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Zinc in PDB 1s4i: Crystal Structure of A Sod-Like Protein From Bacillus Subtilis

Enzymatic activity of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis, PDB code: 1s4i was solved by L.Banci, I.Bertini, V.Calderone, F.Cramaro, R.Del Conte, A.Fantoni, S.Mangani, A.Quattrone, M.S.Viezzoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.01 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.225, 61.108, 64.915, 84.35, 76.02, 90.42
R / Rfree (%) 22.1 / 25.8

Other elements in 1s4i:

The structure of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis (pdb code 1s4i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis, PDB code: 1s4i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1s4i

Go back to Zinc Binding Sites List in 1s4i
Zinc binding site 1 out of 6 in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:33.1
occ:1.00
 OD2 B:ASP124 1.9 32.0 1.0
CL B:CL402 2.1 28.8 1.0
ND1 B:HIS121 2.1 30.4 1.0
ND1 B:HIS112 2.2 30.1 1.0
CG B:ASP124 2.9 31.1 1.0
CE1 B:HIS121 2.9 33.6 1.0
CE1 B:HIS112 3.0 32.4 1.0
OD1 B:ASP124 3.1 33.4 1.0
CG B:HIS121 3.3 35.2 1.0
CG B:HIS112 3.3 34.6 1.0
O B:PRO176 3.5 34.3 1.0
CB B:HIS121 3.8 33.0 1.0
CB B:HIS112 3.8 31.6 1.0
O B:HOH861 4.0 38.1 1.0
CA B:HIS112 4.1 34.9 1.0
NE2 B:HIS121 4.1 33.3 1.0
NE2 B:HIS112 4.2 28.2 1.0
CB B:ASP124 4.3 28.9 1.0
CD2 B:HIS121 4.3 28.8 1.0
CB B:PRO104 4.3 39.3 1.0
CD2 B:HIS112 4.4 32.7 1.0
O B:HOH830 4.4 43.5 1.0
CG B:PRO104 4.7 40.7 1.0
C B:PRO176 4.7 38.5 1.0
CA B:ASP124 4.7 29.6 1.0
CG B:HIS86 4.7 29.4 1.0
CA B:SER177 4.8 38.7 1.0
N B:GLY113 4.8 33.9 1.0
N B:ASP124 4.8 28.4 1.0
ND1 B:HIS86 4.9 34.5 1.0
CA B:HIS121 4.9 34.6 1.0
CD2 B:HIS86 4.9 31.5 1.0
N B:HIS121 4.9 36.0 1.0
C B:HIS112 5.0 34.0 1.0

Zinc binding site 2 out of 6 in 1s4i

Go back to Zinc Binding Sites List in 1s4i
Zinc binding site 2 out of 6 in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.6
occ:1.00
 OD1 D:ASP137 1.8 22.0 1.0
OD1 B:ASP137 1.9 23.5 1.0
NE2 B:HIS71 2.0 23.8 1.0
NE2 D:HIS71 2.1 20.1 1.0
CG D:ASP137 2.7 24.9 1.0
CE1 B:HIS71 2.8 21.4 1.0
CG B:ASP137 2.8 24.6 1.0
OD2 D:ASP137 2.8 24.9 1.0
OD2 B:ASP137 3.0 27.5 1.0
CE1 D:HIS71 3.0 21.4 1.0
CD2 B:HIS71 3.1 23.1 1.0
CD2 D:HIS71 3.2 21.1 1.0
ND1 B:HIS71 4.0 24.7 1.0
CB D:ASP137 4.2 18.5 1.0
CG B:HIS71 4.2 19.8 1.0
ND1 D:HIS71 4.2 23.1 1.0
CB B:ASP137 4.2 20.9 1.0
CB B:SER73 4.2 24.1 1.0
OG B:SER73 4.3 24.3 1.0
CG D:HIS71 4.3 25.1 1.0
OG D:SER73 4.3 25.1 1.0
CB D:SER73 4.3 26.4 1.0
C D:ASP137 4.5 17.9 1.0
C B:ASP137 4.6 19.0 1.0
CA D:ASP137 4.6 21.6 1.0
CA B:ASP137 4.7 20.4 1.0
O D:ASP137 4.8 23.5 1.0
O B:ASP137 4.8 20.4 1.0
N B:VAL138 5.0 20.0 1.0
N D:VAL138 5.0 20.5 1.0

Zinc binding site 3 out of 6 in 1s4i

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Zinc binding site 3 out of 6 in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:36.5
occ:1.00
 ND1 A:HIS121 1.8 15.0 1.0
OD2 A:ASP124 1.9 31.9 1.0
ND1 A:HIS112 2.0 30.9 1.0
CL A:CL502 2.1 34.3 1.0
CE1 A:HIS112 2.8 33.8 1.0
CE1 A:HIS121 2.8 15.0 1.0
CG A:ASP124 2.9 36.2 1.0
CG A:HIS121 3.0 15.0 1.0
OD1 A:ASP124 3.2 35.9 1.0
CG A:HIS112 3.2 36.6 1.0
CB A:HIS121 3.5 15.0 1.0
CB A:HIS112 3.7 38.5 1.0
O A:PRO176 3.7 41.9 1.0
O A:HOH824 3.9 42.9 1.0
NE2 A:HIS121 3.9 15.0 1.0
NE2 A:HIS112 4.0 34.2 1.0
CD2 A:HIS121 4.1 15.0 1.0
CA A:HIS112 4.1 37.0 1.0
CD2 A:HIS112 4.2 39.2 1.0
CB A:ASP124 4.3 32.9 1.0
CD2 A:HIS86 4.4 34.6 1.0
CA A:SER177 4.5 40.8 1.0
NE2 A:HIS86 4.6 40.5 1.0
CB A:PRO104 4.7 41.6 1.0
CG A:HIS86 4.7 34.6 1.0
CA A:ASP124 4.7 33.2 1.0
C A:PRO176 4.8 41.9 1.0
N A:GLY113 4.8 35.3 1.0
N A:ASP124 4.8 32.4 1.0
CA A:HIS121 4.9 15.0 1.0
CB A:SER177 4.9 43.0 1.0
CE1 A:HIS86 5.0 38.4 1.0
C A:HIS112 5.0 37.2 1.0
ND1 A:HIS86 5.0 39.8 1.0

Zinc binding site 4 out of 6 in 1s4i

Go back to Zinc Binding Sites List in 1s4i
Zinc binding site 4 out of 6 in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:32.9
occ:1.00
 OD1 A:ASP137 1.8 27.5 1.0
OD1 C:ASP137 1.8 25.1 1.0
NE2 C:HIS71 2.0 38.0 1.0
NE2 A:HIS71 2.1 24.7 1.0
CG A:ASP137 2.7 33.8 1.0
CE1 C:HIS71 2.9 33.3 1.0
OD2 A:ASP137 2.9 31.7 1.0
CG C:ASP137 2.9 31.9 1.0
CE1 A:HIS71 3.1 25.8 1.0
CD2 A:HIS71 3.1 29.5 1.0
CD2 C:HIS71 3.1 31.1 1.0
OD2 C:ASP137 3.2 31.5 1.0
ND1 C:HIS71 4.0 30.1 1.0
CB A:ASP137 4.1 35.1 1.0
CG C:HIS71 4.2 32.1 1.0
ND1 A:HIS71 4.2 27.1 1.0
CG A:HIS71 4.2 29.9 1.0
OG A:SER73 4.2 34.0 1.0
OG C:SER73 4.3 34.5 1.0
CB C:SER73 4.3 30.2 1.0
CB A:SER73 4.4 32.9 1.0
CB C:ASP137 4.4 28.6 1.0
C A:ASP137 4.4 34.7 1.0
CA A:ASP137 4.5 34.7 1.0
O A:ASP137 4.5 35.5 1.0
N A:VAL138 4.8 32.5 1.0
C C:ASP137 4.8 28.5 1.0
CA C:ASP137 4.9 27.6 1.0

Zinc binding site 5 out of 6 in 1s4i

Go back to Zinc Binding Sites List in 1s4i
Zinc binding site 5 out of 6 in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:33.5
occ:1.00
 ND1 C:HIS121 1.9 34.3 1.0
ND1 C:HIS112 2.0 27.4 1.0
OD2 C:ASP124 2.0 31.3 1.0
CL C:CL602 2.2 30.3 1.0
CE1 C:HIS121 2.8 37.5 1.0
CG C:ASP124 2.8 34.0 1.0
OD1 C:ASP124 2.8 36.7 1.0
CE1 C:HIS112 2.9 27.7 1.0
CG C:HIS112 3.0 33.0 1.0
CG C:HIS121 3.0 35.4 1.0
CB C:HIS112 3.4 34.8 1.0
CB C:HIS121 3.6 33.2 1.0
O C:PRO176 3.6 43.7 1.0
O C:HOH618 3.8 38.3 1.0
NE2 C:HIS121 3.9 36.9 1.0
CA C:HIS112 4.0 33.7 1.0
NE2 C:HIS112 4.0 30.3 1.0
CD2 C:HIS121 4.1 39.0 1.0
CD2 C:HIS112 4.1 30.6 1.0
CB C:ASP124 4.3 29.4 1.0
CB C:PRO104 4.5 39.9 1.0
CA C:SER177 4.6 40.1 1.0
OG C:SER177 4.6 44.7 1.0
N C:GLY113 4.7 32.6 1.0
CG C:PRO104 4.7 39.5 1.0
N C:HIS121 4.7 37.0 1.0
CA C:ASP124 4.7 30.3 1.0
C C:PRO176 4.7 43.0 1.0
CD2 C:HIS86 4.8 33.4 1.0
CA C:HIS121 4.8 34.8 1.0
C C:HIS112 4.8 33.1 1.0
CG C:HIS86 4.9 31.4 1.0
NE2 C:HIS86 4.9 35.0 1.0
N C:ASP124 5.0 30.0 1.0

Zinc binding site 6 out of 6 in 1s4i

Go back to Zinc Binding Sites List in 1s4i
Zinc binding site 6 out of 6 in the Crystal Structure of A Sod-Like Protein From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Sod-Like Protein From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:38.2
occ:1.00
 ND1 D:HIS121 1.9 40.9 1.0
OD2 D:ASP124 1.9 38.9 1.0
ND1 D:HIS112 2.0 33.6 1.0
CL D:CL702 2.2 38.4 1.0
CE1 D:HIS121 2.8 41.6 1.0
CG D:ASP124 2.8 39.8 1.0
CE1 D:HIS112 2.9 30.4 1.0
OD1 D:ASP124 3.0 42.6 1.0
CG D:HIS121 3.1 40.8 1.0
CG D:HIS112 3.1 37.7 1.0
CB D:HIS121 3.5 41.3 1.0
CB D:HIS112 3.5 40.7 1.0
O D:PRO176 3.7 46.1 1.0
CA D:HIS112 3.8 41.0 1.0
NE2 D:HIS121 3.9 43.6 1.0
O D:HOH784 4.0 47.1 1.0
NE2 D:HIS112 4.1 35.9 1.0
CD2 D:HIS121 4.1 41.6 1.0
CD2 D:HIS112 4.2 36.4 1.0
CB D:ASP124 4.3 34.7 1.0
N D:GLY113 4.5 41.1 1.0
CB D:PRO104 4.6 42.8 1.0
C D:HIS112 4.7 42.0 1.0
CA D:SER177 4.7 43.2 1.0
CA D:ASP124 4.8 34.6 1.0
N D:HIS112 4.8 42.8 1.0
C D:PRO176 4.8 44.5 1.0
CA D:HIS121 4.9 40.2 1.0
CD2 D:HIS86 4.9 38.3 1.0
N D:ASP124 4.9 35.5 1.0

Reference:

L.Banci, I.Bertini, V.Calderone, F.Cramaro, R.Del Conte, A.Fantoni, S.Mangani, A.Quattrone, M.S.Viezzoli. A Prokaryotic Superoxide Dismutase Paralog Lacking Two Cu Ligands: From Largely Unstructured in Solution to Ordered in the Crystal. Proc.Natl.Acad.Sci.Usa V. 102 7541 2005.
ISSN: ISSN 0027-8424
PubMed: 15897454
DOI: 10.1073/PNAS.0502450102
Page generated: Wed Oct 16 18:43:47 2024

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