Iron in PDB 5kh0: Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster

Protein crystallography data

The structure of Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster, PDB code: 5kh0 was solved by G.Caserta, L.Pecqueur, M.Fontecave, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.62 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.010, 173.480, 89.320, 90.00, 110.01, 90.00
R / Rfree (%) 23.3 / 26.2

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster (pdb code 5kh0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster, PDB code: 5kh0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 5kh0

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Iron binding site 1 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:72.3
occ:0.83
 FE1 A:SF4401 0.0 72.3 0.8
S4 A:SF4401 2.3 70.5 0.8
S3 A:SF4401 2.3 69.0 0.8
S2 A:SF4401 2.3 69.4 0.8
SG A:CYS352 2.3 70.4 1.0
FE2 A:SF4401 2.7 69.8 0.8
FE3 A:SF4401 2.7 69.7 0.8
FE4 A:SF4401 2.8 68.6 0.8
CB A:CYS352 3.4 66.5 1.0
N A:CYS352 3.5 66.1 1.0
S1 A:SF4401 3.9 69.9 0.8
CA A:CYS352 3.9 66.2 1.0
N A:VAL353 4.0 66.8 1.0
OE1 A:GLU305 4.3 0.4 1.0
C A:GLY351 4.3 68.7 1.0
C A:CYS352 4.5 69.7 1.0
CB A:VAL353 4.6 69.8 1.0
CA A:GLY351 4.6 65.2 1.0
SG A:CYS298 4.7 77.4 1.0
N A:GLY351 4.8 65.4 1.0
SG A:CYS349 4.8 66.1 1.0
CG2 A:VAL353 4.9 69.1 1.0

Iron binding site 2 out of 16 in 5kh0

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Iron binding site 2 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:69.8
occ:0.83
 FE2 A:SF4401 0.0 69.8 0.8
SG A:CYS349 2.3 66.1 1.0
S3 A:SF4401 2.3 69.0 0.8
S1 A:SF4401 2.3 69.9 0.8
S4 A:SF4401 2.3 70.5 0.8
FE4 A:SF4401 2.7 68.6 0.8
FE1 A:SF4401 2.7 72.3 0.8
FE3 A:SF4401 2.7 69.7 0.8
CB A:CYS349 3.2 61.9 1.0
N A:GLY297 3.9 70.5 1.0
S2 A:SF4401 3.9 69.4 0.8
N A:GLY351 3.9 65.4 1.0
CA A:GLY351 4.0 65.2 1.0
N A:CYS352 4.5 66.1 1.0
CA A:GLY297 4.5 70.5 1.0
CA A:CYS349 4.6 61.7 1.0
OE2 A:GLU305 4.6 0.7 1.0
C A:GLY351 4.6 68.7 1.0
N A:GLY350 4.7 63.5 1.0
CA A:GLU296 4.7 70.0 1.0
CB A:GLU296 4.7 71.0 1.0
OE1 A:GLU305 4.8 0.4 1.0
C A:CYS349 4.8 67.1 1.0
C A:GLU296 4.8 74.0 1.0
N A:CYS298 4.8 73.5 1.0
C A:GLY297 4.8 75.1 1.0
SG A:CYS298 4.9 77.4 1.0
SG A:CYS352 5.0 70.4 1.0

Iron binding site 3 out of 16 in 5kh0

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Iron binding site 3 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:69.7
occ:0.83
 FE3 A:SF4401 0.0 69.7 0.8
OE1 A:GLU305 2.1 0.4 1.0
S1 A:SF4401 2.3 69.9 0.8
S2 A:SF4401 2.3 69.4 0.8
S4 A:SF4401 2.3 70.5 0.8
OE2 A:GLU305 2.7 0.7 1.0
FE4 A:SF4401 2.7 68.6 0.8
CD A:GLU305 2.7 0.4 1.0
FE2 A:SF4401 2.7 69.8 0.8
FE1 A:SF4401 2.7 72.3 0.8
S3 A:SF4401 3.9 69.0 0.8
CG A:GLU305 4.2 96.3 1.0
CB A:ARG301 4.3 80.0 1.0
OE2 A:GLU296 4.6 87.4 1.0
SG A:CYS349 4.6 66.1 1.0
CB A:CYS349 4.6 61.9 1.0
CD A:PRO302 4.7 82.4 1.0
CA A:ARG301 4.7 81.5 1.0
SG A:CYS352 4.8 70.4 1.0
SG A:CYS298 4.9 77.4 1.0
CB A:GLU305 4.9 88.8 1.0

Iron binding site 4 out of 16 in 5kh0

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Iron binding site 4 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:68.6
occ:0.83
 FE4 A:SF4401 0.0 68.6 0.8
S1 A:SF4401 2.3 69.9 0.8
S2 A:SF4401 2.3 69.4 0.8
S3 A:SF4401 2.3 69.0 0.8
SG A:CYS298 2.3 77.4 1.0
FE3 A:SF4401 2.7 69.7 0.8
FE2 A:SF4401 2.7 69.8 0.8
FE1 A:SF4401 2.8 72.3 0.8
CB A:CYS298 3.3 73.7 1.0
S4 A:SF4401 3.9 70.5 0.8
N A:CYS298 4.0 73.5 1.0
CA A:CYS298 4.1 73.9 1.0
O A:CYS298 4.3 79.2 1.0
CA A:ARG301 4.4 81.5 1.0
CB A:ARG301 4.4 80.0 1.0
C A:CYS298 4.5 79.6 1.0
OE1 A:GLU305 4.6 0.4 1.0
C A:GLY297 4.6 75.1 1.0
N A:ARG301 4.6 81.7 1.0
SG A:CYS352 4.7 70.4 1.0
N A:GLY297 4.7 70.5 1.0
SG A:CYS349 4.8 66.1 1.0

Iron binding site 5 out of 16 in 5kh0

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Iron binding site 5 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:78.2
occ:0.82
 FE1 B:SF4401 0.0 78.2 0.8
S3 B:SF4401 2.3 75.4 0.8
S4 B:SF4401 2.3 76.8 0.8
S2 B:SF4401 2.3 78.0 0.8
SG B:CYS352 2.3 72.2 1.0
FE4 B:SF4401 2.7 78.0 0.8
FE2 B:SF4401 2.7 77.2 0.8
FE3 B:SF4401 2.8 77.1 0.8
CB B:CYS352 3.5 68.4 1.0
N B:CYS352 3.8 68.3 1.0
S1 B:SF4401 3.9 77.7 0.8
CA B:CYS352 4.1 68.3 1.0
N B:VAL353 4.1 69.5 1.0
OE1 B:GLU305 4.3 95.6 1.0
C B:GLY351 4.5 71.3 1.0
SG B:CYS298 4.6 87.2 1.0
CB B:VAL353 4.6 72.7 1.0
C B:CYS352 4.6 72.6 1.0
CA B:GLY351 4.8 66.4 1.0
SG B:CYS349 4.8 65.4 1.0
CG2 B:VAL353 4.9 72.1 1.0
N B:GLY351 4.9 66.4 1.0

Iron binding site 6 out of 16 in 5kh0

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Iron binding site 6 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:77.2
occ:0.82
 FE2 B:SF4401 0.0 77.2 0.8
SG B:CYS349 2.3 65.4 1.0
S4 B:SF4401 2.3 76.8 0.8
S3 B:SF4401 2.3 75.4 0.8
S1 B:SF4401 2.3 77.7 0.8
FE1 B:SF4401 2.7 78.2 0.8
FE3 B:SF4401 2.7 77.1 0.8
FE4 B:SF4401 2.8 78.0 0.8
CB B:CYS349 3.2 61.8 1.0
S2 B:SF4401 3.9 78.0 0.8
N B:GLY297 4.0 78.5 1.0
N B:GLY351 4.1 66.4 1.0
CA B:GLY351 4.2 66.4 1.0
OE2 B:GLU305 4.5 0.3 1.0
CA B:CYS349 4.6 62.0 1.0
OE1 B:GLU305 4.6 95.6 1.0
CA B:GLY297 4.7 79.1 1.0
N B:CYS352 4.7 68.3 1.0
N B:GLY350 4.8 62.6 1.0
C B:CYS349 4.8 65.2 1.0
N B:CYS298 4.8 82.3 1.0
C B:GLY351 4.9 71.3 1.0
CA B:GLU296 4.9 76.2 1.0
SG B:CYS298 4.9 87.2 1.0
CB B:GLU296 4.9 77.5 1.0
SG B:CYS352 4.9 72.2 1.0
C B:GLY297 5.0 84.8 1.0
C B:GLU296 5.0 80.2 1.0
CD B:GLU305 5.0 0.7 1.0

Iron binding site 7 out of 16 in 5kh0

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Iron binding site 7 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:77.1
occ:0.82
 FE3 B:SF4401 0.0 77.1 0.8
OE1 B:GLU305 2.0 95.6 1.0
S1 B:SF4401 2.3 77.7 0.8
S2 B:SF4401 2.3 78.0 0.8
S4 B:SF4401 2.3 76.8 0.8
CD B:GLU305 2.7 0.7 1.0
FE4 B:SF4401 2.7 78.0 0.8
FE2 B:SF4401 2.7 77.2 0.8
FE1 B:SF4401 2.8 78.2 0.8
OE2 B:GLU305 2.8 0.3 1.0
S3 B:SF4401 3.9 75.4 0.8
CG B:GLU305 4.2 0.6 1.0
CD B:PRO302 4.5 91.8 1.0
CB B:ARG301 4.5 85.2 1.0
CA B:ARG301 4.7 86.5 1.0
SG B:CYS349 4.7 65.4 1.0
SG B:CYS352 4.8 72.2 1.0
CB B:CYS349 4.8 61.8 1.0
OE2 B:GLU296 4.8 95.9 1.0
CG B:ARG301 4.8 91.2 1.0
CB B:GLU305 4.9 98.1 1.0
SG B:CYS298 4.9 87.2 1.0

Iron binding site 8 out of 16 in 5kh0

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Iron binding site 8 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:78.0
occ:0.82
 FE4 B:SF4401 0.0 78.0 0.8
S2 B:SF4401 2.3 78.0 0.8
S1 B:SF4401 2.3 77.7 0.8
S3 B:SF4401 2.3 75.4 0.8
SG B:CYS298 2.3 87.2 1.0
FE1 B:SF4401 2.7 78.2 0.8
FE3 B:SF4401 2.7 77.1 0.8
FE2 B:SF4401 2.8 77.2 0.8
CB B:CYS298 3.5 83.1 1.0
S4 B:SF4401 3.9 76.8 0.8
N B:CYS298 4.1 82.3 1.0
CA B:CYS298 4.2 82.5 1.0
CA B:ARG301 4.3 86.5 1.0
CB B:ARG301 4.4 85.2 1.0
O B:CYS298 4.4 86.3 1.0
N B:ARG301 4.5 86.3 1.0
C B:CYS298 4.5 86.7 1.0
OE1 B:GLU305 4.6 95.6 1.0
C B:GLY297 4.8 84.8 1.0
SG B:CYS352 4.8 72.2 1.0
SG B:CYS349 4.8 65.4 1.0
C B:HIS300 4.9 88.5 1.0
N B:GLY297 4.9 78.5 1.0

Iron binding site 9 out of 16 in 5kh0

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Iron binding site 9 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:65.6
occ:0.85
 FE1 C:SF4401 0.0 65.6 0.8
S4 C:SF4401 2.3 66.1 0.8
S2 C:SF4401 2.3 65.1 0.8
S3 C:SF4401 2.3 65.4 0.8
SG C:CYS349 2.3 69.4 1.0
FE3 C:SF4401 2.7 67.5 0.8
FE4 C:SF4401 2.8 65.8 0.8
FE2 C:SF4401 2.8 66.9 0.8
CB C:CYS349 3.3 65.8 1.0
N C:GLY297 3.7 70.2 1.0
N C:GLY351 3.9 67.6 1.0
CA C:GLY351 3.9 67.6 1.0
S1 C:SF4401 3.9 66.5 0.8
CA C:GLY297 4.2 69.7 1.0
N C:CYS352 4.4 68.5 1.0
N C:CYS298 4.6 72.6 1.0
C C:GLY351 4.6 71.7 1.0
OE2 C:GLU305 4.6 88.6 1.0
CA C:CYS349 4.7 66.0 1.0
OE1 C:GLU305 4.7 69.4 1.0
C C:GLY297 4.7 73.5 1.0
C C:GLU296 4.7 74.1 1.0
CA C:GLU296 4.8 71.8 1.0
N C:GLY350 4.8 66.8 1.0
SG C:CYS298 4.9 79.4 1.0
C C:CYS349 4.9 70.5 1.0
SG C:CYS352 4.9 72.7 1.0
CB C:GLU296 5.0 73.1 1.0

Iron binding site 10 out of 16 in 5kh0

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Iron binding site 10 out of 16 in the Crystal Structure of Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster


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 Hydf From Thermosipho Melanesiensis in Complex with A [4FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:66.9
occ:0.85
 FE2 C:SF4401 0.0 66.9 0.8
S3 C:SF4401 2.3 65.4 0.8
S4 C:SF4401 2.3 66.1 0.8
SG C:CYS352 2.3 72.7 1.0
S1 C:SF4401 2.3 66.5 0.8
FE1 C:SF4401 2.8 65.6 0.8
FE3 C:SF4401 2.8 67.5 0.8
FE4 C:SF4401 2.8 65.8 0.8
CB C:CYS352 3.5 68.9 1.0
N C:CYS352 3.5 68.5 1.0
S2 C:SF4401 3.9 65.1 0.8
CA C:CYS352 4.0 68.8 1.0
N C:VAL353 4.0 74.3 1.0
OE1 C:GLU305 4.2 69.4 1.0
C C:GLY351 4.3 71.7 1.0
C C:CYS352 4.5 74.9 1.0
CB C:VAL353 4.5 79.3 1.0
CA C:GLY351 4.6 67.6 1.0
SG C:CYS298 4.7 79.4 1.0
N C:GLY351 4.8 67.6 1.0
SG C:CYS349 4.9 69.4 1.0
CG2 C:VAL353 4.9 78.6 1.0
CA C:VAL353 5.0 74.8 1.0

Reference:

G.Caserta, L.Pecqueur, A.Adamska-Venkatesh, C.Papini, S.Roy, V.Artero, M.Atta, E.Reijerse, W.Lubitz, M.Fontecave. Structural and Functional Characterization of the Hydrogenase-Maturation Hydf Protein. Nat. Chem. Biol. V. 13 779 2017.
ISSN: ESSN 1552-4469
PubMed: 28553946
DOI: 10.1038/NCHEMBIO.2385
Page generated: Sun Dec 13 16:05:27 2020

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