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Iron in PDB 5xle: Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase

Enzymatic activity of Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase

All present enzymatic activity of Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase, PDB code: 5xle was solved by K.Nishikawa, S.Mochida, T.Hiromoto, N.Shibata, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.06 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.640, 98.650, 127.590, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 17.6

Other elements in 5xle:

The structure of Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase (pdb code 5xle). 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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase, PDB code: 5xle:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 5xle

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Iron binding site 1 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:10.4
occ:1.00
 FE1 S:SF41001 0.0 10.4 1.0
S4 S:SF41001 2.2 9.0 1.0
S3 S:SF41001 2.2 8.8 1.0
S2 S:SF41001 2.2 9.7 1.0
SG S:CYS17 2.3 8.6 1.0
FE2 S:SF41001 2.6 10.3 1.0
FE3 S:SF41001 2.7 10.6 1.0
FE4 S:SF41001 2.7 10.3 1.0
CB S:CYS17 3.5 9.2 1.0
N S:CYS17 3.8 9.7 1.0
S1 S:SF41001 3.8 8.1 1.0
CA S:CYS17 4.1 7.9 1.0
NE2 L:HIS235 4.2 8.2 1.0
N S:GLY19 4.2 9.3 1.0
CA S:GLY19 4.5 8.6 1.0
O S:HOH1202 4.5 8.7 1.0
N S:THR18 4.5 8.8 1.0
C S:CYS17 4.6 9.8 1.0
N S:CYS20 4.6 6.9 1.0
CG L:ARG79 4.6 7.0 1.0
SG S:CYS114 4.8 9.5 1.0
SG S:CYS150 4.8 8.7 1.0
CD2 L:HIS235 4.8 6.8 1.0
C S:GLU16 4.9 9.3 1.0
SG S:CYS20 4.9 8.9 1.0
C S:GLY19 5.0 7.6 1.0

Iron binding site 2 out of 12 in 5xle

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Iron binding site 2 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:10.3
occ:1.00
 FE2 S:SF41001 0.0 10.3 1.0
S3 S:SF41001 2.2 8.8 1.0
S4 S:SF41001 2.2 9.0 1.0
S1 S:SF41001 2.3 8.1 1.0
SG S:CYS114 2.3 9.5 1.0
FE3 S:SF41001 2.6 10.6 1.0
FE1 S:SF41001 2.6 10.4 1.0
FE4 S:SF41001 2.7 10.3 1.0
CB S:CYS114 3.2 7.8 1.0
S2 S:SF41001 3.7 9.7 1.0
O S:HOH1156 4.0 10.3 1.0
O S:HOH1314 4.0 8.9 1.0
N S:CYS114 4.1 9.0 1.0
O S:HOH1202 4.1 8.7 1.0
CA S:CYS114 4.2 8.9 1.0
SG S:CYS150 4.6 8.7 1.0
SG S:CYS20 4.8 8.9 1.0
N S:CYS17 4.9 9.7 1.0
SG S:CYS17 4.9 8.6 1.0
CA S:GLU16 5.0 7.9 1.0

Iron binding site 3 out of 12 in 5xle

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Iron binding site 3 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:10.6
occ:1.00
 FE3 S:SF41001 0.0 10.6 1.0
S2 S:SF41001 2.2 9.7 1.0
S4 S:SF41001 2.2 9.0 1.0
S1 S:SF41001 2.2 8.1 1.0
SG S:CYS150 2.4 8.7 1.0
FE2 S:SF41001 2.6 10.3 1.0
FE1 S:SF41001 2.7 10.4 1.0
FE4 S:SF41001 2.8 10.3 1.0
CB S:CYS150 3.4 7.8 1.0
CA S:CYS150 3.5 6.4 1.0
S3 S:SF41001 3.8 8.8 1.0
C S:CYS150 3.9 7.4 1.0
O S:HOH1314 3.9 8.9 1.0
CG L:ARG79 4.1 7.0 1.0
O S:CYS150 4.2 8.5 1.0
N S:PRO151 4.4 8.3 1.0
SG S:CYS114 4.4 9.5 1.0
CD2 L:HIS235 4.6 6.8 1.0
SG S:CYS17 4.6 8.6 1.0
NE L:ARG79 4.7 8.0 1.0
NE2 L:HIS235 4.7 8.2 1.0
CA S:PRO151 4.7 8.0 1.0
O S:GLY149 4.7 9.3 1.0
N S:CYS150 4.8 8.9 1.0
SG S:CYS20 4.8 8.9 1.0

Iron binding site 4 out of 12 in 5xle

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Iron binding site 4 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:10.3
occ:1.00
 FE4 S:SF41001 0.0 10.3 1.0
S1 S:SF41001 2.2 8.1 1.0
S3 S:SF41001 2.2 8.8 1.0
S2 S:SF41001 2.2 9.7 1.0
SG S:CYS20 2.4 8.9 1.0
FE1 S:SF41001 2.7 10.4 1.0
FE2 S:SF41001 2.7 10.3 1.0
FE3 S:SF41001 2.8 10.6 1.0
CB S:CYS20 3.5 7.7 1.0
N S:CYS20 3.6 6.9 1.0
O S:HOH1156 3.8 10.3 1.0
S4 S:SF41001 3.9 9.0 1.0
CA S:CYS20 4.1 9.1 1.0
CA S:PRO151 4.4 8.0 1.0
CB S:PRO151 4.4 9.4 1.0
C S:GLY19 4.5 7.6 1.0
CA S:GLY112 4.5 7.0 1.0
SG S:CYS17 4.7 8.6 1.0
OE1 S:GLU75 4.7 11.4 1.0
CA S:CYS150 4.8 6.4 1.0
O S:GLY149 4.8 9.3 1.0
N S:PRO151 4.9 8.3 1.0
CA S:GLY19 4.9 8.6 1.0
SG S:CYS114 5.0 9.5 1.0
SG S:CYS150 5.0 8.7 1.0
N S:GLY19 5.0 9.3 1.0

Iron binding site 5 out of 12 in 5xle

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Iron binding site 5 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:12.0
occ:1.00
 FE1 S:SF41002 0.0 12.0 1.0
S4 S:SF41002 2.2 11.6 1.0
S3 S:SF41002 2.2 11.4 1.0
S2 S:SF41002 2.2 12.5 1.0
ND1 S:HIS188 2.2 12.3 1.0
FE3 S:SF41002 2.7 12.1 1.0
FE2 S:SF41002 2.7 12.3 1.0
FE4 S:SF41002 2.7 13.3 1.0
CE1 S:HIS188 3.1 14.5 1.0
CG S:HIS188 3.3 11.8 1.0
S1 S:SF41002 3.7 11.1 1.0
CB S:HIS188 3.7 11.4 1.0
CA S:HIS188 3.9 12.4 1.0
CD S:PRO225 4.2 12.4 1.0
NE2 S:HIS188 4.3 11.3 1.0
CG S:PRO225 4.4 13.2 1.0
CD2 S:HIS188 4.4 12.5 1.0
CB S:CYS191 4.5 11.5 1.0
O S:HIS188 4.5 11.3 1.0
SG S:CYS191 4.7 10.7 1.0
C S:HIS188 4.7 8.6 1.0
CD2 S:PHE197 4.7 13.1 1.0
SG S:CYS216 4.7 12.0 1.0
SG S:CYS222 4.8 9.6 1.0
N S:PRO225 4.8 10.4 1.0
CA S:GLY224 4.9 11.0 1.0

Iron binding site 6 out of 12 in 5xle

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Iron binding site 6 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:12.3
occ:1.00
 FE2 S:SF41002 0.0 12.3 1.0
S4 S:SF41002 2.2 11.6 1.0
S1 S:SF41002 2.2 11.1 1.0
S3 S:SF41002 2.2 11.4 1.0
SG S:CYS222 2.4 9.6 1.0
FE3 S:SF41002 2.7 12.1 1.0
FE1 S:SF41002 2.7 12.0 1.0
FE4 S:SF41002 2.8 13.3 1.0
CB S:CYS222 3.2 10.6 1.0
S2 S:SF41002 3.8 12.5 1.0
CG2 S:VAL243 4.3 10.9 1.0
CA S:GLY224 4.5 11.0 1.0
N S:GLY224 4.5 8.7 1.0
CA S:CYS222 4.6 7.7 1.0
CD S:PRO225 4.6 12.4 1.0
ND1 S:HIS188 4.8 12.3 1.0
SG S:CYS216 4.8 12.0 1.0
N S:LEU217 4.8 11.3 1.0
SG S:CYS191 4.8 10.7 1.0
N S:TYR218 4.9 9.7 1.0
C S:CYS222 4.9 10.1 1.0
CB S:LEU217 4.9 11.4 1.0

Iron binding site 7 out of 12 in 5xle

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Iron binding site 7 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:12.1
occ:1.00
 FE3 S:SF41002 0.0 12.1 1.0
S1 S:SF41002 2.2 11.1 1.0
S4 S:SF41002 2.2 11.6 1.0
S2 S:SF41002 2.2 12.5 1.0
SG S:CYS191 2.4 10.7 1.0
FE1 S:SF41002 2.7 12.0 1.0
FE2 S:SF41002 2.7 12.3 1.0
FE4 S:SF41002 2.7 13.3 1.0
CB S:CYS191 3.1 11.5 1.0
S3 S:SF41002 3.8 11.4 1.0
CB S:ARG193 4.0 12.3 1.0
CG1 S:VAL243 4.3 10.5 1.0
CG2 S:VAL243 4.5 10.9 1.0
CA S:CYS191 4.6 12.6 1.0
ND1 S:HIS188 4.6 12.3 1.0
N S:ARG193 4.7 12.3 1.0
CA S:ARG193 4.7 13.4 1.0
C S:ARG193 4.7 17.4 1.0
CG S:ARG193 4.7 11.5 1.0
N S:LEU194 4.7 14.5 1.0
SG S:CYS222 4.8 9.6 1.0
CB S:VAL243 4.9 11.3 1.0
CD S:ARG193 5.0 12.5 1.0

Iron binding site 8 out of 12 in 5xle

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Iron binding site 8 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:13.3
occ:1.00
 FE4 S:SF41002 0.0 13.3 1.0
S2 S:SF41002 2.2 12.5 1.0
S1 S:SF41002 2.2 11.1 1.0
S3 S:SF41002 2.3 11.4 1.0
SG S:CYS216 2.4 12.0 1.0
FE1 S:SF41002 2.7 12.0 1.0
FE3 S:SF41002 2.7 12.1 1.0
FE2 S:SF41002 2.8 12.3 1.0
CB S:CYS216 3.4 10.6 1.0
N S:LEU217 3.7 11.3 1.0
S4 S:SF41002 3.8 11.6 1.0
CA S:CYS216 3.9 11.6 1.0
C S:CYS216 4.2 10.5 1.0
N S:TYR218 4.2 9.7 1.0
CD2 S:PHE197 4.4 13.1 1.0
CB S:PHE197 4.4 13.8 1.0
CB S:ARG193 4.5 12.3 1.0
ND1 S:HIS188 4.6 12.3 1.0
CB S:TYR218 4.7 11.8 1.0
CA S:LEU217 4.7 10.8 1.0
CE1 S:HIS188 4.8 14.5 1.0
C S:LEU217 4.8 10.8 1.0
CG S:PHE197 4.8 13.8 1.0
O S:ARG193 4.9 16.0 1.0
SG S:CYS222 4.9 9.6 1.0
CA S:TYR218 4.9 13.2 1.0
SG S:CYS191 4.9 10.7 1.0

Iron binding site 9 out of 12 in 5xle

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Iron binding site 9 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:10.9
occ:1.00
 FE1 S:F3S1003 0.0 10.9 1.0
S1 S:F3S1003 2.2 9.8 1.0
S3 S:F3S1003 2.2 8.9 1.0
S2 S:F3S1003 2.2 9.4 1.0
SG S:CYS249 2.4 9.7 1.0
FE4 S:F3S1003 2.6 11.2 1.0
FE3 S:F3S1003 2.7 10.8 1.0
CB S:CYS249 3.3 7.7 1.0
CA S:CYS249 3.7 7.1 1.0
S4 S:F3S1003 3.9 8.4 1.0
N S:ILE250 4.1 9.3 1.0
N S:GLY251 4.2 10.9 1.0
C S:CYS249 4.4 11.8 1.0
N S:CYS252 4.5 9.2 1.0
CG2 S:THR227 4.6 11.6 1.0
CG2 S:VAL187 4.7 10.9 1.0
CA S:GLY251 4.8 10.2 1.0
SG S:CYS252 4.8 9.8 1.0
NE2 L:GLN237 4.9 10.5 1.0
SG S:CYS231 4.9 9.5 1.0
CG S:PRO242 5.0 7.0 1.0

Iron binding site 10 out of 12 in 5xle

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Iron binding site 10 out of 12 in the Crystal Structure of Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase


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 Anaerobically Purified and Anaerobically Crystallized D. Vulgaris Miyazaki F [Nife]-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:10.8
occ:1.00
 FE3 S:F3S1003 0.0 10.8 1.0
S1 S:F3S1003 2.2 9.8 1.0
S4 S:F3S1003 2.2 8.4 1.0
S3 S:F3S1003 2.2 8.9 1.0
SG S:CYS231 2.4 9.5 1.0
FE4 S:F3S1003 2.6 11.2 1.0
FE1 S:F3S1003 2.7 10.9 1.0
CB S:CYS231 3.4 8.9 1.0
ND2 S:ASN229 3.8 8.6 1.0
S2 S:F3S1003 3.9 9.4 1.0
O S:HOH1262 4.3 9.2 1.0
CE2 S:PHE236 4.4 9.2 1.0
CZ S:PHE236 4.5 9.4 1.0
CG S:ASN229 4.5 11.3 1.0
CB S:ASN229 4.6 9.4 1.0
CG2 S:VAL187 4.6 10.9 1.0
SG S:CYS252 4.8 9.8 1.0
CD S:PRO242 4.8 9.4 1.0
CA S:CYS231 4.8 8.7 1.0
CG S:PRO242 4.8 7.0 1.0
SG S:CYS249 4.9 9.7 1.0

Reference:

K.Nishikawa, S.Mochida, T.Hiromoto, N.Shibata, Y.Higuchi. Ni-Elimination From the Active Site of the Standard [Nife]‐Hydrogenase Upon Oxidation By O2. J. Inorg. Biochem. V. 177 435 2017.
ISSN: ISSN 1873-3344
PubMed: 28967475
DOI: 10.1016/J.JINORGBIO.2017.09.011
Page generated: Tue Aug 6 11:45:49 2024

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