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Iron in PDB 5mdl: Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method

Enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method

All present enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method, PDB code: 5mdl was solved by J.Kalms, A.Schmidt, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.134, 95.568, 119.686, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 16.3

Other elements in 5mdl:

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method (pdb code 5mdl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method, PDB code: 5mdl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 5mdl

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Iron binding site 1 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe701

b:13.0
occ:1.00
FE L:NFV701 0.0 13.0 1.0
C2 L:NFV701 1.8 13.2 1.0
C3 L:NFV701 1.8 13.1 1.0
C1 L:NFV701 1.9 13.0 1.0
O4 L:NFV701 2.1 14.4 1.0
SG L:CYS78 2.3 12.7 1.0
SG L:CYS600 2.3 13.9 1.0
NI L:NFV701 2.9 16.2 1.0
N2 L:NFV701 3.0 12.5 1.0
N3 L:NFV701 3.0 13.6 1.0
O1 L:NFV701 3.3 15.3 1.0
CB L:CYS78 3.4 11.6 1.0
CB L:CYS600 3.5 11.5 1.0
CG1 L:VAL551 4.2 16.4 1.0
NE2 L:HIS82 4.2 11.5 1.0
CD L:ARG530 4.2 13.0 1.0
CB L:CYS597 4.3 15.0 1.0
NH1 L:ARG530 4.4 15.4 1.0
SG L:CYS81 4.4 13.4 1.0
SG L:CYS597 4.4 18.1 1.0
CD L:PRO552 4.7 12.0 1.0
CA L:CYS600 4.8 12.3 1.0
SG L:CYS75 4.8 16.2 1.0
CA L:CYS78 4.8 11.8 1.0
CB L:CYS75 4.9 14.6 1.0
CD2 L:HIS82 4.9 11.1 1.0
NE L:ARG530 5.0 14.1 1.0
CG L:PRO552 5.0 12.7 1.0

Iron binding site 2 out of 12 in 5mdl

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Iron binding site 2 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:16.6
occ:1.00
FE1 S:SF41001 0.0 16.6 1.0
S3 S:SF41001 2.3 16.8 1.0
SG S:CYS221 2.3 14.8 1.0
S2 S:SF41001 2.3 17.3 1.0
S4 S:SF41001 2.3 16.4 1.0
FE2 S:SF41001 2.7 17.1 1.0
FE3 S:SF41001 2.7 17.7 1.0
FE4 S:SF41001 2.8 18.2 1.0
CB S:CYS221 3.2 14.6 1.0
CD1 S:ILE243 3.9 16.2 1.0
S1 S:SF41001 3.9 19.1 1.0
CD S:PRO224 4.4 15.7 1.0
CG1 S:ILE243 4.4 15.4 1.0
CA S:GLY223 4.5 17.3 1.0
N S:GLY223 4.5 15.2 1.0
CA S:CYS221 4.6 14.2 1.0
SG S:CYS215 4.6 17.1 1.0
N S:TYR217 4.7 15.0 1.0
ND1 S:HIS187 4.8 16.5 1.0
SG S:CYS190 4.8 16.7 1.0
N S:LEU216 4.8 15.2 1.0
C S:CYS221 4.8 14.4 1.0
C S:LEU216 4.9 14.0 1.0
CB S:LEU216 5.0 14.4 1.0
O S:CYS221 5.0 15.8 1.0

Iron binding site 3 out of 12 in 5mdl

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Iron binding site 3 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:17.1
occ:1.00
FE2 S:SF41001 0.0 17.1 1.0
S1 S:SF41001 2.2 19.1 1.0
SG S:CYS215 2.3 17.1 1.0
S4 S:SF41001 2.3 16.4 1.0
S3 S:SF41001 2.3 16.8 1.0
FE4 S:SF41001 2.7 18.2 1.0
FE3 S:SF41001 2.7 17.7 1.0
FE1 S:SF41001 2.7 16.6 1.0
CB S:CYS215 3.4 17.9 1.0
N S:LEU216 3.8 15.2 1.0
S2 S:SF41001 3.9 17.3 1.0
CA S:CYS215 3.9 16.6 1.0
N S:TYR217 4.2 15.0 1.0
C S:CYS215 4.3 17.4 1.0
CB S:PHE196 4.4 19.9 1.0
ND1 S:HIS187 4.5 16.5 1.0
CD2 S:PHE196 4.5 19.3 1.0
CB S:ARG192 4.7 18.1 1.0
CB S:TYR217 4.7 16.8 1.0
O S:ARG192 4.7 20.1 1.0
CE1 S:HIS187 4.8 23.0 1.0
CA S:LEU216 4.8 15.0 1.0
C S:LEU216 4.8 14.0 1.0
SG S:CYS221 4.8 14.8 1.0
CG S:PHE196 4.8 18.9 1.0
SG S:CYS190 4.9 16.7 1.0
CA S:TYR217 4.9 15.6 1.0
C S:ARG192 5.0 19.6 1.0

Iron binding site 4 out of 12 in 5mdl

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Iron binding site 4 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:17.7
occ:1.00
FE3 S:SF41001 0.0 17.7 1.0
S1 S:SF41001 2.3 19.1 1.0
S2 S:SF41001 2.3 17.3 1.0
SG S:CYS190 2.3 16.7 1.0
S4 S:SF41001 2.3 16.4 1.0
FE2 S:SF41001 2.7 17.1 1.0
FE1 S:SF41001 2.7 16.6 1.0
FE4 S:SF41001 2.8 18.2 1.0
CB S:CYS190 3.1 17.4 1.0
S3 S:SF41001 3.9 16.8 1.0
CB S:ARG192 4.1 18.1 1.0
CD1 S:ILE243 4.2 16.2 1.0
CG2 S:ILE243 4.2 14.7 1.0
CA S:CYS190 4.5 17.1 1.0
ND1 S:HIS187 4.6 16.5 1.0
N S:ARG193 4.6 18.6 1.0
C S:ARG192 4.6 19.6 1.0
CA S:ARG192 4.8 19.1 1.0
SG S:CYS221 4.8 14.8 1.0
CG1 S:ILE243 4.8 15.4 1.0
N S:ARG192 4.8 18.6 1.0
SG S:CYS215 4.9 17.1 1.0
C S:CYS190 4.9 18.4 1.0
CA S:HIS187 4.9 18.2 1.0

Iron binding site 5 out of 12 in 5mdl

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Iron binding site 5 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:18.2
occ:1.00
FE4 S:SF41001 0.0 18.2 1.0
ND1 S:HIS187 2.1 16.5 1.0
S1 S:SF41001 2.3 19.1 1.0
S2 S:SF41001 2.3 17.3 1.0
S3 S:SF41001 2.3 16.8 1.0
FE2 S:SF41001 2.7 17.1 1.0
FE3 S:SF41001 2.8 17.7 1.0
FE1 S:SF41001 2.8 16.6 1.0
CE1 S:HIS187 2.9 23.0 1.0
CG S:HIS187 3.2 20.8 1.0
CB S:HIS187 3.6 19.1 1.0
CA S:HIS187 3.9 18.2 1.0
S4 S:SF41001 3.9 16.4 1.0
NE2 S:HIS187 4.1 23.3 1.0
CD2 S:HIS187 4.2 22.6 1.0
CG S:PRO224 4.3 16.3 1.0
CD S:PRO224 4.3 15.7 1.0
SG S:CYS215 4.6 17.1 1.0
CB S:CYS190 4.6 17.4 1.0
O S:HIS187 4.7 22.5 1.0
SG S:CYS190 4.8 16.7 1.0
N S:PRO224 4.8 16.2 1.0
C S:HIS187 4.8 20.7 1.0
CD2 S:PHE196 4.8 19.3 1.0
N S:HIS187 4.8 17.2 1.0
SG S:CYS221 4.9 14.8 1.0

Iron binding site 6 out of 12 in 5mdl

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Iron binding site 6 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:13.6
occ:1.00
FE1 S:F3S1002 0.0 13.6 1.0
S2 S:F3S1002 2.3 13.6 1.0
S1 S:F3S1002 2.3 14.1 1.0
S3 S:F3S1002 2.3 14.1 1.0
SG S:CYS249 2.3 13.4 1.0
FE3 S:F3S1002 2.7 13.5 1.0
FE4 S:F3S1002 2.7 13.5 1.0
CB S:CYS249 3.2 12.8 1.0
CA S:CYS249 3.6 13.0 1.0
S4 S:F3S1002 3.9 13.5 1.0
N S:ILE250 4.1 12.0 1.0
N S:GLY251 4.2 12.9 1.0
C S:CYS249 4.3 12.7 1.0
N S:CYS252 4.4 13.8 1.0
CG2 S:THR226 4.6 15.2 1.0
CG1 S:ILE186 4.6 21.7 1.0
CA S:GLY251 4.7 14.2 1.0
SG S:CYS252 4.8 14.3 1.0
O L:HOH1021 4.8 15.3 0.4
SG S:CYS230 4.8 13.9 1.0
CG S:PRO242 4.9 13.1 1.0
N S:CYS249 4.9 14.1 1.0
CD1 S:ILE186 4.9 21.3 1.0

Iron binding site 7 out of 12 in 5mdl

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Iron binding site 7 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:13.5
occ:1.00
FE3 S:F3S1002 0.0 13.5 1.0
S4 S:F3S1002 2.3 13.5 1.0
S1 S:F3S1002 2.3 14.1 1.0
S3 S:F3S1002 2.3 14.1 1.0
SG S:CYS230 2.3 13.9 1.0
FE1 S:F3S1002 2.7 13.6 1.0
FE4 S:F3S1002 2.7 13.5 1.0
CB S:CYS230 3.3 15.1 1.0
S2 S:F3S1002 3.9 13.6 1.0
ND2 S:ASN228 4.1 14.0 1.0
NE1 S:TRP235 4.3 12.7 1.0
CD1 S:ILE186 4.4 21.3 1.0
O S:HOH1166 4.5 14.0 1.0
CD S:PRO242 4.5 13.4 1.0
CG S:PRO242 4.5 13.1 1.0
CG S:ASN228 4.6 14.2 1.0
CB S:ASN228 4.6 14.7 1.0
CA S:CYS230 4.7 14.8 1.0
SG S:CYS252 4.7 14.3 1.0
SG S:CYS249 4.8 13.4 1.0
CG1 S:ILE186 4.9 21.7 1.0

Iron binding site 8 out of 12 in 5mdl

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Iron binding site 8 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:13.5
occ:1.00
FE4 S:F3S1002 0.0 13.5 1.0
S2 S:F3S1002 2.3 13.6 1.0
S4 S:F3S1002 2.3 13.5 1.0
SG S:CYS252 2.3 14.3 1.0
S3 S:F3S1002 2.3 14.1 1.0
FE1 S:F3S1002 2.7 13.6 1.0
FE3 S:F3S1002 2.7 13.5 1.0
CB S:CYS252 3.4 14.1 1.0
N S:CYS252 3.8 13.8 1.0
O L:HOH871 3.8 16.2 1.0
S1 S:F3S1002 4.0 14.1 1.0
CA S:CYS252 4.0 13.2 1.0
O S:HOH1166 4.0 14.0 1.0
NZ L:LYS226 4.0 16.7 1.0
N S:SER253 4.5 14.2 1.0
C S:CYS252 4.5 14.4 1.0
O L:HOH1021 4.6 14.9 0.6
ND2 S:ASN228 4.7 14.0 1.0
SG S:CYS230 4.7 13.9 1.0
SG S:CYS249 4.7 13.4 1.0
C S:GLY251 4.9 13.6 1.0

Iron binding site 9 out of 12 in 5mdl

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Iron binding site 9 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:15.5
occ:1.00
FE1 S:F4S1003 0.0 15.5 1.0
O S:O1006 1.8 19.9 0.5
SG S:CYS17 2.3 12.7 1.0
S1 S:F4S1003 2.3 15.5 1.0
SG S:CYS19 2.3 14.4 1.0
S2 S:F4S1003 2.3 14.4 1.0
FE2 S:F4S1003 2.6 15.2 1.0
FE4 S:F4S1003 3.1 20.1 1.0
CB S:CYS19 3.4 13.9 1.0
CB S:CYS17 3.4 13.0 1.0
FE3 S:F4S1003 3.5 13.8 1.0
S3 S:F4S1003 3.6 14.0 1.0
N S:CYS19 3.7 13.2 1.0
N S:CYS17 3.8 14.2 1.0
CA S:CYS17 4.0 13.8 1.0
CA S:CYS19 4.1 13.3 1.0
N S:THR18 4.2 13.6 1.0
NE2 L:HIS229 4.2 12.4 1.0
C S:CYS17 4.3 13.1 1.0
SG S:CYS149 4.3 13.2 1.0
SG S:CYS115 4.6 14.3 1.0
O S:HOH1144 4.7 14.0 1.0
N S:CYS20 4.8 12.9 1.0
CD2 L:HIS229 4.8 11.8 1.0
C S:THR18 4.8 13.5 1.0
SG S:CYS20 4.9 14.6 1.0
C S:CYS19 4.9 12.5 1.0
C S:GLU16 5.0 14.9 1.0

Iron binding site 10 out of 12 in 5mdl

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Iron binding site 10 out of 12 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:15.2
occ:1.00
FE2 S:F4S1003 0.0 15.2 1.0
S3 S:F4S1003 2.2 14.0 1.0
S1 S:F4S1003 2.3 15.5 1.0
SG S:CYS115 2.3 14.3 1.0
S2 S:F4S1003 2.3 14.4 1.0
FE1 S:F4S1003 2.6 15.5 1.0
FE3 S:F4S1003 2.8 13.8 1.0
CB S:CYS115 3.4 15.0 1.0
O S:HOH1113 3.7 17.9 1.0
FE4 S:F4S1003 3.9 20.1 1.0
O S:O1006 3.9 19.9 0.5
N S:CYS115 4.0 13.5 1.0
SG S:CYS19 4.1 14.4 1.0
O S:HOH1144 4.2 14.0 1.0
CA S:CYS115 4.2 14.0 1.0
SG S:CYS120 4.3 13.6 1.0
CB S:CYS120 4.4 14.6 1.0
N S:CYS17 4.5 14.2 1.0
SG S:CYS17 4.6 12.7 1.0
SG S:CYS20 4.6 14.6 1.0
SG S:CYS149 4.7 13.2 1.0
CA S:GLU16 4.8 15.0 0.5
CA S:GLU16 4.8 14.8 0.5
CB S:GLU16 4.8 16.3 0.5

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: Sun Dec 13 16:08:31 2020

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