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Iodine in PDB 4aw7: BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius

Enzymatic activity of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius

All present enzymatic activity of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius:
3.2.1.178;

Protein crystallography data

The structure of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius, PDB code: 4aw7 was solved by J.H.Hehemann, A.G.Kelly, N.A.Pudlo, E.C.Martens, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.61 / 1.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.330, 87.700, 114.450, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 15.2

Other elements in 4aw7:

The structure of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius (pdb code 4aw7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius, PDB code: 4aw7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in 4aw7

Go back to Iodine Binding Sites List in 4aw7
Iodine binding site 1 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1700

b:10.5
occ:0.70
 N A:ALA202 3.5 10.1 1.0
N A:PHE154 3.6 8.6 1.0
K A:K1616 3.6 23.3 0.5
N A:VAL155 3.7 10.4 1.0
C A:GLU152 3.7 8.1 1.0
CG1 A:VAL155 3.8 19.1 1.0
CA A:GLU152 3.8 8.5 0.5
CB A:ALA202 3.8 15.8 1.0
CA A:GLU152 3.8 8.6 0.5
N A:PRO153 3.9 8.0 1.0
CB A:PHE154 3.9 10.2 1.0
CE1 A:TYR199 3.9 8.2 1.0
O A:GLU152 4.1 9.1 1.0
CA A:PHE154 4.1 9.6 1.0
CA A:ALA201 4.2 8.8 1.0
CD A:PRO153 4.2 8.2 1.0
CB A:GLU152 4.2 9.4 0.5
CA A:ALA202 4.3 12.8 1.0
CG2 A:VAL155 4.3 14.6 1.0
C A:PHE154 4.3 9.5 1.0
C A:ALA201 4.3 9.1 1.0
CB A:VAL155 4.4 14.4 1.0
CB A:GLU152 4.4 9.5 0.5
CD1 A:TYR199 4.4 7.8 1.0
C A:PRO153 4.5 7.9 1.0
CG A:PHE154 4.6 9.4 1.0
CA A:VAL155 4.6 12.6 1.0
O A:ALA200 4.6 8.8 1.0
N A:TYR203 4.6 12.2 1.0
CD2 A:PHE154 4.7 9.9 1.0
CA A:PRO153 4.8 8.7 1.0
CG A:GLU152 4.9 8.7 0.5
CG A:PRO153 4.9 9.4 1.0
C A:ALA202 5.0 14.5 1.0
OH A:TYR213 5.0 14.0 1.0

Iodine binding site 2 out of 13 in 4aw7

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Iodine binding site 2 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1701

b:17.6
occ:0.30
 O A:HOH2031 2.9 14.3 1.0
N A:GLY40 3.6 9.6 1.0
CA A:GLY40 3.7 10.1 1.0
C A:GLY40 3.9 9.9 1.0
O A:HOH2024 4.0 40.9 1.0
CB A:ASP316 4.0 7.9 1.0
N A:VAL41 4.0 8.9 1.0
CB A:VAL41 4.4 8.6 1.0
CG1 A:VAL41 4.4 9.5 1.0
O A:LEU38 4.5 8.0 1.0
CA A:ASP316 4.5 7.5 1.0
O A:ASP316 4.5 11.7 1.0
O A:HOH2021 4.5 34.6 1.0
O A:GLY40 4.6 13.1 1.0
CB A:SER39 4.8 12.0 1.0
C A:SER39 4.8 9.2 1.0
CA A:VAL41 4.8 8.8 1.0

Iodine binding site 3 out of 13 in 4aw7

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Iodine binding site 3 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1702

b:23.4
occ:0.50
 ND2 A:ASN186 3.4 25.7 1.0
CD2 A:HIS183 3.7 15.6 1.0
NE2 A:HIS183 3.9 16.0 1.0
CE A:LYS182 3.9 21.6 1.0
CG A:HIS183 4.0 13.6 1.0
CB A:ASN186 4.1 15.9 1.0
CG A:LYS182 4.2 16.2 1.0
CA A:HIS183 4.2 12.9 1.0
CG A:ASN186 4.2 20.8 1.0
CE1 A:HIS183 4.3 15.1 1.0
O A:LYS182 4.4 13.6 1.0
ND1 A:HIS183 4.4 13.8 1.0
CD A:LYS182 4.4 19.8 1.0
O A:HOH2224 4.4 26.4 1.0
N A:HIS183 4.6 12.3 1.0
C A:LYS182 4.6 12.4 1.0
CB A:HIS183 4.7 13.0 1.0
NZ A:LYS182 4.7 24.5 1.0
O A:HOH2098 5.0 47.3 1.0

Iodine binding site 4 out of 13 in 4aw7

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Iodine binding site 4 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1703

b:31.2
occ:0.30
 O A:HOH2014 2.7 22.1 1.0
N A:SER598 3.5 24.2 1.0
OG A:SER477 3.6 16.9 0.5
C A:ASN476 3.8 13.9 1.0
N A:SER477 3.8 12.3 1.0
CA A:ASN476 4.0 18.0 1.0
O A:THR596 4.2 19.4 1.0
CB A:SER477 4.3 11.3 0.5
CA A:SER598 4.3 25.8 1.0
CB A:SER477 4.3 12.4 0.5
O A:ASN476 4.3 14.0 1.0
CA A:VAL597 4.3 20.4 1.0
N A:ASN476 4.4 18.9 1.0
C A:VAL597 4.4 21.6 1.0
C A:SER598 4.5 26.8 1.0
OG A:SER477 4.6 12.7 0.5
CA A:SER477 4.7 11.3 0.5
CA A:SER477 4.7 10.6 0.5
C A:THR475 4.8 20.5 1.0
O A:THR475 4.8 22.2 1.0
CG1 A:VAL597 4.9 20.3 1.0

Iodine binding site 5 out of 13 in 4aw7

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Iodine binding site 5 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1704

b:21.6
occ:0.30
 O A:HOH2057 2.0 25.5 1.0
O A:LEU318 3.7 8.2 1.0
NZ A:LYS48 3.8 8.0 1.0
N A:LEU318 3.8 7.5 1.0
O A:ASP316 3.9 11.7 1.0
CG A:PRO274 3.9 10.7 1.0
C A:LEU318 3.9 7.1 1.0
CB A:PRO274 4.0 9.4 1.0
CD1 A:PHE319 4.2 10.1 1.0
C A:ASP316 4.3 8.5 1.0
C A:ASN317 4.3 7.8 1.0
N A:PHE319 4.3 6.8 1.0
CA A:ASN317 4.4 7.8 1.0
O A:GLN315 4.4 7.5 1.0
O A:HOH2056 4.4 40.4 1.0
O A:HOH2032 4.5 50.3 1.0
CA A:LEU318 4.5 7.3 1.0
CE1 A:PHE319 4.6 11.3 1.0
N A:ASN317 4.6 7.0 1.0
CA A:PHE319 4.6 6.8 1.0
CE A:LYS48 4.8 7.1 1.0
O A:HOH2031 4.8 14.3 1.0
O A:HOH2342 5.0 34.3 1.0

Iodine binding site 6 out of 13 in 4aw7

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Iodine binding site 6 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1705

b:7.3
occ:0.40
 O A:HOH2280 3.4 27.4 1.0
ND2 A:ASN212 3.6 11.9 1.0
N A:TYR213 4.0 8.6 1.0
CB A:TYR213 4.0 7.6 1.0
CA A:TYR213 4.1 8.3 1.0
O A:ASP208 4.2 9.0 1.0
CB A:ASN212 4.2 10.1 1.0
CD2 A:TYR213 4.3 9.6 1.0
CA A:GLY209 4.3 9.9 1.0
C A:ASP208 4.3 9.2 1.0
CG A:ASN212 4.4 10.4 1.0
N A:GLY209 4.4 10.2 1.0
CB A:ASP208 4.5 9.7 1.0
C A:ASN212 4.5 9.2 1.0
NH1 A:ARG217 4.6 13.5 1.0
CG A:TYR213 4.7 8.5 1.0
O A:HOH2130 4.9 24.2 1.0
CA A:ASN212 5.0 8.9 1.0

Iodine binding site 7 out of 13 in 4aw7

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Iodine binding site 7 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1706

b:17.1
occ:0.40
 O A:HOH2463 3.5 23.7 1.0
N A:VAL272 3.8 14.0 1.0
CA A:HIS271 3.9 15.4 1.0
CD1 A:TYR266 4.1 15.5 1.0
CG2 A:VAL272 4.2 15.4 1.0
CE1 A:TYR484 4.3 11.3 1.0
CB A:HIS271 4.3 16.7 1.0
CG1 A:VAL272 4.3 15.4 1.0
CD1 A:TYR484 4.3 11.4 1.0
C A:HIS271 4.4 14.4 1.0
CE1 A:TYR266 4.4 17.4 1.0
CB A:VAL272 4.7 13.5 1.0
CA A:VAL272 4.8 13.6 1.0
O A:GLY270 4.9 17.9 1.0

Iodine binding site 8 out of 13 in 4aw7

Go back to Iodine Binding Sites List in 4aw7
Iodine binding site 8 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1707

b:18.3
occ:0.40
 OG1 A:THR383 3.2 17.6 1.0
O A:MET27 3.7 16.4 1.0
N A:SER385 3.8 11.3 1.0
C A:MET27 4.0 16.0 1.0
CB A:THR383 4.1 15.5 1.0
O A:THR383 4.1 12.4 1.0
C A:THR383 4.1 12.0 1.0
C A:SER384 4.2 11.4 1.0
CB A:SER385 4.2 14.4 1.0
N A:SER29 4.2 14.8 1.0
N A:SER384 4.2 11.8 1.0
CB A:MET27 4.2 19.7 1.0
CA A:SER384 4.3 10.9 1.0
CA A:ALA28 4.3 15.7 1.0
CB A:SER29 4.4 18.5 1.0
N A:ALA28 4.4 15.6 1.0
CA A:SER385 4.4 12.3 1.0
C A:ALA28 4.5 15.7 1.0
O A:HOH2390 4.6 46.6 1.0
CA A:MET27 4.8 16.9 1.0
CA A:THR383 4.8 12.9 1.0
OG A:SER385 5.0 16.1 1.0
CA A:SER29 5.0 16.7 1.0
O A:SER384 5.0 12.9 1.0
O A:HOH2389 5.0 30.2 1.0

Iodine binding site 9 out of 13 in 4aw7

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Iodine binding site 9 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1708

b:18.7
occ:0.30
 O A:HOH2272 3.2 31.3 1.0
ND2 A:ASN542 3.6 12.2 1.0
O A:HOH2002 3.6 21.2 1.0
O A:HOH2271 3.6 32.8 1.0
OD1 A:ASN386 3.9 11.2 1.0
CG A:ASN386 4.0 11.6 1.0
CD A:PRO387 4.0 11.6 1.0
O A:HOH2013 4.0 35.5 1.0
CA A:ASN386 4.1 11.2 1.0
CE1 A:HIS26 4.1 20.7 1.0
O A:HOH2538 4.1 23.7 1.0
CB A:ASN386 4.2 11.7 1.0
CB A:ASN542 4.2 11.4 1.0
ND1 A:HIS26 4.3 18.6 1.0
O A:SER385 4.4 15.3 1.0
CG A:ASN542 4.4 11.8 1.0
ND2 A:ASN386 4.5 14.1 1.0
N A:PRO387 4.9 10.0 1.0
N A:ASN386 5.0 11.1 1.0

Iodine binding site 10 out of 13 in 4aw7

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Iodine binding site 10 out of 13 in the BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of BPGH86A: A Beta-Porphyranase of Glycoside Hydrolase Family 86 From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1719

b:28.1
occ:0.40
 O A:HOH2591 2.8 33.3 1.0
CB A:TRP331 4.0 14.8 1.0
C6 A:AAL1612 4.0 18.4 1.0
C4 A:GAL1611 4.0 14.5 1.0
C6 A:GAL1611 4.1 16.8 1.0
O A:HOH2354 4.2 29.6 1.0
O5 A:AAL1612 4.2 15.4 1.0
C5 A:AAL1612 4.4 17.3 1.0
O4 A:GAL1611 4.5 13.4 1.0
C5 A:GAL1611 4.5 14.9 1.0
CG A:TRP331 4.8 14.5 1.0
C1 A:AAL1612 5.0 15.3 1.0
CE3 A:TRP331 5.0 14.9 1.0

Reference:

J.H.Hehemann, A.G.Kelly, N.A.Pudlo, E.C.Martens, A.B.Boraston. Bacteria of the Human Gut Microbiome Catabolize Red Seaweed Glycans with Carbohydrate-Active Enzyme Updates From Extrinsic Microbes. Proc. Natl. Acad. Sci. V. 109 19786 2012U.S.A..
ISSN: ESSN 1091-6490
PubMed: 23150581
DOI: 10.1073/PNAS.1211002109
Page generated: Sun Aug 11 17:23:38 2024

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