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Chlorine in PDB 8iq1: Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State

Enzymatic activity of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State

All present enzymatic activity of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State, PDB code: 8iq1 was solved by J.H.Zhou, W.X.Huang, R.X.Cheng, P.J.Zhang, Y.C.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.28 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.126, 69.961, 91.345, 98.69, 94.83, 103.31
R / Rfree (%) 18.4 / 21.7

Other elements in 8iq1:

The structure of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Copper (Cu) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State (pdb code 8iq1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State, PDB code: 8iq1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8iq1

Go back to Chlorine Binding Sites List in 8iq1
Chlorine binding site 1 out of 7 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl209

b:49.7
occ:1.00
CB B:ASN63 3.1 20.2 1.0
O B:HIS61 3.2 15.4 1.0
ND2 B:ASN63 3.3 17.2 1.0
CG B:ASN63 3.7 19.5 1.0
CB B:PRO60 3.9 21.7 1.0
O B:HOH313 4.0 26.2 1.0
CG B:PRO60 4.1 19.9 1.0
O B:HOH378 4.1 33.1 1.0
C B:HIS61 4.4 15.2 1.0
NE2 B:HIS78 4.5 21.2 1.0
CA B:ASN63 4.5 18.2 1.0
N B:HIS61 4.5 16.4 1.0
N B:ASN63 4.6 12.1 1.0
CD2 B:HIS78 4.7 19.5 1.0
CE1 B:HIS78 4.8 20.1 1.0
CA B:HIS61 4.9 17.6 1.0
O B:HOH387 4.9 29.7 1.0
C B:PRO60 4.9 16.6 1.0
O B:HOH360 4.9 20.1 1.0
O B:ASN63 4.9 18.8 1.0
OD1 B:ASN63 5.0 19.7 1.0

Chlorine binding site 2 out of 7 in 8iq1

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Chlorine binding site 2 out of 7 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl206

b:55.9
occ:1.00
O C:ASP40 2.9 25.3 1.0
OG1 C:THR37 3.4 42.4 1.0
O C:GLU119 3.5 26.8 1.0
CE1 C:HIS41 3.5 30.0 1.0
O C:HOH321 3.7 48.7 1.0
NE2 C:HIS41 3.7 30.4 1.0
CD C:PRO121 3.9 29.8 1.0
ND1 C:HIS41 4.0 29.5 1.0
O C:HOH392 4.0 36.8 1.0
C C:ASP40 4.1 27.9 1.0
O C:GLU38 4.2 36.0 1.0
CD2 C:HIS41 4.2 30.0 1.0
CG C:PRO121 4.3 30.3 1.0
N C:ASP40 4.3 30.9 1.0
CA C:LYS120 4.3 24.7 1.0
CG C:HIS41 4.4 29.2 1.0
N C:PRO121 4.4 27.7 1.0
C C:GLU119 4.5 24.5 1.0
C C:LYS120 4.6 26.8 1.0
C C:GLY39 4.6 32.8 1.0
CA C:ASP40 4.8 31.2 1.0
CB C:THR37 4.8 41.7 1.0
CA C:GLY39 4.8 32.6 1.0
N C:LYS120 4.9 24.5 1.0

Chlorine binding site 3 out of 7 in 8iq1

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Chlorine binding site 3 out of 7 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl205

b:34.5
occ:1.00
O D:HOH428 2.8 23.7 1.0
O D:HOH375 2.9 29.7 1.0
NH2 D:ARG141 3.2 17.0 1.0
O D:HOH318 3.3 27.0 1.0
O D:HOH339 3.3 23.5 1.0
NE2 D:HIS61 3.6 17.3 1.0
CE1 D:HIS46 3.6 13.7 1.0
CE1 D:HIS118 3.7 13.8 1.0
CG2 D:THR135 3.7 25.0 1.0
NE D:ARG141 3.9 17.2 1.0
CD2 D:HIS61 3.9 15.9 1.0
CZ D:ARG141 3.9 16.1 1.0
CB D:THR135 4.1 23.7 1.0
CU D:CU201 4.3 17.1 1.0
NE2 D:HIS118 4.3 12.9 1.0
NE2 D:HIS46 4.4 13.3 1.0
ND1 D:HIS46 4.5 13.8 1.0
CE1 D:HIS61 4.7 15.2 1.0
ND1 D:HIS118 4.7 15.9 1.0

Chlorine binding site 4 out of 7 in 8iq1

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Chlorine binding site 4 out of 7 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl204

b:45.6
occ:1.00
OE2 E:GLU76 2.6 29.2 1.0
O E:HOH430 2.7 37.7 1.0
NZ E:LYS68 2.9 41.6 1.0
O E:HOH384 2.9 28.9 1.0
CD E:GLU76 3.6 30.4 1.0
OE1 E:GLU76 4.0 32.1 1.0
N E:LYS68 4.1 17.8 1.0
CA E:LYS67 4.2 18.1 1.0
CE E:LYS68 4.3 40.1 1.0
O E:SER66 4.3 18.4 1.0
CG E:LYS68 4.3 29.6 1.0
C E:LYS67 4.5 19.3 1.0
CD E:LYS67 4.6 29.6 1.0
CD E:LYS68 4.6 35.8 1.0
CB E:LYS68 4.7 22.6 1.0
O E:HOH469 4.8 45.9 1.0
CG E:GLU76 4.9 30.6 1.0
CB E:LYS67 4.9 21.0 1.0

Chlorine binding site 5 out of 7 in 8iq1

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Chlorine binding site 5 out of 7 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl205

b:45.7
occ:1.00
O F:HOH401 3.1 26.7 1.0
O2 F:EDO204 3.5 32.0 1.0
O F:HOH305 3.7 31.3 1.0
N E:ALA1 3.8 29.0 1.0
CB E:ALA1 3.8 22.5 1.0
NH2 F:ARG113 3.9 15.2 1.0
O E:HOH325 3.9 30.4 1.0
CD1 E:ILE149 4.1 11.6 1.0
CA E:ALA1 4.1 23.0 1.0
O E:HOH353 4.2 37.6 1.0
O F:HOH380 4.4 32.4 1.0
O F:HOH320 4.4 22.4 1.0
CG1 E:ILE149 4.8 11.4 1.0
C2 F:EDO204 4.9 29.5 1.0
CZ F:ARG113 4.9 15.2 1.0
O F:HOH324 4.9 20.2 1.0

Chlorine binding site 6 out of 7 in 8iq1

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Chlorine binding site 6 out of 7 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl207

b:46.4
occ:1.00
N H:GLY106 3.4 19.6 1.0
O H:HOH334 3.7 24.9 1.0
O H:HOH354 3.7 26.6 1.0
CB H:SER105 4.0 19.2 1.0
O H:HOH385 4.0 29.5 1.0
CA H:SER105 4.1 17.7 1.0
C H:SER105 4.3 18.5 1.0
O G:HOH387 4.3 38.1 1.0
CA H:GLY106 4.3 20.3 1.0
O G:HOH416 5.0 28.3 1.0

Chlorine binding site 7 out of 7 in 8iq1

Go back to Chlorine Binding Sites List in 8iq1
Chlorine binding site 7 out of 7 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl208

b:42.0
occ:1.00
NH1 H:ARG113 3.0 15.7 1.0
NE2 H:GLN47 3.2 25.1 1.0
NH2 H:ARG113 3.7 16.1 1.0
O H:HOH409 3.8 32.6 1.0
CZ H:ARG113 3.8 17.4 1.0
O G:HOH420 3.8 35.1 1.0
CG H:GLN47 3.8 24.7 1.0
CD H:GLN47 4.0 26.8 1.0
CE1 H:PHE48 4.2 21.8 1.0
CG2 G:ILE149 4.3 18.8 1.0
O H:HOH408 4.4 30.7 1.0
O H:GLN47 4.8 18.4 1.0
CD1 H:PHE48 4.8 20.7 1.0

Reference:

D.D.Wu, S.Jin, R.X.Cheng, W.J.Cai, W.L.Xue, Q.Q.Zhang, L.J.Yang, Q.Zhu, M.Y.Li, G.Lin, Y.Z.Wang, X.P.Mu, Y.Wang, I.Y.Zhang, Q.Zhang, Y.Chen, S.Y.Cai, B.Tan, Y.Li, Y.Q.Chen, P.J.Zhang, C.Sun, Y.Yin, M.J.Wang, Y.Z.Zhu, B.B.Tao, J.H.Zhou, W.X.Huang, Y.C.Zhu. Hydrogen Sulfide Functions As A Micro-Modulator Bound at the Copper Active Site of Cu/Zn-Sod to Regulate the Catalytic Activity of the Enzyme. Cell Rep V. 42 12750 2023.
ISSN: ESSN 2211-1247
PubMed: 37421623
DOI: 10.1016/J.CELREP.2023.112750
Page generated: Thu Dec 28 03:19:33 2023

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