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Iron in PDB 5d51: Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network

Enzymatic activity of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network

All present enzymatic activity of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network:
1.12.99.6;

Protein crystallography data

The structure of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network, PDB code: 5d51 was solved by J.Kalms, A.Schmidt, S.Frielingsdorf, P.Van Der Linden, D.Von Stetten, O.Lenz, P.Carpentier, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.79 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.387, 95.574, 119.752, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15

Other elements in 5d51:

The structure of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom
Krypton (Kr) 23 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network (pdb code 5d51). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network, PDB code: 5d51:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 5d51

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Iron binding site 1 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe701

b:13.9
occ:1.00
FE L:NFV701 0.0 13.9 1.0
C2 L:NFV701 1.8 13.4 1.0
C3 L:NFV701 1.9 13.9 1.0
C1 L:NFV701 1.9 13.8 1.0
O4 L:NFV701 2.2 16.6 1.0
SG L:CYS78 2.3 14.6 1.0
SG L:CYS600 2.3 15.1 1.0
NI L:NFV701 2.8 15.9 1.0
O1 L:NFV701 2.9 15.5 1.0
N3 L:NFV701 3.0 13.9 1.0
N2 L:NFV701 3.0 13.8 1.0
CB L:CYS78 3.4 14.8 1.0
CB L:CYS600 3.4 14.8 1.0
CG1 L:VAL551 4.2 17.4 1.0
NE2 L:HIS82 4.2 13.2 1.0
CD L:ARG530 4.3 15.6 1.0
NH1 L:ARG530 4.4 18.8 1.0
SG L:CYS597 4.4 18.7 1.0
SG L:CYS81 4.4 16.5 1.0
CB L:CYS597 4.4 15.1 1.0
CD L:PRO552 4.7 13.0 1.0
CA L:CYS78 4.8 13.9 1.0
CA L:CYS600 4.8 14.6 1.0
SG L:CYS75 4.8 18.6 1.0
CB L:CYS75 4.9 15.4 1.0
CD2 L:HIS82 5.0 11.7 1.0
CG L:PRO552 5.0 13.4 1.0
NE L:ARG530 5.0 16.9 1.0

Iron binding site 2 out of 13 in 5d51

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Iron binding site 2 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:18.3
occ:1.00
FE1 S:SF41001 0.0 18.3 1.0
S3 S:SF41001 2.3 19.7 1.0
SG S:CYS221 2.3 17.5 1.0
S4 S:SF41001 2.3 18.5 1.0
S2 S:SF41001 2.3 20.3 1.0
FE3 S:SF41001 2.7 19.8 1.0
FE2 S:SF41001 2.7 19.3 1.0
FE4 S:SF41001 2.8 20.3 1.0
CB S:CYS221 3.2 16.1 1.0
S1 S:SF41001 3.9 21.8 1.0
CD1 S:ILE243 3.9 20.4 1.0
CG1 S:ILE243 4.4 18.6 1.0
CD S:PRO224 4.5 17.9 1.0
CA S:GLY223 4.5 17.6 1.0
N S:GLY223 4.5 17.5 1.0
CA S:CYS221 4.6 14.5 1.0
SG S:CYS215 4.7 19.5 1.0
N S:TYR217 4.7 16.9 1.0
ND1 S:HIS187 4.7 20.9 1.0
SG S:CYS190 4.8 20.2 1.0
N S:LEU216 4.8 18.0 1.0
C S:CYS221 4.8 15.2 1.0
CB S:LEU216 4.9 16.5 1.0
C S:LEU216 4.9 17.4 1.0
O S:CYS221 5.0 17.2 1.0

Iron binding site 3 out of 13 in 5d51

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Iron binding site 3 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:19.3
occ:1.00
FE2 S:SF41001 0.0 19.3 1.0
S4 S:SF41001 2.3 18.5 1.0
SG S:CYS215 2.3 19.5 1.0
S1 S:SF41001 2.3 21.8 1.0
S3 S:SF41001 2.3 19.7 1.0
FE4 S:SF41001 2.7 20.3 1.0
FE3 S:SF41001 2.7 19.8 1.0
FE1 S:SF41001 2.7 18.3 1.0
CB S:CYS215 3.4 20.1 1.0
N S:LEU216 3.8 18.0 1.0
S2 S:SF41001 3.9 20.3 1.0
CA S:CYS215 3.9 19.3 1.0
N S:TYR217 4.2 16.9 1.0
C S:CYS215 4.3 18.4 1.0
CB S:PHE196 4.4 22.3 1.0
ND1 S:HIS187 4.5 20.9 1.0
CD1 S:PHE196 4.5 23.5 1.0
CB S:ARG192 4.7 21.5 1.0
CB S:TYR217 4.7 17.8 1.0
CE1 S:HIS187 4.7 22.7 1.0
CA S:LEU216 4.7 17.4 1.0
O S:ARG192 4.8 24.3 1.0
C S:LEU216 4.8 17.4 1.0
CG S:PHE196 4.8 22.7 1.0
CA S:TYR217 4.8 16.7 1.0
SG S:CYS221 4.9 17.5 1.0
SG S:CYS190 4.9 20.2 1.0

Iron binding site 4 out of 13 in 5d51

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Iron binding site 4 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:19.8
occ:1.00
FE3 S:SF41001 0.0 19.8 1.0
S1 S:SF41001 2.3 21.8 1.0
S2 S:SF41001 2.3 20.3 1.0
S4 S:SF41001 2.3 18.5 1.0
SG S:CYS190 2.3 20.2 1.0
FE4 S:SF41001 2.7 20.3 1.0
FE2 S:SF41001 2.7 19.3 1.0
FE1 S:SF41001 2.7 18.3 1.0
CB S:CYS190 3.1 21.9 1.0
S3 S:SF41001 3.9 19.7 1.0
CB S:ARG192 4.1 21.5 1.0
CD1 S:ILE243 4.2 20.4 1.0
CG2 S:ILE243 4.3 18.1 1.0
ND1 S:HIS187 4.6 20.9 1.0
CA S:CYS190 4.6 21.7 1.0
N S:ARG193 4.7 23.1 1.0
C S:ARG192 4.7 22.8 1.0
CA S:ARG192 4.8 22.2 1.0
SG S:CYS221 4.8 17.5 1.0
CG1 S:ILE243 4.8 18.6 1.0
N S:ARG192 4.8 22.3 1.0
SG S:CYS215 4.9 19.5 1.0
CG S:ARG192 4.9 20.8 1.0
C S:CYS190 4.9 22.7 1.0
CA S:HIS187 5.0 21.8 1.0

Iron binding site 5 out of 13 in 5d51

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Iron binding site 5 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:20.3
occ:1.00
FE4 S:SF41001 0.0 20.3 1.0
ND1 S:HIS187 2.1 20.9 1.0
S2 S:SF41001 2.3 20.3 1.0
S1 S:SF41001 2.3 21.8 1.0
S3 S:SF41001 2.3 19.7 1.0
FE2 S:SF41001 2.7 19.3 1.0
FE3 S:SF41001 2.7 19.8 1.0
FE1 S:SF41001 2.8 18.3 1.0
CE1 S:HIS187 2.9 22.7 1.0
CG S:HIS187 3.2 23.5 1.0
CB S:HIS187 3.6 21.7 1.0
CA S:HIS187 3.9 21.8 1.0
S4 S:SF41001 3.9 18.5 1.0
NE2 S:HIS187 4.1 26.4 1.0
CD2 S:HIS187 4.2 27.1 1.0
CG S:PRO224 4.3 19.4 1.0
CD S:PRO224 4.3 17.9 1.0
SG S:CYS215 4.6 19.5 1.0
CB S:CYS190 4.6 21.9 1.0
O S:HIS187 4.7 25.3 1.0
SG S:CYS190 4.7 20.2 1.0
N S:PRO224 4.8 18.8 1.0
CD1 S:PHE196 4.8 23.5 1.0
SG S:CYS221 4.8 17.5 1.0
N S:HIS187 4.8 20.7 1.0
C S:HIS187 4.9 22.4 1.0

Iron binding site 6 out of 13 in 5d51

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Iron binding site 6 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:15.6
occ:1.00
FE1 S:F3S1002 0.0 15.6 1.0
S1 S:F3S1002 2.3 16.2 1.0
SG S:CYS249 2.3 16.1 1.0
S2 S:F3S1002 2.3 15.7 1.0
S3 S:F3S1002 2.3 16.7 1.0
FE3 S:F3S1002 2.7 15.8 1.0
FE4 S:F3S1002 2.7 15.6 1.0
CB S:CYS249 3.2 15.9 1.0
CA S:CYS249 3.6 13.8 1.0
S4 S:F3S1002 3.9 15.4 1.0
N S:ILE250 4.1 14.5 1.0
N S:GLY251 4.2 14.9 1.0
C S:CYS249 4.3 14.8 1.0
N S:CYS252 4.4 17.1 1.0
CG2 S:THR226 4.5 16.5 1.0
CG1 S:ILE186 4.6 24.0 1.0
O S:HOH1234 4.7 19.5 0.5
CA S:GLY251 4.8 16.7 1.0
SG S:CYS252 4.8 16.1 1.0
CG S:PRO242 4.8 14.7 1.0
SG S:CYS230 4.9 16.6 1.0
N S:CYS249 4.9 13.4 1.0
CD1 S:ILE186 4.9 24.6 1.0
O S:HOH1234 5.0 20.6 0.5

Iron binding site 7 out of 13 in 5d51

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Iron binding site 7 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:15.8
occ:1.00
FE3 S:F3S1002 0.0 15.8 1.0
S3 S:F3S1002 2.3 16.7 1.0
S1 S:F3S1002 2.3 16.2 1.0
S4 S:F3S1002 2.3 15.4 1.0
SG S:CYS230 2.3 16.6 1.0
FE1 S:F3S1002 2.7 15.6 1.0
FE4 S:F3S1002 2.7 15.6 1.0
CB S:CYS230 3.3 16.8 1.0
ND2 S:ASN228 4.0 16.1 1.0
S2 S:F3S1002 4.0 15.7 1.0
NE1 S:TRP235 4.3 14.3 1.0
CD1 S:ILE186 4.3 24.6 1.0
O S:HOH1165 4.5 15.7 1.0
CG S:ASN228 4.5 15.9 1.0
CG S:PRO242 4.5 14.7 1.0
CD S:PRO242 4.5 14.7 1.0
CB S:ASN228 4.6 16.2 1.0
SG S:CYS252 4.7 16.1 1.0
CA S:CYS230 4.8 16.8 1.0
SG S:CYS249 4.8 16.1 1.0
CG1 S:ILE186 4.9 24.0 1.0

Iron binding site 8 out of 13 in 5d51

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Iron binding site 8 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:15.6
occ:1.00
FE4 S:F3S1002 0.0 15.6 1.0
SG S:CYS252 2.3 16.1 1.0
S4 S:F3S1002 2.3 15.4 1.0
S2 S:F3S1002 2.3 15.7 1.0
S3 S:F3S1002 2.3 16.7 1.0
FE3 S:F3S1002 2.7 15.8 1.0
FE1 S:F3S1002 2.7 15.6 1.0
CB S:CYS252 3.4 16.8 1.0
N S:CYS252 3.8 17.1 1.0
O L:HOH877 3.9 17.2 1.0
S1 S:F3S1002 3.9 16.2 1.0
O S:HOH1165 4.0 15.7 1.0
CA S:CYS252 4.0 17.5 1.0
NZ L:LYS226 4.1 16.5 1.0
N S:SER253 4.5 17.9 1.0
ND2 S:ASN228 4.5 16.1 1.0
C S:CYS252 4.6 17.9 1.0
O S:HOH1234 4.6 20.6 0.5
SG S:CYS249 4.7 16.1 1.0
SG S:CYS230 4.7 16.6 1.0
C S:GLY251 5.0 17.2 1.0

Iron binding site 9 out of 13 in 5d51

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Iron binding site 9 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:18.1
occ:1.00
FE1 S:F4S1003 0.0 18.1 1.0
SG S:CYS17 2.3 14.7 1.0
SG S:CYS19 2.3 15.8 1.0
S2 S:F4S1003 2.3 16.1 1.0
S1 S:F4S1003 2.3 17.8 1.0
FE2 S:F4S1003 2.6 17.3 1.0
FE4 S:F4S1003 2.9 27.0 0.5
FE4 S:F4S1003 3.0 21.7 0.5
CB S:CYS17 3.4 13.8 1.0
CB S:CYS19 3.5 15.4 1.0
FE3 S:F4S1003 3.6 16.5 1.0
N S:CYS19 3.7 14.4 1.0
S3 S:F4S1003 3.7 15.9 1.0
N S:CYS17 3.7 15.2 1.0
CA S:CYS17 4.0 14.5 1.0
N S:THR18 4.1 13.9 1.0
NE2 L:HIS229 4.1 14.5 1.0
CA S:CYS19 4.1 14.5 1.0
C S:CYS17 4.2 13.5 1.0
SG S:CYS149 4.4 15.0 1.0
SG S:CYS115 4.6 18.1 1.0
O S:HOH1140 4.6 15.9 1.0
N S:CYS20 4.8 14.2 1.0
C S:THR18 4.8 14.8 1.0
CD2 L:HIS229 4.8 14.3 1.0
C S:GLU16 4.9 16.5 0.5
C S:GLU16 4.9 16.5 0.6
C S:CYS19 4.9 13.9 1.0
SG S:CYS20 5.0 17.7 1.0

Iron binding site 10 out of 13 in 5d51

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Iron binding site 10 out of 13 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:17.3
occ:1.00
FE2 S:F4S1003 0.0 17.3 1.0
S3 S:F4S1003 2.3 15.9 1.0
SG S:CYS115 2.3 18.1 1.0
S2 S:F4S1003 2.3 16.1 1.0
S1 S:F4S1003 2.3 17.8 1.0
FE1 S:F4S1003 2.6 18.1 1.0
FE3 S:F4S1003 2.7 16.5 1.0
FE4 S:F4S1003 3.3 27.0 0.5
CB S:CYS115 3.3 18.5 1.0
FE4 S:F4S1003 3.8 21.7 0.5
O S:HOH1113 3.9 19.0 1.0
N S:CYS115 4.0 15.3 1.0
SG S:CYS19 4.0 15.8 1.0
O S:HOH1140 4.1 15.9 1.0
CA S:CYS115 4.2 15.5 1.0
SG S:CYS120 4.3 15.8 1.0
CB S:CYS120 4.4 14.5 1.0
N S:CYS17 4.5 15.2 1.0
SG S:CYS149 4.7 15.0 1.0
SG S:CYS17 4.7 14.7 1.0
SG S:CYS20 4.7 17.7 1.0
CA S:GLU16 4.7 17.1 0.5
CA S:GLU16 4.8 17.2 0.6
CB S:GLU16 4.9 20.5 0.5

Reference:

J.Kalms, A.Schmidt, S.Frielingsdorf, P.Van Der Linden, D.Von Stetten, O.Lenz, P.Carpentier, P.Scheerer. Krypton Derivatization of An O2 -Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Tunnel Network For Gas Transport. Angew.Chem.Int.Ed.Engl. V. 55 5586 2016.
ISSN: ESSN 1521-3773
PubMed: 26913499
DOI: 10.1002/ANIE.201508976
Page generated: Sun Dec 13 15:58:45 2020

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