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Zinc in PDB 2yav: Zn Inhibited Sulfur Oxygenase Reductase

Enzymatic activity of Zn Inhibited Sulfur Oxygenase Reductase

All present enzymatic activity of Zn Inhibited Sulfur Oxygenase Reductase:
1.13.11.55;

Protein crystallography data

The structure of Zn Inhibited Sulfur Oxygenase Reductase, PDB code: 2yav was solved by A.Veith, T.Urich, K.Seyfarth, J.Protze, C.Frazao, A.Kletzin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.20 / 1.70
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 162.074, 162.074, 154.237, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.3

Other elements in 2yav:

The structure of Zn Inhibited Sulfur Oxygenase Reductase also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Iron (Fe) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Zn Inhibited Sulfur Oxygenase Reductase (pdb code 2yav). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Zn Inhibited Sulfur Oxygenase Reductase, PDB code: 2yav:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2yav

Go back to Zinc Binding Sites List in 2yav
Zinc binding site 1 out of 6 in the Zn Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:23.5
occ:0.80
 O A:HOH2233 1.8 19.2 0.8
OXT A:ACT406 2.0 28.3 0.8
NE2 A:HIS277 2.0 14.2 1.0
CL A:CL407 2.3 20.9 0.8
O A:HOH2232 2.8 26.0 0.8
C A:ACT406 2.9 24.6 0.8
CE1 A:HIS277 3.0 13.0 1.0
O A:ACT406 3.0 23.0 0.8
CD2 A:HIS277 3.0 17.8 1.0
O A:HOH2198 3.8 44.8 1.0
ND1 A:HIS277 4.1 14.8 1.0
CG A:HIS277 4.1 14.3 1.0
NE2 A:HIS166 4.2 19.4 1.0
CH3 A:ACT406 4.3 29.4 0.8
CG2 A:VAL267 4.4 14.4 1.0
CB A:PRO288 4.5 21.0 1.0
CG A:PRO288 4.6 19.2 1.0

Zinc binding site 2 out of 6 in 2yav

Go back to Zinc Binding Sites List in 2yav
Zinc binding site 2 out of 6 in the Zn Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:24.2
occ:0.80
 O B:HOH2221 1.8 24.0 0.8
NE2 B:HIS277 2.1 16.7 1.0
CL B:CL407 2.2 21.1 0.8
O B:HOH2222 2.2 26.9 0.8
OXT B:ACT406 2.3 26.3 0.8
CE1 B:HIS277 2.9 18.3 1.0
CD2 B:HIS277 3.1 15.4 1.0
C B:ACT406 3.2 27.9 0.8
O B:ACT406 3.3 26.3 0.8
ND1 B:HIS277 4.1 15.2 1.0
CG B:HIS277 4.2 16.0 1.0
NE2 B:HIS166 4.2 18.6 1.0
CB B:PRO288 4.4 20.4 1.0
CG2 B:VAL267 4.5 15.6 1.0
CG B:PRO288 4.5 20.1 1.0
CH3 B:ACT406 4.6 21.9 0.8
CE1 B:HIS166 5.0 15.3 1.0

Zinc binding site 3 out of 6 in 2yav

Go back to Zinc Binding Sites List in 2yav
Zinc binding site 3 out of 6 in the Zn Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn405

b:22.1
occ:0.80
 O C:HOH2221 1.7 19.0 0.8
OXT C:ACT406 2.1 28.2 0.8
NE2 C:HIS277 2.1 18.1 1.0
CL C:CL407 2.2 20.9 0.8
O C:HOH2220 2.6 28.5 0.8
CE1 C:HIS277 3.0 16.5 1.0
C C:ACT406 3.1 21.2 0.8
CD2 C:HIS277 3.1 16.2 1.0
O C:ACT406 3.2 22.4 0.8
O C:HOH2189 4.1 41.8 1.0
ND1 C:HIS277 4.1 16.9 1.0
NE2 C:HIS166 4.2 18.0 1.0
CG C:HIS277 4.2 14.5 1.0
CB C:PRO288 4.5 21.2 1.0
CH3 C:ACT406 4.5 21.4 0.8
CG2 C:VAL267 4.5 12.0 1.0
CG C:PRO288 4.6 17.6 1.0
CE1 C:HIS166 5.0 15.2 1.0

Zinc binding site 4 out of 6 in 2yav

Go back to Zinc Binding Sites List in 2yav
Zinc binding site 4 out of 6 in the Zn Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn405

b:24.2
occ:0.80
 O D:HOH2225 2.0 25.0 0.8
OXT D:ACT406 2.0 26.7 0.8
NE2 D:HIS277 2.1 16.6 1.0
CL D:CL407 2.2 23.5 0.8
O D:HOH2226 2.7 29.9 0.8
C D:ACT406 2.9 24.5 0.8
O D:ACT406 3.0 24.6 0.8
CE1 D:HIS277 3.0 15.9 1.0
CD2 D:HIS277 3.2 17.1 1.0
ND1 D:HIS277 4.2 14.8 1.0
NE2 D:HIS166 4.2 17.5 1.0
CG D:HIS277 4.2 15.2 1.0
O D:HOH2193 4.3 35.8 1.0
CH3 D:ACT406 4.3 29.6 0.8
CB D:PRO288 4.4 18.4 1.0
CG2 D:VAL267 4.4 12.8 1.0
CG D:PRO288 4.5 23.1 1.0

Zinc binding site 5 out of 6 in 2yav

Go back to Zinc Binding Sites List in 2yav
Zinc binding site 5 out of 6 in the Zn Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn405

b:24.3
occ:0.80
 O E:HOH2214 1.9 19.0 0.8
NE2 E:HIS277 2.1 18.8 1.0
OXT E:ACT406 2.1 30.9 0.8
CL E:CL407 2.2 21.5 0.8
O E:HOH2215 2.4 36.4 0.8
CE1 E:HIS277 2.9 14.7 1.0
C E:ACT406 3.1 26.7 0.8
CD2 E:HIS277 3.1 16.4 1.0
O E:ACT406 3.2 25.8 0.8
ND1 E:HIS277 4.1 12.0 1.0
CG E:HIS277 4.2 14.2 1.0
NE2 E:HIS166 4.3 16.3 1.0
CG2 E:VAL267 4.4 13.2 1.0
CH3 E:ACT406 4.4 26.9 0.8
O E:HOH2183 4.5 43.4 1.0
CB E:PRO288 4.5 22.1 1.0
CG E:PRO288 4.5 17.5 1.0

Zinc binding site 6 out of 6 in 2yav

Go back to Zinc Binding Sites List in 2yav
Zinc binding site 6 out of 6 in the Zn Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn405

b:24.0
occ:0.80
 O F:HOH2240 1.9 24.2 0.8
OXT F:ACT406 2.1 28.9 0.8
NE2 F:HIS277 2.1 16.8 1.0
CL F:CL407 2.2 21.7 0.8
O F:HOH2241 2.8 28.2 0.8
CE1 F:HIS277 3.0 13.7 1.0
C F:ACT406 3.0 20.9 0.8
O F:ACT406 3.1 25.1 0.8
CD2 F:HIS277 3.2 17.9 1.0
ND1 F:HIS277 4.1 14.6 1.0
NE2 F:HIS166 4.2 17.4 1.0
CG F:HIS277 4.2 16.3 1.0
CB F:PRO288 4.4 18.8 1.0
CH3 F:ACT406 4.4 24.5 0.8
CG F:PRO288 4.5 21.8 1.0
CG2 F:VAL267 4.5 16.2 1.0
CE1 F:HIS166 5.0 13.4 1.0

Reference:

A.Veith, T.Urich, K.Seyfarth, J.Protze, C.Frazao, A.Kletzin. Substrate Pathways and Mechanisms of Inhibition in the Sulfur Oxygenase Reductase of Acidianus Ambivalens. Front.Microbiol. V. 2 37 2011.
ISSN: ESSN 1664-302X
PubMed: 21747782
DOI: 10.3389/FMICB.2011.00037
Page generated: Thu Oct 17 05:47:23 2024

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