0
CG L:ARG266 4.4 93.1 1.0
CB L:ARG266 4.5 91.1 1.0
CZ L:PHE212 4.7 91.1 1.0
CG L:PHE212 4.8 89.2 1.0

Chlorine binding site 4 out of 10 in 4gd3

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Chlorine binding site 4 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl601

b:92.3
occ:1.00
 NH2 T:ARG26 2.7 81.1 1.0
O M:VAL78 2.9 83.0 1.0
CE1 M:HIS117 3.0 80.8 1.0
ND1 M:HIS117 3.2 78.0 1.0
OE2 T:GLU22 3.4 77.5 1.0
CD T:GLU22 3.6 78.4 1.0
O M:GLY77 3.8 80.3 1.0
OE1 T:GLU22 3.8 76.1 1.0
CZ T:ARG26 3.8 80.7 1.0
CG2 M:THR80 3.9 83.6 1.0
C M:VAL78 3.9 84.1 1.0
NE2 M:HIS117 4.2 78.2 1.0
CG T:GLU22 4.3 80.1 1.0
CA M:VAL78 4.3 84.3 1.0
CD1 M:LEU114 4.3 74.8 1.0
NH1 T:ARG26 4.3 79.9 1.0
CG M:HIS117 4.5 77.6 1.0
ND2 M:ASN227 4.7 71.0 1.0
N M:THR80 4.8 83.6 1.0
OD1 M:ASN227 4.8 75.8 1.0
CB M:THR80 4.8 82.6 1.0
C M:GLY77 4.8 81.4 1.0
CB T:GLU22 4.8 80.0 1.0
NE T:ARG26 4.9 77.6 1.0
CD2 M:HIS117 5.0 78.2 1.0

Chlorine binding site 5 out of 10 in 4gd3

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Chlorine binding site 5 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl605

b:91.2
occ:1.00
 N M:MET254 2.7 66.8 1.0
O M:ILE243 3.0 77.6 1.0
CB M:ASN253 3.0 61.3 1.0
CB M:MET254 3.3 67.8 0.5
CB M:MET254 3.3 67.7 0.6
CA M:ASN253 3.5 62.1 1.0
CA M:MET254 3.5 66.9 0.5
CA M:MET254 3.5 66.9 0.6
C M:ASN253 3.6 64.7 1.0
SD S:MET180 3.6 82.3 1.0
C M:ILE243 3.7 77.0 1.0
CA M:ILE243 3.7 73.9 1.0
O M:ASN242 3.8 70.1 1.0
CB S:MET180 3.9 72.4 1.0
CG M:ASN253 3.9 58.5 1.0
CD1 M:ILE243 4.2 76.1 1.0
CZ S:PHE181 4.2 76.7 1.0
CB M:ALA248 4.3 65.1 1.0
OD1 M:ASN253 4.3 56.6 1.0
CG S:MET180 4.5 75.6 1.0
CG2 M:ILE243 4.5 76.0 1.0
N M:GLU255 4.6 66.4 1.0
C M:MET254 4.6 66.0 1.0
CB M:ILE243 4.6 73.8 1.0
C M:ASN242 4.6 71.3 1.0
CG M:MET254 4.7 69.5 0.6
N M:ILE243 4.7 72.3 1.0
CE1 S:PHE181 4.7 73.3 1.0
CG M:MET254 4.7 69.9 0.5
O M:ASN253 4.7 64.7 1.0
ND2 M:ASN253 4.8 58.2 1.0
CE2 S:PHE181 4.9 75.9 1.0
N M:ASP244 4.9 81.0 1.0
N M:ASN253 4.9 61.5 1.0

Chlorine binding site 6 out of 10 in 4gd3

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Chlorine binding site 6 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cl404

b:82.6
occ:1.00
 N Q:GLY256 3.1 77.5 1.0
N Q:CYS120 3.2 70.9 1.0
CA Q:GLY256 3.5 79.9 1.0
CB Q:TRP118 3.6 74.3 1.0
CA Q:CYS120 3.8 70.9 1.0
C Q:TRP118 3.8 73.7 1.0
N Q:GLY119 3.9 72.2 1.0
O Q:TRP118 4.0 74.8 1.0
OD1 Q:ASN255 4.0 85.0 1.0
C Q:GLY119 4.0 72.1 1.0
CG2 Q:THR114 4.0 65.3 1.0
CA Q:GLY119 4.1 71.9 1.0
O Q:CYS120 4.1 74.8 1.0
C Q:ASN255 4.2 76.2 1.0
CA Q:TRP118 4.4 74.0 1.0
C Q:CYS120 4.4 73.0 1.0
C Q:GLY256 4.5 79.8 1.0
CA Q:ASN255 4.5 75.2 1.0
N Q:PHE257 4.6 77.9 1.0
O Q:GLU254 4.6 76.2 1.0
CG Q:TRP118 4.7 76.2 1.0
CD1 Q:TRP258 4.8 73.6 1.0
O Q:THR114 4.9 70.6 1.0

Chlorine binding site 7 out of 10 in 4gd3

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Chlorine binding site 7 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cl405

b:92.1
occ:1.00
 ND1 Q:HIS29 3.3 82.5 1.0
CD1 K:LEU259 3.4 73.2 0.5
OD1 Q:ASP237 3.7 95.6 1.0
OD2 Q:ASP237 3.7 0.2 1.0
CE1 Q:HIS29 3.8 82.7 1.0
CG Q:ASP237 4.1 95.6 1.0
CG Q:HIS29 4.3 78.1 1.0
NZ K:LYS218 4.3 82.3 1.0
OG K:SER262 4.4 79.4 0.6
O Q:ALA28 4.4 83.3 1.0
CG K:LEU259 4.5 71.2 0.5
CB Q:ALA28 4.5 80.0 1.0
CD2 K:LEU259 4.6 69.1 0.5
NH1 K:ARG266 4.7 93.6 1.0
CB Q:HIS29 4.7 75.5 1.0
C Q:ALA28 4.8 80.3 1.0
CD1 K:ILE263 4.8 75.5 1.0
CG K:LEU259 4.9 71.9 0.5
NE2 Q:HIS29 5.0 82.0 1.0

Chlorine binding site 8 out of 10 in 4gd3

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Chlorine binding site 8 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl604

b:96.5
occ:1.00
 NE J:ARG266 3.1 90.3 1.0
NH2 J:ARG266 3.5 91.5 1.0
CE1 J:PHE212 3.5 85.8 1.0
CD1 J:PHE212 3.6 85.2 1.0
CZ J:ARG266 3.7 91.4 1.0
CG J:ARG266 4.2 88.4 1.0
CD J:ARG266 4.2 89.8 1.0
CB J:ARG266 4.3 86.5 1.0
CZ J:PHE212 4.5 86.4 1.0
CG J:PHE212 4.7 83.7 1.0

Chlorine binding site 9 out of 10 in 4gd3

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Chlorine binding site 9 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl601

b:0.9
occ:1.00
 O K:VAL78 2.7 89.8 1.0
NH2 R:ARG26 2.9 87.0 1.0
OE2 R:GLU22 3.2 83.4 1.0
CE1 K:HIS117 3.2 86.6 1.0
ND1 K:HIS117 3.3 84.1 1.0
CD R:GLU22 3.6 84.0 1.0
O K:GLY77 3.7 84.6 1.0
CG2 K:THR80 3.7 90.8 1.0
C K:VAL78 3.7 89.7 1.0
OE1 R:GLU22 4.0 82.7 1.0
CZ R:ARG26 4.0 84.8 1.0
CA K:VAL78 4.1 88.5 1.0
CD1 K:LEU114 4.2 83.5 1.0
CG R:GLU22 4.4 85.0 1.0
NE2 K:HIS117 4.5 83.7 1.0
NH1 R:ARG26 4.5 84.2 1.0
N K:THR80 4.5 91.0 1.0
CG K:HIS117 4.6 84.5 1.0
CB K:THR80 4.7 89.9 1.0
C K:GLY77 4.7 85.7 1.0
ND2 K:ASN227 4.7 79.8 1.0
N K:CYS79 4.8 91.3 1.0
OD1 K:ASN227 4.9 82.0 1.0
N K:VAL78 4.9 87.2 1.0
CB R:GLU22 4.9 84.2 1.0

Chlorine binding site 10 out of 10 in 4gd3

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Chlorine binding site 10 out of 10 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl605

b:0.8
occ:1.00
 O K:ILE243 2.7 88.5 1.0
N K:MET254 2.8 78.2 1.0
CB K:ASN253 3.2 73.0 1.0
CB K:MET254 3.3 79.3 0.5
CB K:MET254 3.3 79.3 0.6
SD Q:MET180 3.5 78.5 1.0
C K:ILE243 3.5 88.1 1.0
CA K:MET254 3.6 78.5 0.5
CA K:MET254 3.6 78.5 0.6
CA K:ILE243 3.7 85.9 1.0
C K:ASN253 3.7 76.0 1.0
CA K:ASN253 3.7 73.9 1.0
O K:ASN242 3.9 80.9 1.0
CB Q:MET180 3.9 68.2 1.0
CG K:ASN253 4.1 70.4 1.0
CZ Q:PHE181 4.3 72.7 1.0
CD1 K:ILE243 4.3 88.5 1.0
CB K:ALA248 4.3 77.2 1.0
CG2 K:ILE243 4.4 87.1 1.0
OD1 K:ASN253 4.4 70.0 1.0
CG Q:MET180 4.4 70.9 1.0
CB K:ILE243 4.6 85.5 1.0
N K:ILE243 4.6 85.1 1.0
CG K:MET254 4.7 80.9 0.6
C K:ASN242 4.7 82.7 1.0
N K:GLU255 4.7 77.7 1.0
C K:MET254 4.7 77.7 1.0
CG K:MET254 4.7 81.2 0.5
CE1 Q:PHE181 4.7 69.7 1.0
N K:ASP244 4.8 92.1 1.0
O K:ASN253 4.9 76.2 1.0
CE2 Q:PHE181 4.9 71.4 1.0

Reference:

A.Volbeda, C.Darnault, A.Parkin, F.Sargent, F.A.Armstrong, J.C.Fontecilla-Camps. Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 From Escherichia Coli in Complex with Its Cognate Cytochrome B. Structure V. 21 184 2013.
ISSN: ISSN 0969-2126
PubMed: 23260654
DOI: 10.1016/J.STR.2012.11.010
Page generated: Sun Jul 21 14:30:26 2024

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