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Iodine in PDB 4ur2: Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide

Enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide

All present enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide:
1.97.1.8;

Protein crystallography data

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide, PDB code: 4ur2 was solved by M.Bommer, C.Kunze, J.Fesseler, T.Schubert, G.Diekert, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.047 / 2.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.243, 73.243, 184.154, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.59

Other elements in 4ur2:

The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Iron (Fe) 16 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide (pdb code 4ur2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide, PDB code: 4ur2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 1 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1463

b:33.8
occ:0.74
 CO A:BVQ503 2.9 23.0 1.0
OH A:TYR246 3.1 18.1 1.0
I A:IOD1464 3.3 40.1 0.3
N22 A:BVQ503 3.5 15.8 1.0
N24 A:BVQ503 3.6 20.4 1.0
N23 A:BVQ503 3.7 17.0 1.0
N21 A:BVQ503 3.7 21.4 1.0
NH2 A:ARG305 3.8 18.2 1.0
C6 A:BVQ503 3.9 19.2 1.0
CE2 A:PHE38 3.9 21.4 1.0
CZ A:PHE38 4.0 31.6 1.0
C19 A:BVQ503 4.0 20.6 1.0
CH2 A:TRP376 4.1 25.6 1.0
C4 A:BVQ503 4.1 19.8 1.0
C9 A:BVQ503 4.1 20.9 1.0
C5 A:BVQ503 4.2 20.5 1.0
C37 A:BVQ503 4.2 26.1 1.0
C11 A:BVQ503 4.3 19.1 1.0
C16 A:BVQ503 4.3 22.1 1.0
CZ A:TYR246 4.3 24.4 1.0
ND2 A:ASN272 4.4 16.9 1.0
C14 A:BVQ503 4.4 17.9 1.0
C1 A:BVQ503 4.5 28.5 1.0
C10 A:BVQ503 4.5 17.5 1.0
C26 A:BVQ503 4.6 17.8 1.0
O39 A:BVQ503 4.6 22.2 1.0
C15 A:BVQ503 4.7 18.8 1.0
C7 A:BVQ503 4.7 14.7 1.0
CE2 A:TYR246 4.8 18.9 1.0
C38 A:BVQ503 4.8 24.8 1.0
CZ2 A:TRP376 4.8 24.3 1.0

Iodine binding site 2 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 2 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1464

b:40.1
occ:0.34
 I A:IOD1463 3.3 33.8 0.7
OH A:TYR246 3.4 18.1 1.0
O A:TYR102 3.6 27.5 1.0
CZ A:PHE38 3.8 31.6 1.0
CZ A:TYR246 3.8 24.4 1.0
CE2 A:PHE38 3.9 21.4 1.0
O A:HOH2124 4.0 21.2 1.0
O A:HOH2125 4.1 25.6 1.0
CE2 A:TYR246 4.1 18.9 1.0
CH2 A:TRP96 4.1 23.5 1.0
ND2 A:ASN272 4.2 16.9 1.0
C A:TYR102 4.2 21.6 1.0
CB A:TYR102 4.2 20.6 1.0
CE1 A:TYR246 4.6 23.6 1.0
CA A:TYR102 4.6 22.4 1.0
CE1 A:PHE38 4.7 26.2 1.0
CZ3 A:TRP376 4.7 25.8 1.0
CH2 A:TRP376 4.8 25.6 1.0
CZ3 A:TRP96 4.8 15.6 1.0
CD2 A:PHE38 4.9 25.4 1.0
CZ2 A:TRP96 5.0 23.7 1.0

Iodine binding site 3 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 3 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1465

b:32.7
occ:0.90
 OG A:SER455 3.4 23.8 1.0
O A:HOH2187 3.5 30.5 1.0
CG1 A:VAL159 3.5 26.6 1.0
O A:HOH2196 3.5 28.7 1.0
CB A:SER455 3.8 24.2 1.0
NH1 A:ARG152 3.8 19.0 1.0
CG A:ARG460 3.9 28.3 1.0
CD A:ARG152 4.0 22.9 1.0
O A:HOH2347 4.1 39.3 1.0
CG A:ARG152 4.2 19.6 1.0
CD A:LYS148 4.4 22.0 1.0
CD A:ARG460 4.4 29.8 1.0
CB A:LYS148 4.6 24.9 1.0
O A:ASP459 4.6 28.9 1.0
O A:VAL159 4.8 21.2 1.0
CZ A:ARG152 4.8 19.1 1.0
CB A:ARG460 4.8 26.1 1.0
NE A:ARG152 4.8 22.4 1.0
CG A:LYS148 4.8 20.3 1.0
CA A:ARG460 4.9 30.7 1.0
O A:HOH2194 4.9 26.6 1.0
CB A:VAL159 4.9 24.9 1.0

Iodine binding site 4 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 4 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1466

b:52.8
occ:0.71
 N A:PHE196 3.6 33.7 1.0
NH1 A:ARG30 3.7 32.2 1.0
O A:HOH2212 3.8 43.4 1.0
CA A:VAL195 3.9 27.5 1.0
CB A:VAL195 4.1 35.3 1.0
O A:HOH2050 4.2 46.7 1.0
C A:VAL195 4.3 32.2 1.0
CD1 A:PHE196 4.3 31.1 1.0
CG1 A:VAL195 4.5 36.8 1.0
O A:ILE194 4.5 30.3 1.0
CB A:PHE196 4.5 32.2 1.0
O A:PHE196 4.5 33.4 1.0
CA A:PHE196 4.6 35.2 1.0
O A:HOH2215 4.8 44.5 1.0
CZ A:ARG30 4.9 41.1 1.0
CG A:PHE196 5.0 32.2 1.0
O A:HOH2051 5.0 44.0 1.0

Iodine binding site 5 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 5 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1467

b:61.8
occ:0.66
 ND2 A:ASN235 3.3 32.9 1.0
CG1 A:ILE432 3.9 37.2 1.0
N A:ILE432 4.0 35.4 1.0
CB A:THR232 4.1 31.0 1.0
CA A:ASN431 4.1 45.1 1.0
CG2 A:THR232 4.3 26.7 1.0
CD1 A:ILE432 4.3 39.4 1.0
CA A:THR232 4.4 29.7 1.0
C A:ASN431 4.4 40.4 1.0
O A:THR232 4.4 26.6 1.0
CG A:ASN235 4.5 33.8 1.0
SD A:MET77 4.5 63.5 1.0
CG A:MET77 4.6 42.0 1.0
CB A:ILE432 4.6 31.4 1.0
CB A:ASN431 4.6 46.8 1.0
CE A:MET77 4.7 41.3 1.0
CB A:ASN235 4.8 29.8 1.0
CA A:ILE432 4.8 35.7 1.0
C A:THR232 4.9 30.0 1.0

Iodine binding site 6 out of 11 in 4ur2

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Iodine binding site 6 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1462

b:36.7
occ:0.68
 CO B:BVQ503 2.9 27.4 1.0
OH B:TYR246 3.1 19.2 1.0
I B:IOD1463 3.3 38.5 0.3
N22 B:BVQ503 3.5 27.3 1.0
N24 B:BVQ503 3.5 22.4 1.0
N23 B:BVQ503 3.6 29.3 1.0
N21 B:BVQ503 3.7 27.6 1.0
NH2 B:ARG305 3.8 24.8 1.0
CE2 B:PHE38 3.8 28.2 1.0
C6 B:BVQ503 3.9 28.6 1.0
CZ B:PHE38 3.9 24.3 1.0
C19 B:BVQ503 4.0 25.1 1.0
C4 B:BVQ503 4.1 22.3 1.0
CH2 B:TRP376 4.1 28.2 1.0
C5 B:BVQ503 4.2 20.0 1.0
C9 B:BVQ503 4.2 28.4 1.0
C16 B:BVQ503 4.3 23.9 1.0
C11 B:BVQ503 4.3 28.2 1.0
C37 B:BVQ503 4.3 25.5 1.0
CZ B:TYR246 4.3 25.4 1.0
C14 B:BVQ503 4.4 25.3 1.0
ND2 B:ASN272 4.5 22.4 1.0
C1 B:BVQ503 4.5 23.5 1.0
O39 B:BVQ503 4.5 24.9 1.0
C10 B:BVQ503 4.5 20.4 1.0
C26 B:BVQ503 4.6 21.4 1.0
C15 B:BVQ503 4.7 23.6 1.0
C7 B:BVQ503 4.7 23.1 1.0
C38 B:BVQ503 4.8 28.4 1.0
CE2 B:TYR246 4.8 24.9 1.0
CZ2 B:TRP376 4.9 26.0 1.0

Iodine binding site 7 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 7 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1463

b:38.5
occ:0.33
 I B:IOD1462 3.3 36.7 0.7
OH B:TYR246 3.5 19.2 1.0
CZ B:PHE38 3.6 24.3 1.0
O B:TYR102 3.6 32.5 1.0
CE2 B:PHE38 3.8 28.2 1.0
O B:HOH2095 3.9 30.7 1.0
O B:HOH2096 3.9 29.6 1.0
CZ B:TYR246 3.9 25.4 1.0
CH2 B:TRP96 4.1 23.0 1.0
C B:TYR102 4.2 28.6 1.0
CE2 B:TYR246 4.2 24.9 1.0
CB B:TYR102 4.2 25.0 1.0
ND2 B:ASN272 4.3 22.4 1.0
CA B:TYR102 4.6 25.7 1.0
CE1 B:PHE38 4.6 28.6 1.0
CE1 B:TYR246 4.7 21.4 1.0
CZ3 B:TRP376 4.7 31.9 1.0
CH2 B:TRP376 4.8 28.2 1.0
CZ3 B:TRP96 4.8 18.6 1.0
CD2 B:PHE38 4.8 27.9 1.0
CZ2 B:TRP96 4.9 27.3 1.0
N B:GLY103 5.0 21.7 1.0

Iodine binding site 8 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 8 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1464

b:42.5
occ:0.83
 O B:HOH2144 3.3 31.5 1.0
OG B:SER455 3.3 29.0 1.0
CG1 B:VAL159 3.5 32.4 1.0
NH1 B:ARG152 3.8 21.9 1.0
CB B:SER455 3.8 25.8 1.0
CD B:ARG152 4.0 24.7 1.0
O B:HOH2140 4.0 39.5 1.0
CG B:ARG460 4.1 31.9 1.0
CG B:ARG152 4.3 23.0 1.0
CD B:LYS148 4.5 24.8 1.0
CB B:LYS148 4.6 26.2 1.0
O B:HOH2139 4.6 27.6 1.0
CD B:ARG460 4.7 28.9 1.0
CZ B:ARG152 4.7 27.9 1.0
O B:ASP459 4.8 40.8 1.0
NE B:ARG152 4.8 27.4 1.0
CB B:VAL159 4.8 26.7 1.0
O B:VAL159 4.8 25.9 1.0
CA B:ARG460 4.9 33.7 1.0
CG B:LYS148 5.0 22.1 1.0
N B:VAL159 5.0 20.4 1.0
CB B:ARG460 5.0 34.9 1.0

Iodine binding site 9 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 9 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1465

b:58.1
occ:0.65
 N B:PHE196 3.5 40.0 1.0
NH1 B:ARG30 3.6 33.2 1.0
CA B:VAL195 3.7 31.9 1.0
CB B:VAL195 3.9 39.7 1.0
O B:HOH2159 3.9 50.9 1.0
CG1 B:VAL195 4.1 31.6 1.0
C B:VAL195 4.2 37.3 1.0
O B:HOH2033 4.2 41.1 1.0
CD1 B:PHE196 4.3 45.5 1.0
O B:ILE194 4.4 30.5 1.0
O B:PHE196 4.6 38.4 1.0
CA B:PHE196 4.6 35.2 1.0
CB B:PHE196 4.6 41.3 1.0
O B:HOH2161 4.7 40.9 1.0
CZ B:ARG30 4.8 40.6 1.0
N B:VAL195 4.9 31.2 1.0
CG B:PHE196 5.0 44.2 1.0

Iodine binding site 10 out of 11 in 4ur2

Go back to Iodine Binding Sites List in 4ur2
Iodine binding site 10 out of 11 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans in Complex with Iodide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1466

b:68.0
occ:0.66
 NZ B:LYS192 3.3 31.5 1.0
O B:HOH2187 3.4 42.1 1.0
O B:HOH2175 3.8 42.6 1.0
CA B:PRO177 3.8 30.6 1.0
N B:ALA178 3.9 41.2 1.0
NH2 B:ARG109 4.0 28.3 1.0
O B:ASP206 4.3 40.2 1.0
CB B:PRO177 4.4 32.3 1.0
C B:PRO177 4.4 29.5 1.0
O B:HOH2162 4.5 51.4 1.0
CE B:LYS192 4.5 35.2 1.0
CD1 B:ILE190 4.7 26.2 1.0
OE2 B:GLU204 4.7 34.4 1.0
O B:ILE176 4.8 28.1 1.0
CB B:ALA178 4.8 53.5 1.0
N B:PRO177 4.9 29.2 1.0
CA B:ASP206 4.9 31.7 1.0
CD B:LYS192 5.0 36.4 1.0
CA B:ALA178 5.0 47.6 1.0

Reference:

M.Bommer, C.Kunze, J.Fesseler, T.Schubert, G.Diekert, H.Dobbek. Structural Basis For Organohalide Respiration. Science V. 346 455 2014.
ISSN: ISSN 0036-8075
PubMed: 25278505
DOI: 10.1126/SCIENCE.1258118
Page generated: Sun Aug 11 19:58:33 2024

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