Iron in PDB 2v4j: The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration

All present enzymatic activity of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration:
1.8.99.3;

The structure of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration, PDB code: 2v4j was solved by T.F.Oliveira, C.Vonrhein, P.M.Matias, S.S.Venceslau, I.A.C.Pereira, M.Archer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	128.04 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.410, 118.900, 132.240, 90.00, 104.13, 90.00
R / Rfree (%)	19.01 / 21.88

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Iron atom in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration (pdb code 2v4j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 34 binding sites of Iron where determined in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration, PDB code: 2v4j:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:26.1 occ:1.00 FE1 A:SF4501 0.0 26.1 1.0 SG A:CYS225 2.3 25.0 1.0 S3 A:SF4501 2.3 23.1 1.0 S2 A:SF4501 2.3 27.1 1.0 S4 A:SF4501 2.3 26.7 1.0 FE2 A:SF4501 2.6 25.7 1.0 FE4 A:SF4501 2.7 26.3 1.0 FE3 A:SF4501 2.7 24.7 1.0 CB A:CYS225 3.1 21.6 1.0 S1 A:SF4501 3.9 26.5 1.0 N A:CYS225 4.0 22.9 1.0 CA A:CYS225 4.2 22.1 1.0 N23 A:SH0503 4.3 21.9 1.0 CB A:ASN223 4.4 24.2 1.0 CB A:CYS177 4.4 23.4 1.0 SG A:CYS177 4.6 27.6 1.0 SG A:CYS221 4.7 25.4 1.0 C81 A:SH0503 4.7 25.7 1.0 C11 A:SH0503 4.7 22.6 1.0 SG A:CYS183 4.8 25.4 1.0 N22 A:SH0503 4.8 23.1 1.0 C14 A:SH0503 4.9 20.8 1.0 N24 A:SH0503 4.9 19.7 1.0 C6 A:SH0503 5.0 24.9 1.0

Iron binding site 2 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:25.7 occ:1.00 FE2 A:SF4501 0.0 25.7 1.0 S4 A:SF4501 2.3 26.7 1.0 S1 A:SF4501 2.3 26.5 1.0 S3 A:SF4501 2.3 23.1 1.0 SG A:CYS177 2.3 27.6 1.0 FE1 A:SF4501 2.6 26.1 1.0 FE4 A:SF4501 2.7 26.3 1.0 FE3 A:SF4501 2.8 24.7 1.0 CB A:CYS177 3.2 23.4 1.0 N A:ALA220 3.8 23.4 1.0 S2 A:SF4501 3.9 27.1 1.0 CB A:ALA220 3.9 23.9 1.0 N A:GLY179 4.1 25.3 1.0 CA A:ALA220 4.3 23.0 1.0 CA A:GLY179 4.3 26.7 1.0 N A:CYS221 4.5 22.9 1.0 CB A:CYS225 4.5 21.6 1.0 CA A:CYS177 4.6 23.0 1.0 SG A:CYS225 4.6 25.0 1.0 C A:ALA220 4.6 26.4 1.0 N A:LEU178 4.7 22.0 1.0 SG A:CYS183 4.8 25.4 1.0 C A:CYS177 4.8 25.7 1.0 C A:ASP219 4.9 26.2 1.0 SG A:CYS221 4.9 25.4 1.0

Iron binding site 3 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:24.7 occ:1.00 FE3 A:SF4501 0.0 24.7 1.0 SG A:CYS221 2.2 25.4 1.0 S4 A:SF4501 2.3 26.7 1.0 S2 A:SF4501 2.3 27.1 1.0 S1 A:SF4501 2.3 26.5 1.0 FE4 A:SF4501 2.7 26.3 1.0 FE1 A:SF4501 2.7 26.1 1.0 FE2 A:SF4501 2.8 25.7 1.0 CB A:CYS221 3.2 21.5 1.0 N A:CYS221 3.6 22.9 1.0 CA A:CYS221 3.8 21.9 1.0 S3 A:SF4501 4.0 23.1 1.0 CB A:ASN223 4.0 24.2 1.0 C A:CYS221 4.2 25.4 1.0 O A:CYS221 4.2 26.2 1.0 CB A:PHE185 4.3 28.0 1.0 C A:ALA220 4.3 26.4 1.0 ND2 A:ASN223 4.4 27.3 1.0 SG A:CYS183 4.5 25.4 1.0 N A:ASN223 4.6 24.6 1.0 CG A:ASN223 4.7 32.5 1.0 SG A:CYS225 4.7 25.0 1.0 N A:ALA220 4.8 23.4 1.0 CA A:ASN223 4.8 25.0 1.0 CD2 A:PHE185 4.8 31.1 1.0 CA A:ALA220 4.8 23.0 1.0 O A:ALA220 4.9 26.0 1.0 SG A:CYS177 4.9 27.6 1.0 N A:GLY224 4.9 25.9 1.0 CB A:ALA220 4.9 23.9 1.0 O A:PHE185 5.0 27.5 1.0 C A:PHE185 5.0 28.1 1.0

Iron binding site 4 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:26.3 occ:1.00 FE4 A:SF4501 0.0 26.3 1.0 SG A:CYS183 2.3 25.4 1.0 S2 A:SF4501 2.3 27.1 1.0 S1 A:SF4501 2.3 26.5 1.0 S3 A:SF4501 2.3 23.1 1.0 FE2 A:SF4501 2.7 25.7 1.0 FE3 A:SF4501 2.7 24.7 1.0 FE1 A:SF4501 2.7 26.1 1.0 CB A:CYS183 3.2 22.1 1.0 S4 A:SF4501 3.8 26.7 1.0 C81 A:SH0503 4.0 25.7 1.0 CB A:PHE185 4.2 28.0 1.0 CD2 A:PHE185 4.5 31.1 1.0 SG A:CYS221 4.5 25.4 1.0 C82 A:SH0503 4.7 27.8 1.0 CA A:CYS183 4.7 23.4 1.0 N A:ALA186 4.7 24.7 1.0 SG A:CYS225 4.8 25.0 1.0 CG A:PHE185 4.8 29.4 1.0 SG A:CYS177 4.8 27.6 1.0 CD2 A:LEU178 4.9 25.6 1.0 C A:PHE185 5.0 28.1 1.0 CA A:PHE185 5.0 26.0 1.0 N A:PHE185 5.0 26.4 1.0

Iron binding site 5 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:29.0 occ:1.00 FE1 A:SF4502 0.0 29.0 1.0 SG A:CYS306 2.3 26.6 1.0 S3 A:SF4502 2.3 30.6 1.0 S4 A:SF4502 2.3 30.1 1.0 S2 A:SF4502 2.3 32.1 1.0 FE3 A:SF4502 2.7 34.8 1.0 FE4 A:SF4502 2.7 32.4 1.0 FE2 A:SF4502 2.7 29.3 1.0 CB A:CYS306 3.4 23.2 1.0 N A:CYS306 3.4 24.1 1.0 CA A:CYS306 3.8 23.3 1.0 N A:MET307 3.9 24.2 1.0 S1 A:SF4502 3.9 35.4 1.0 CD A:PRO285 4.0 27.1 1.0 N A:HIS308 4.1 23.0 1.0 C A:CYS306 4.2 27.1 1.0 CG A:PRO285 4.4 30.6 1.0 C A:ARG305 4.5 26.9 1.0 CB A:HIS308 4.6 23.8 1.0 SG A:CYS284 4.6 33.2 1.0 N A:ARG305 4.7 25.3 1.0 N A:CYS309 4.7 25.2 1.0 SG A:CYS309 4.7 28.0 1.0 CA A:ARG305 4.8 23.5 1.0 CA A:HIS308 4.8 23.4 1.0 SG A:CYS303 4.8 28.0 1.0 C A:MET307 4.9 26.6 1.0 CA A:MET307 4.9 23.3 1.0 CG2 A:VAL304 5.0 30.8 1.0

Iron binding site 6 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:29.3 occ:1.00 FE2 A:SF4502 0.0 29.3 1.0 S4 A:SF4502 2.3 30.1 1.0 S3 A:SF4502 2.3 30.6 1.0 SG A:CYS303 2.3 28.0 1.0 S1 A:SF4502 2.3 35.4 1.0 FE3 A:SF4502 2.6 34.8 1.0 FE4 A:SF4502 2.7 32.4 1.0 FE1 A:SF4502 2.7 29.0 1.0 CB A:CYS303 3.3 24.9 1.0 N A:ARG305 3.8 25.3 1.0 CA A:CYS303 3.8 25.3 1.0 S2 A:SF4502 3.9 32.1 1.0 N A:VAL304 4.0 28.3 1.0 CA A:ARG305 4.1 23.5 1.0 C A:CYS303 4.2 30.7 1.0 CD1 A:ILE244 4.3 28.6 1.0 N A:CYS306 4.3 24.1 1.0 SG A:CYS288 4.4 33.7 1.0 SG A:CYS284 4.6 33.2 1.0 SG A:CYS309 4.7 28.0 1.0 C A:VAL304 4.8 30.4 1.0 C A:ARG305 4.8 26.9 1.0 SG A:CYS306 4.9 26.6 1.0 CA A:VAL304 5.0 27.4 1.0

Iron binding site 7 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:34.8 occ:1.00 FE3 A:SF4502 0.0 34.8 1.0 SG A:CYS284 2.2 33.2 1.0 S1 A:SF4502 2.3 35.4 1.0 S4 A:SF4502 2.3 30.1 1.0 S2 A:SF4502 2.3 32.1 1.0 FE2 A:SF4502 2.6 29.3 1.0 FE1 A:SF4502 2.7 29.0 1.0 FE4 A:SF4502 2.7 32.4 1.0 CB A:CYS284 3.4 29.4 1.0 S3 A:SF4502 3.8 30.6 1.0 SG A:CYS288 4.0 33.7 1.0 CA A:CYS284 4.0 29.1 1.0 CD A:PRO285 4.2 27.1 1.0 CG A:MET289 4.2 31.7 1.0 SD A:MET289 4.3 33.5 1.0 SG A:CYS306 4.6 26.6 1.0 C A:CYS284 4.7 31.8 1.0 N A:PRO285 4.7 26.6 1.0 SG A:CYS303 4.8 28.0 1.0 SG A:CYS309 4.8 28.0 1.0 CB A:SER286 4.9 30.8 1.0 CG A:PRO285 4.9 30.6 1.0 N A:SER286 4.9 29.0 1.0

Iron binding site 8 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:32.4 occ:1.00 FE4 A:SF4502 0.0 32.4 1.0 SG A:CYS309 2.3 28.0 1.0 S2 A:SF4502 2.3 32.1 1.0 S1 A:SF4502 2.3 35.4 1.0 S3 A:SF4502 2.3 30.6 1.0 FE3 A:SF4502 2.7 34.8 1.0 FE2 A:SF4502 2.7 29.3 1.0 FE1 A:SF4502 2.7 29.0 1.0 CB A:CYS309 3.2 24.9 1.0 N A:CYS309 3.7 25.2 1.0 S4 A:SF4502 3.9 30.1 1.0 CA A:CYS309 4.1 24.6 1.0 CD1 A:ILE244 4.2 28.6 1.0 SD A:MET289 4.4 33.5 1.0 CE A:MET289 4.4 29.3 1.0 SG A:CYS303 4.6 28.0 1.0 SG A:CYS306 4.7 26.6 1.0 SG A:CYS284 4.8 33.2 1.0 N A:HIS308 4.8 23.0 1.0 C A:HIS308 4.9 29.8 1.0 N A:ILE310 5.0 26.6 1.0

Iron binding site 9 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:32.2 occ:1.00 FE1 B:SF4501 0.0 32.2 1.0 S2 B:SF4501 2.3 31.0 1.0 S3 B:SF4501 2.3 28.6 1.0 SG B:CYS151 2.3 28.3 1.0 S4 B:SF4501 2.3 30.4 1.0 FE4 B:SF4501 2.6 37.8 1.0 FE3 B:SF4501 2.7 30.8 1.0 FE2 B:SF4501 2.8 28.1 1.0 CB B:CYS151 3.3 24.9 1.0 OG1 B:THR153 3.6 26.1 1.0 S1 B:SF4501 3.9 29.0 1.0 C3A B:SRM503 4.0 31.2 1.0 CDA B:SRM503 4.3 30.0 1.0 SG B:CYS188 4.5 34.2 1.0 C4A B:SRM503 4.5 31.7 1.0 SG B:CYS189 4.7 28.7 1.0 CA B:CYS151 4.7 24.5 1.0 CBA B:SRM503 4.8 34.2 1.0 C2A B:SRM503 4.8 29.1 1.0 CD B:PRO154 4.8 24.2 1.0 CHB B:SRM503 4.9 32.1 1.0 N B:THR153 4.9 24.3 1.0 N B:PRO154 4.9 22.4 1.0 O B:HOH2150 4.9 35.0 1.0 CB B:THR153 4.9 26.3 1.0 C B:THR153 4.9 25.3 1.0 SG B:CYS193 5.0 30.9 1.0 CAA B:SRM503 5.0 32.4 1.0

Iron binding site 10 out of 34 in the The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:28.1 occ:1.00 FE2 B:SF4501 0.0 28.1 1.0 S4 B:SF4501 2.3 30.4 1.0 S1 B:SF4501 2.3 29.0 1.0 S3 B:SF4501 2.3 28.6 1.0 SG B:CYS193 2.4 30.9 1.0 FE3 B:SF4501 2.7 30.8 1.0 FE4 B:SF4501 2.7 37.8 1.0 FE1 B:SF4501 2.8 32.2 1.0 CB B:CYS193 3.3 28.2 1.0 C4A B:SRM503 3.7 31.7 1.0 CHB B:SRM503 3.7 32.1 1.0 NA B:SRM503 3.9 30.4 1.0 S2 B:SF4501 4.0 31.0 1.0 C3A B:SRM503 4.2 31.2 1.0 N B:CYS193 4.3 32.7 1.0 CG2 B:THR145 4.3 28.0 1.0 FE B:SRM503 4.4 28.1 1.0 CA B:CYS193 4.4 30.2 1.0 C1B B:SRM503 4.5 31.4 1.0 C1A B:SRM503 4.5 27.9 1.0 CB B:ASN191 4.5 25.8 1.0 CB B:THR145 4.6 29.2 1.0 NB B:SRM503 4.7 29.4 1.0 SG B:CYS189 4.8 28.7 1.0 ND B:SRM503 4.9 27.6 1.0 C2A B:SRM503 4.9 29.1 1.0 SG B:CYS188 4.9 34.2 1.0 SG B:CYS151 5.0 28.3 1.0

T.F.Oliveira, C.Vonrhein, P.M.Matias, S.S.Venceslau, I.A.C.Pereira, M.Archer. The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration. J.Biol.Chem. V. 283 34141 2008.
ISSN: ISSN 0021-9258
PubMed: 18829451
DOI: 10.1074/JBC.M805643200