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Chlorine in PDB 6spj: A4V Mutant of Human SOD1 with Ebselen Derivative 1

Enzymatic activity of A4V Mutant of Human SOD1 with Ebselen Derivative 1

All present enzymatic activity of A4V Mutant of Human SOD1 with Ebselen Derivative 1:
1.15.1.1;

Protein crystallography data

The structure of A4V Mutant of Human SOD1 with Ebselen Derivative 1, PDB code: 6spj was solved by V.Chantadul, K.Amporndanai, G.Wright, S.Antonyuk, S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.33 / 1.97
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.506, 194.658, 75.169, 90.00, 96.97, 90.00
R / Rfree (%) 18.3 / 22.5

Other elements in 6spj:

The structure of A4V Mutant of Human SOD1 with Ebselen Derivative 1 also contains other interesting chemical elements:

Zinc (Zn) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the A4V Mutant of Human SOD1 with Ebselen Derivative 1 (pdb code 6spj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the A4V Mutant of Human SOD1 with Ebselen Derivative 1, PDB code: 6spj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6spj

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Chlorine binding site 1 out of 6 in the A4V Mutant of Human SOD1 with Ebselen Derivative 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A4V Mutant of Human SOD1 with Ebselen Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:29.2
occ:0.80
 NZ I:LYS128 3.1 27.5 0.8
O A:HOH406 3.2 32.4 1.0
N A:LYS75 3.4 30.1 1.0
CB A:LYS75 3.5 33.5 1.0
CD A:PRO74 3.6 29.2 1.0
CA A:GLY73 3.6 26.9 1.0
N A:PRO74 3.6 26.9 1.0
C A:GLY73 3.7 26.7 1.0
CE I:LYS128 3.8 27.9 0.8
O I:HOH433 3.9 48.2 1.0
CA A:LYS75 4.0 32.3 1.0
CD I:LYS128 4.0 29.7 1.0
CG A:LYS75 4.1 33.1 0.5
CG A:PRO74 4.1 28.1 1.0
O A:GLY73 4.3 25.6 1.0
CD1 A:LEU126 4.4 26.1 1.0
C A:PRO74 4.4 29.5 1.0
CA A:PRO74 4.5 28.9 1.0
CG I:LYS128 4.5 26.7 1.0
O I:HOH434 4.6 38.9 1.0
CD A:LYS75 4.6 36.7 0.5
C A:LYS75 4.6 34.5 1.0
N A:ASP76 4.6 34.9 1.0
O I:HOH359 4.7 42.5 1.0
N A:GLY73 4.7 26.7 1.0
CB A:PRO74 4.9 27.8 1.0
OD2 A:ASP76 4.9 45.5 1.0

Chlorine binding site 2 out of 6 in 6spj

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Chlorine binding site 2 out of 6 in the A4V Mutant of Human SOD1 with Ebselen Derivative 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A4V Mutant of Human SOD1 with Ebselen Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl213

b:35.1
occ:0.70
 O B:HOH365 3.1 37.9 1.0
CB B:SER98 3.4 31.5 1.0
CB B:ASP96 3.7 37.5 1.0
O B:VAL97 4.0 26.6 1.0
C B:VAL97 4.1 28.0 1.0
N B:SER98 4.1 28.9 1.0
C B:ASP96 4.2 30.0 1.0
N B:VAL97 4.4 28.4 1.0
CA B:SER98 4.4 28.3 1.0
OG B:SER98 4.4 30.7 1.0
O B:ASP96 4.4 29.4 1.0
CA B:ASP96 4.6 31.7 1.0
CG B:ASP96 4.7 43.6 1.0
CA B:VAL97 4.8 27.8 1.0
O B:HOH385 4.9 45.8 1.0

Chlorine binding site 3 out of 6 in 6spj

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Chlorine binding site 3 out of 6 in the A4V Mutant of Human SOD1 with Ebselen Derivative 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A4V Mutant of Human SOD1 with Ebselen Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl213

b:40.1
occ:0.80
 O E:HOH358 2.7 34.5 0.6
O E:HOH431 2.8 25.5 0.7
O E:HOH408 3.1 52.1 1.0
NH2 E:ARG143 3.4 27.0 1.0
O E:HOH442 3.4 33.0 0.5
CE1 E:HIS120 3.5 20.2 1.0
O E:HOH344 3.5 27.5 1.0
ZN E:ZN203 3.5 21.8 0.1
CE1 E:HIS48 3.6 23.5 1.0
CG2 E:THR137 3.6 28.0 1.0
O E:HOH428 3.7 42.0 1.0
NE E:ARG143 3.9 26.3 1.0
CZ E:ARG143 4.0 28.9 1.0
CB E:THR137 4.1 25.3 1.0
NE2 E:HIS63 4.1 24.9 1.0
NE2 E:HIS120 4.2 21.4 1.0
NE2 E:HIS48 4.4 22.3 1.0
ND1 E:HIS120 4.4 21.1 1.0
CD2 E:HIS63 4.5 26.1 1.0
ND1 E:HIS48 4.6 21.9 1.0
O E:GLY141 4.7 26.6 1.0
CA E:THR137 4.9 24.9 1.0

Chlorine binding site 4 out of 6 in 6spj

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Chlorine binding site 4 out of 6 in the A4V Mutant of Human SOD1 with Ebselen Derivative 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of A4V Mutant of Human SOD1 with Ebselen Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl208

b:40.9
occ:0.80
 O E:HOH384 2.7 22.8 1.0
O F:HOH354 2.9 43.4 1.0
O F:HOH418 2.9 28.9 1.0
N F:VAL148 3.0 22.2 1.0
CA F:GLY147 3.4 24.0 1.0
O F:HOH357 3.6 22.1 1.0
O E:HOH426 3.6 50.8 1.0
C F:GLY147 3.7 25.0 1.0
CG2 F:VAL148 4.0 24.6 1.0
CB F:VAL148 4.0 22.3 1.0
CA F:VAL148 4.1 21.7 1.0
O F:VAL148 4.4 21.4 1.0
O F:VAL7 4.4 24.8 1.0
O F:HOH374 4.5 37.9 1.0
O E:HOH314 4.5 33.9 0.8
CG2 E:VAL148 4.6 23.1 1.0
O E:HOH425 4.6 34.4 1.0
N F:GLY147 4.8 23.9 1.0
C F:VAL148 4.8 20.3 1.0
CB E:VAL148 4.8 22.1 1.0
O E:HOH346 4.8 40.5 1.0
O F:HOH373 4.9 45.5 1.0
O F:CYS146 4.9 24.6 1.0
O F:HOH334 5.0 33.8 0.5

Chlorine binding site 5 out of 6 in 6spj

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Chlorine binding site 5 out of 6 in the A4V Mutant of Human SOD1 with Ebselen Derivative 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of A4V Mutant of Human SOD1 with Ebselen Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl211

b:43.5
occ:0.80
 O I:HOH420 2.9 23.3 0.6
O I:HOH346 3.0 34.9 1.0
O I:HOH358 3.3 29.8 1.0
NH2 I:ARG143 3.3 25.5 1.0
CE1 I:HIS120 3.4 22.8 1.0
CE1 I:HIS48 3.5 20.3 1.0
ZN I:ZN203 3.6 29.2 0.1
O I:HOH301 3.7 42.5 0.8
CG2 I:THR137 3.8 27.9 1.0
NE I:ARG143 3.9 26.9 1.0
O I:HOH418 4.0 42.5 1.0
CZ I:ARG143 4.0 25.6 1.0
CB I:THR137 4.0 26.9 1.0
NE2 I:HIS63 4.1 26.0 1.0
NE2 I:HIS120 4.2 22.9 1.0
ND1 I:HIS120 4.3 24.9 1.0
NE2 I:HIS48 4.4 22.0 1.0
CD2 I:HIS63 4.5 24.7 1.0
ND1 I:HIS48 4.5 20.8 1.0
O I:HOH334 4.7 52.1 1.0
O I:GLY141 4.7 31.9 1.0
CA I:THR137 5.0 25.3 1.0

Chlorine binding site 6 out of 6 in 6spj

Go back to Chlorine Binding Sites List in 6spj
Chlorine binding site 6 out of 6 in the A4V Mutant of Human SOD1 with Ebselen Derivative 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of A4V Mutant of Human SOD1 with Ebselen Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl211

b:33.5
occ:0.80
 O J:HOH423 3.3 41.1 1.0
N J:LYS75 3.4 32.5 1.0
CD J:PRO74 3.5 27.0 1.0
CA J:GLY73 3.5 29.8 1.0
N J:PRO74 3.6 26.8 1.0
CB J:LYS75 3.6 36.3 1.0
C J:GLY73 3.6 28.1 1.0
CG J:LYS75 4.0 37.6 1.0
CG J:PRO74 4.0 26.1 1.0
CA J:LYS75 4.1 32.8 1.0
O J:GLY73 4.3 28.1 1.0
CD J:LYS75 4.4 41.7 0.7
C J:PRO74 4.4 29.5 1.0
CA J:PRO74 4.4 27.7 1.0
CD1 J:LEU126 4.5 28.5 1.0
N J:GLY73 4.6 28.0 1.0
N J:ASP76 4.6 32.4 1.0
C J:LYS75 4.7 34.5 1.0
CB J:PRO74 4.9 26.3 1.0
OD1 J:ASP76 4.9 38.7 1.0

Reference:

V.Chantadul, G.S.A.Wright, K.Amporndanai, M.Shahid, S.V.Antonyuk, G.Washbourn, M.Rogers, N.Roberts, M.Pye, P.M.O'neill, S.S.Hasnain. Ebselen As Template For Stabilization of A4V Mutant Dimer For Motor Neuron Disease Therapy. Commun Biol V. 3 97 2020.
ISSN: ESSN 2399-3642
PubMed: 32139772
DOI: 10.1038/S42003-020-0826-3
Page generated: Mon Jul 29 15:05:46 2024

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