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Iron in PDB 5mms: Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant

Enzymatic activity of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant

All present enzymatic activity of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant:
4.2.1.22;

Protein crystallography data

The structure of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant, PDB code: 5mms was solved by J.B.Vicente, H.G.Colaco, F.Malagrino, P.E.Santo, A.Gutierres, T.M.Bandeiras, P.Leandro, J.A.Brito, A.Giuffre, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.35 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 86.174, 86.783, 97.786, 102.67, 103.07, 111.19
R / Rfree (%) 18.2 / 22.1

Other elements in 5mms:

The structure of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant (pdb code 5mms). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant, PDB code: 5mms:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5mms

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Iron binding site 1 out of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:47.2
occ:1.00
 FE A:HEM1001 0.0 47.2 1.0
NC A:HEM1001 1.9 46.1 1.0
NB A:HEM1001 2.0 47.4 1.0
ND A:HEM1001 2.0 46.9 1.0
NA A:HEM1001 2.0 48.3 1.0
NE2 A:HIS65 2.2 46.3 1.0
SG A:CYS52 2.4 43.3 1.0
C1D A:HEM1001 3.0 46.6 1.0
C4B A:HEM1001 3.0 47.4 1.0
C1C A:HEM1001 3.0 46.0 1.0
C4C A:HEM1001 3.0 45.7 1.0
C4D A:HEM1001 3.0 47.7 1.0
C1B A:HEM1001 3.0 48.5 1.0
C4A A:HEM1001 3.0 49.0 1.0
C1A A:HEM1001 3.0 48.8 1.0
CD2 A:HIS65 3.1 46.5 1.0
CE1 A:HIS65 3.2 46.1 1.0
CHC A:HEM1001 3.3 47.2 1.0
CHD A:HEM1001 3.4 46.4 1.0
CHA A:HEM1001 3.4 48.8 1.0
CHB A:HEM1001 3.4 49.5 1.0
CB A:CYS52 3.6 40.3 1.0
C2C A:HEM1001 4.2 45.9 1.0
C2A A:HEM1001 4.2 50.1 1.0
C3C A:HEM1001 4.2 45.7 1.0
C2D A:HEM1001 4.2 47.0 1.0
C3A A:HEM1001 4.2 50.3 1.0
CA A:CYS52 4.2 40.8 1.0
C3D A:HEM1001 4.2 47.8 1.0
CG A:HIS65 4.3 46.8 1.0
C2B A:HEM1001 4.3 48.9 1.0
C3B A:HEM1001 4.3 48.5 1.0
ND1 A:HIS65 4.3 47.2 1.0
NH1 A:ARG266 4.4 36.6 1.0
CB A:TRP54 4.9 42.1 1.0
C A:CYS52 4.9 48.0 1.0
N A:THR53 4.9 48.1 1.0
CD A:PRO64 5.0 54.0 1.0
CG A:PRO64 5.0 57.8 1.0

Iron binding site 2 out of 6 in 5mms

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Iron binding site 2 out of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:41.1
occ:1.00
 FE B:HEM1001 0.0 41.1 1.0
NC B:HEM1001 1.9 40.0 1.0
ND B:HEM1001 1.9 40.6 1.0
NA B:HEM1001 2.0 42.6 1.0
NB B:HEM1001 2.0 41.7 1.0
NE2 B:HIS65 2.2 48.8 1.0
SG B:CYS52 2.5 44.0 1.0
C1D B:HEM1001 2.9 40.1 1.0
C4C B:HEM1001 2.9 39.4 1.0
C1C B:HEM1001 3.0 39.9 1.0
C4D B:HEM1001 3.0 41.3 1.0
C4B B:HEM1001 3.0 41.8 1.0
C4A B:HEM1001 3.0 43.5 1.0
C1B B:HEM1001 3.0 43.2 1.0
C1A B:HEM1001 3.0 42.8 1.0
CD2 B:HIS65 3.1 49.0 1.0
CE1 B:HIS65 3.2 48.6 1.0
CHD B:HEM1001 3.3 40.0 1.0
CHC B:HEM1001 3.3 41.4 1.0
CHA B:HEM1001 3.4 42.6 1.0
CHB B:HEM1001 3.4 44.2 1.0
CB B:CYS52 3.5 40.5 1.0
C2D B:HEM1001 4.2 40.3 1.0
C2C B:HEM1001 4.2 39.8 1.0
C3C B:HEM1001 4.2 39.3 1.0
C3D B:HEM1001 4.2 41.1 1.0
CA B:CYS52 4.2 40.7 1.0
C2A B:HEM1001 4.2 44.4 1.0
CG B:HIS65 4.2 47.9 1.0
C3A B:HEM1001 4.3 44.8 1.0
C2B B:HEM1001 4.3 43.7 1.0
C3B B:HEM1001 4.3 43.1 1.0
ND1 B:HIS65 4.3 49.7 1.0
NH1 B:ARG266 4.4 23.8 1.0
CB B:TRP54 4.9 39.1 1.0
N B:THR53 5.0 41.6 1.0
C B:CYS52 5.0 44.7 1.0
CD B:PRO64 5.0 44.4 1.0

Iron binding site 3 out of 6 in 5mms

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Iron binding site 3 out of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:32.4
occ:1.00
 FE C:HEM1001 0.0 32.4 1.0
NC C:HEM1001 1.9 31.4 1.0
NB C:HEM1001 2.0 33.1 1.0
NA C:HEM1001 2.0 33.5 1.0
ND C:HEM1001 2.0 31.9 1.0
NE2 C:HIS65 2.2 43.2 1.0
SG C:CYS52 2.4 42.7 1.0
C1D C:HEM1001 2.9 31.8 1.0
C4B C:HEM1001 3.0 33.1 1.0
C1C C:HEM1001 3.0 31.5 1.0
C4D C:HEM1001 3.0 32.5 1.0
C1B C:HEM1001 3.0 34.3 1.0
C4C C:HEM1001 3.0 31.1 1.0
C4A C:HEM1001 3.0 34.4 1.0
C1A C:HEM1001 3.0 33.7 1.0
CD2 C:HIS65 3.1 43.6 1.0
CE1 C:HIS65 3.2 42.6 1.0
CHC C:HEM1001 3.3 32.8 1.0
CHA C:HEM1001 3.4 33.5 1.0
CHD C:HEM1001 3.4 31.7 1.0
CHB C:HEM1001 3.4 35.3 1.0
CB C:CYS52 3.5 40.1 1.0
C2A C:HEM1001 4.2 35.0 1.0
CA C:CYS52 4.2 41.0 1.0
C2C C:HEM1001 4.2 31.4 1.0
C3A C:HEM1001 4.2 35.5 1.0
C2D C:HEM1001 4.2 32.0 1.0
C3C C:HEM1001 4.2 31.0 1.0
C3D C:HEM1001 4.2 32.6 1.0
C2B C:HEM1001 4.2 35.0 1.0
C3B C:HEM1001 4.3 34.6 1.0
CG C:HIS65 4.3 42.5 1.0
ND1 C:HIS65 4.3 43.6 1.0
NH1 C:ARG266 4.4 45.0 1.0
CB C:TRP54 4.9 34.2 1.0
N C:THR53 4.9 39.5 1.0
C C:CYS52 4.9 43.1 1.0
CD C:PRO64 5.0 40.8 1.0
N C:TRP54 5.0 37.6 1.0
CG C:PRO64 5.0 45.2 1.0

Iron binding site 4 out of 6 in 5mms

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Iron binding site 4 out of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:41.0
occ:1.00
 FE D:HEM1001 0.0 41.0 1.0
NC D:HEM1001 1.9 40.1 1.0
NA D:HEM1001 2.0 42.1 1.0
ND D:HEM1001 2.0 40.5 1.0
NB D:HEM1001 2.0 41.5 1.0
NE2 D:HIS65 2.2 51.4 1.0
SG D:CYS52 2.5 49.6 1.0
C1C D:HEM1001 2.9 40.2 1.0
C4B D:HEM1001 2.9 41.7 1.0
C4C D:HEM1001 3.0 39.6 1.0
C4D D:HEM1001 3.0 41.0 1.0
C1D D:HEM1001 3.0 40.1 1.0
C1A D:HEM1001 3.0 42.1 1.0
CD2 D:HIS65 3.0 51.8 1.0
C1B D:HEM1001 3.0 42.8 1.0
C4A D:HEM1001 3.0 42.8 1.0
CE1 D:HIS65 3.2 51.1 1.0
CHC D:HEM1001 3.2 41.6 1.0
CHD D:HEM1001 3.3 40.1 1.0
CHA D:HEM1001 3.4 42.1 1.0
CHB D:HEM1001 3.4 43.4 1.0
CB D:CYS52 3.6 46.5 1.0
C2C D:HEM1001 4.1 40.1 1.0
C3C D:HEM1001 4.2 39.6 1.0
CG D:HIS65 4.2 50.7 1.0
C2A D:HEM1001 4.2 43.7 1.0
ND1 D:HIS65 4.3 51.8 1.0
C3B D:HEM1001 4.3 43.0 1.0
C2B D:HEM1001 4.3 43.2 1.0
C3A D:HEM1001 4.3 44.0 1.0
C2D D:HEM1001 4.3 40.3 1.0
C3D D:HEM1001 4.3 41.0 1.0
CA D:CYS52 4.4 46.9 1.0
NH1 D:ARG266 4.8 42.4 1.0
CB D:TRP54 4.9 41.4 1.0
CD D:PRO64 4.9 45.6 1.0
CG D:PRO64 5.0 49.8 1.0
N D:THR53 5.0 45.9 1.0

Iron binding site 5 out of 6 in 5mms

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Iron binding site 5 out of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe502

b:42.3
occ:1.00
 FE E:HEM502 0.0 42.3 1.0
NA E:HEM502 1.9 43.7 1.0
ND E:HEM502 2.0 41.5 1.0
NC E:HEM502 2.0 41.2 1.0
NB E:HEM502 2.0 43.2 1.0
NE2 E:HIS65 2.2 49.8 1.0
SG E:CYS52 2.4 47.2 1.0
CE1 E:HIS65 2.9 49.3 1.0
C4D E:HEM502 3.0 42.0 1.0
C1A E:HEM502 3.0 43.8 1.0
C1D E:HEM502 3.0 41.0 1.0
C4A E:HEM502 3.0 44.8 1.0
C4C E:HEM502 3.0 40.6 1.0
C1B E:HEM502 3.0 44.8 1.0
C4B E:HEM502 3.1 43.4 1.0
C1C E:HEM502 3.1 41.3 1.0
CD2 E:HIS65 3.3 49.8 1.0
CHA E:HEM502 3.3 43.4 1.0
CHD E:HEM502 3.4 41.0 1.0
CHB E:HEM502 3.4 45.7 1.0
CHC E:HEM502 3.5 42.9 1.0
CB E:CYS52 3.6 43.7 1.0
ND1 E:HIS65 4.1 49.5 1.0
C2A E:HEM502 4.2 45.4 1.0
CA E:CYS52 4.2 45.1 1.0
C3A E:HEM502 4.2 46.0 1.0
C3C E:HEM502 4.2 40.4 1.0
C2C E:HEM502 4.2 41.0 1.0
C2D E:HEM502 4.3 41.1 1.0
C3D E:HEM502 4.3 41.8 1.0
CG E:HIS65 4.3 48.5 1.0
C2B E:HEM502 4.3 45.6 1.0
C3B E:HEM502 4.4 45.0 1.0
NH1 E:ARG266 4.7 21.9 1.0
N E:THR53 4.8 43.9 1.0
C E:CYS52 4.9 46.9 1.0
CD E:PRO64 4.9 47.2 1.0
CG E:PRO64 5.0 51.2 1.0

Iron binding site 6 out of 6 in 5mms

Go back to Iron Binding Sites List in 5mms
Iron binding site 6 out of 6 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:39.4
occ:1.00
 FE F:HEM502 0.0 39.4 1.0
NB F:HEM502 1.9 39.9 1.0
NC F:HEM502 1.9 38.2 1.0
NA F:HEM502 2.0 40.8 1.0
ND F:HEM502 2.0 38.9 1.0
NE2 F:HIS65 2.3 44.5 1.0
SG F:CYS52 2.7 47.6 1.0
C4B F:HEM502 2.9 40.0 1.0
C1B F:HEM502 3.0 41.3 1.0
C1C F:HEM502 3.0 38.1 1.0
C1D F:HEM502 3.0 38.5 1.0
C4A F:HEM502 3.0 41.7 1.0
C4C F:HEM502 3.0 37.6 1.0
C4D F:HEM502 3.0 39.7 1.0
C1A F:HEM502 3.0 41.1 1.0
CD2 F:HIS65 3.2 44.9 1.0
CHC F:HEM502 3.3 39.6 1.0
CE1 F:HIS65 3.3 44.2 1.0
CHB F:HEM502 3.4 42.4 1.0
CHD F:HEM502 3.4 38.3 1.0
CHA F:HEM502 3.4 40.9 1.0
CB F:CYS52 3.6 43.8 1.0
C2C F:HEM502 4.2 38.0 1.0
C2A F:HEM502 4.2 42.5 1.0
C3A F:HEM502 4.2 43.0 1.0
C2B F:HEM502 4.2 41.9 1.0
C3C F:HEM502 4.2 37.5 1.0
CA F:CYS52 4.2 44.0 1.0
C3B F:HEM502 4.2 41.3 1.0
C2D F:HEM502 4.3 38.9 1.0
C3D F:HEM502 4.3 39.8 1.0
CG F:HIS65 4.3 44.8 1.0
NH1 F:ARG266 4.4 35.5 1.0
ND1 F:HIS65 4.4 45.5 1.0
CB F:TRP54 4.8 42.0 1.0
N F:THR53 4.9 47.3 1.0
C F:CYS52 4.9 49.8 1.0
N F:TRP54 5.0 44.8 1.0
CD F:PRO64 5.0 47.3 1.0

Reference:

J.B.Vicente, H.G.Colaco, F.Malagrino, P.E.Santo, A.Gutierres, T.M.Bandeiras, P.Leandro, J.A.Brito, A.Giuffre. A Clinically Relevant Variant of the Human Hydrogen Sulfide-Synthesizing Enzyme Cystathionine Beta-Synthase: Increased Co Reactivity As A Novel Molecular Mechanism of Pathogenicity? Oxid Med Cell Longev V.2017 40321 2017.
ISSN: ISSN 1942-0994
PubMed: 28421128
DOI: 10.1155/2017/8940321
Page generated: Tue Aug 6 06:01:41 2024

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