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Iodine in PDB 1w2z: Psao and Xenon

Enzymatic activity of Psao and Xenon

All present enzymatic activity of Psao and Xenon:
1.4.3.6;

Protein crystallography data

The structure of Psao and Xenon, PDB code: 1w2z was solved by A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.507, 196.268, 89.665, 90.00, 107.46, 90.00
R / Rfree (%) 17.9 / 22.4

Other elements in 1w2z:

The structure of Psao and Xenon also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Xenon (Xe) 8 atoms
Copper (Cu) 4 atoms

Iodine Binding Sites:

Iodine binding site 1 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 1 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1648

b:39.2
occ:1.00
HA3 A:GLY500 3.1 23.8 1.0
HD2 A:PRO530 3.1 18.1 1.0
HD2 B:PRO530 3.1 17.9 1.0
HA3 B:GLY500 3.2 23.8 1.0
O A:HOH2136 3.3 28.7 1.0
HG3 B:PRO530 3.7 19.9 1.0
HA2 B:GLY500 3.7 23.8 1.0
HD13 A:ILE529 3.7 22.1 1.0
HG2 B:PRO530 3.7 19.9 1.0
HA2 A:GLY500 3.7 23.8 1.0
HD13 B:ILE529 3.7 22.5 1.0
CD A:PRO530 3.7 18.9 1.0
CD B:PRO530 3.8 18.6 1.0
HG3 A:PRO530 3.8 20.1 1.0
HD3 A:PRO530 3.8 18.1 1.0
HG2 A:PRO530 3.8 20.1 1.0
CA A:GLY500 3.9 24.1 1.0
CG B:PRO530 3.9 20.4 1.0
CA B:GLY500 3.9 24.2 1.0
HD3 B:PRO530 3.9 17.9 1.0
CG A:PRO530 4.0 22.4 1.0
HG13 A:ILE529 4.1 21.3 1.0
HG13 B:ILE529 4.2 21.5 1.0
HG23 B:ILE499 4.4 22.2 1.0
HG23 A:ILE499 4.5 22.3 1.0
CD1 A:ILE529 4.5 19.7 1.0
CD1 B:ILE529 4.5 23.8 1.0
HD11 B:ILE529 4.6 22.5 1.0
HD11 A:ILE529 4.6 22.1 1.0
HA A:ILE529 4.7 15.6 1.0
HA B:ILE529 4.7 15.6 1.0
O B:ILE499 4.7 23.9 1.0
N A:GLY500 4.8 22.2 1.0
O A:GLY500 4.8 28.3 1.0
N B:GLY500 4.8 21.9 1.0
O A:ILE499 4.8 24.2 1.0
CG1 A:ILE529 4.8 22.5 1.0
C A:GLY500 4.8 24.9 1.0
O B:GLY500 4.9 27.9 1.0
CG1 B:ILE529 4.9 23.2 1.0
C B:GLY500 4.9 24.8 1.0

Iodine binding site 2 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 2 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1649

b:47.8
occ:0.99
HD2 A:ARG470 3.1 28.4 1.0
HE A:ARG470 3.2 30.9 1.0
NE A:ARG470 3.6 34.2 1.0
CD A:ARG470 3.7 29.2 1.0
HD3 A:ARG470 3.8 28.4 1.0
CZ A:ARG470 4.6 30.7 1.0
HH21 A:ARG470 4.7 25.7 1.0
NZ A:LYS472 4.9 33.7 1.0
HD3 A:LYS472 4.9 23.6 1.0
NH2 A:ARG470 5.0 25.6 1.0

Iodine binding site 3 out of 176 in 1w2z

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Iodine binding site 3 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1650

b:45.2
occ:0.98
H A:ILE186 2.7 17.9 1.0
HB2 A:LYS185 3.1 23.8 1.0
HD21 A:LEU114 3.4 21.3 1.0
HA A:LYS185 3.4 21.4 1.0
HD1 A:TYR118 3.5 19.7 1.0
HB A:ILE186 3.5 17.8 1.0
N A:ILE186 3.6 17.3 1.0
HD11 A:ILE186 3.7 19.2 1.0
HB3 A:LEU114 3.8 19.3 1.0
CB A:LYS185 3.9 25.8 1.0
HG13 A:ILE186 3.9 18.2 1.0
CA A:LYS185 4.0 21.0 1.0
CD1 A:TYR118 4.1 21.2 1.0
HB3 A:LYS185 4.2 23.8 1.0
HE1 A:TYR118 4.2 19.6 1.0
CB A:ILE186 4.2 17.3 1.0
CD2 A:LEU114 4.3 21.3 1.0
C A:LYS185 4.4 19.9 1.0
CG1 A:ILE186 4.4 18.6 1.0
CD1 A:ILE186 4.4 21.2 1.0
HD11 A:LEU114 4.5 20.0 1.0
CA A:ILE186 4.5 17.8 1.0
CE1 A:TYR118 4.5 19.1 1.0
HD13 A:ILE186 4.6 19.2 1.0
CB A:LEU114 4.7 18.2 1.0
HD23 A:LEU114 4.7 21.3 1.0
HB2 A:TYR118 4.7 18.9 1.0
HD22 A:LEU114 4.8 21.3 1.0
O A:ILE186 4.9 16.3 1.0
HD2 A:LYS185 4.9 38.7 1.0
CG A:LEU114 4.9 18.3 1.0

Iodine binding site 4 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 4 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1651

b:52.9
occ:0.97
O A:HOH2032 3.1 21.7 1.0
HB3 A:PRO64 3.5 25.4 1.0
ND2 A:ASN83 3.5 19.4 1.0
HG3 A:PRO64 3.6 27.1 1.0
HG22 A:ILE86 3.8 26.3 1.0
HE A:ARG85 3.8 36.6 1.0
HG2 A:ARG85 3.8 31.7 1.0
HB3 A:ARG85 3.8 28.9 1.0
CB A:PRO64 4.2 25.6 1.0
CG A:PRO64 4.3 27.8 1.0
HG23 A:ILE86 4.4 26.3 1.0
CG A:ASN83 4.5 27.6 1.0
HG12 A:ILE86 4.5 25.1 1.0
CG2 A:ILE86 4.5 25.6 1.0
HH21 A:ARG85 4.5 42.0 1.0
HB2 A:PRO64 4.5 25.4 1.0
OD1 A:ASN83 4.5 26.8 1.0
NE A:ARG85 4.6 37.7 1.0
CG A:ARG85 4.6 31.7 1.0
CB A:ARG85 4.6 28.6 1.0
HB2 A:ARG85 4.8 28.9 1.0
HD3 A:PRO64 4.9 24.3 1.0
O A:HOH2025 4.9 35.2 1.0
HG2 A:PRO64 5.0 27.1 1.0

Iodine binding site 5 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 5 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1652

b:39.9
occ:0.91
HB3 A:PRO216 3.2 20.8 1.0
HD11 B:LEU265 3.2 34.3 1.0
HB3 B:ASN242 3.3 12.3 1.0
HD2 B:TYR263 3.3 20.4 1.0
HA A:PRO216 3.4 20.2 1.0
HB2 B:LEU265 3.6 29.5 1.0
HD3 A:PRO216 3.8 20.9 1.0
HA3 A:GLY215 3.8 20.5 1.0
N A:PRO216 3.9 20.1 1.0
CB A:PRO216 3.9 21.3 1.0
CA A:PRO216 3.9 20.5 1.0
HB3 B:TYR263 3.9 16.9 1.0
HD23 B:LEU265 4.0 35.3 1.0
CD1 B:LEU265 4.1 35.0 1.0
CD2 B:TYR263 4.1 18.7 1.0
CB B:ASN242 4.2 9.3 1.0
C A:GLY215 4.3 20.1 1.0
CD A:PRO216 4.3 22.1 1.0
HA B:ASN242 4.3 12.5 1.0
HB2 B:ASN242 4.4 12.3 1.0
HD12 B:LEU265 4.4 34.3 1.0
CB B:LEU265 4.5 28.4 1.0
CA A:GLY215 4.5 20.9 1.0
HB2 A:PRO216 4.6 20.8 1.0
CG B:LEU265 4.6 32.8 1.0
HD13 B:LEU265 4.7 34.3 1.0
CG A:PRO216 4.7 23.8 1.0
CD2 B:LEU265 4.7 37.1 1.0
HE2 B:TYR263 4.8 21.2 1.0
CB B:TYR263 4.8 16.4 1.0
CA B:ASN242 4.8 12.7 1.0
O B:TYR263 4.8 18.8 1.0
HG3 A:PRO216 4.8 21.6 1.0
HA B:LEU265 4.8 28.7 1.0
CE2 B:TYR263 4.9 22.0 1.0
CG B:TYR263 4.9 19.7 1.0
O A:GLY215 4.9 19.9 1.0
HA2 A:GLY215 5.0 20.5 1.0

Iodine binding site 6 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 6 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1653

b:78.6
occ:0.87
HG13 A:VAL90 2.9 29.1 1.0
HE2 A:LYS66 3.1 36.8 1.0
HB2 A:ASN83 3.5 23.2 1.0
ND2 A:ASN83 3.6 19.4 1.0
CG1 A:VAL90 3.8 30.6 1.0
NZ A:LYS66 3.9 34.5 1.0
CE A:LYS66 3.9 39.7 1.0
HG11 A:VAL90 4.1 29.1 1.0
HB A:VAL90 4.1 26.9 1.0
HG23 A:VAL90 4.2 29.3 1.0
CB A:ASN83 4.3 23.6 1.0
HG12 A:VAL90 4.4 29.1 1.0
HD3 A:LYS66 4.4 32.8 1.0
CB A:VAL90 4.5 27.3 1.0
CG A:ASN83 4.5 27.6 1.0
HE3 A:LYS66 4.6 36.8 1.0
HB3 A:ASN83 4.6 23.2 1.0
CD A:LYS66 4.8 31.0 1.0
CG2 A:VAL90 4.9 30.8 1.0

Iodine binding site 7 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 7 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1654

b:83.4
occ:0.76
HE2 A:LYS217 2.9 46.4 1.0
HG2 A:LYS217 3.0 34.3 1.0
HG3 A:LYS217 3.1 34.3 1.0
O A:HOH2065 3.2 33.6 1.0
HE3 A:LYS217 3.3 46.4 1.0
HG3 B:GLN227 3.3 31.7 1.0
CG A:LYS217 3.4 35.4 1.0
HA A:HIS219 3.5 19.9 1.0
CE A:LYS217 3.5 47.9 1.0
HD2 A:HIS219 3.6 21.5 1.0
CD2 A:HIS219 3.7 21.9 1.0
NE2 A:HIS219 3.9 21.0 1.0
CD A:LYS217 4.1 43.9 1.0
HB2 B:GLN227 4.2 25.1 1.0
CG A:HIS219 4.2 22.0 1.0
CG B:GLN227 4.2 31.7 1.0
CA A:HIS219 4.4 20.1 1.0
HB3 B:GLN227 4.5 25.1 1.0
O A:GLN218 4.5 20.1 1.0
CE1 A:HIS219 4.6 20.7 1.0
CB B:GLN227 4.6 25.5 1.0
HD2 A:LYS217 4.6 42.6 1.0
HG2 B:GLN227 4.6 31.7 1.0
H A:SER220 4.7 20.6 1.0
ND1 A:HIS219 4.7 22.2 1.0
HD3 A:LYS217 4.7 42.6 1.0
HB3 A:LYS217 4.8 23.8 1.0
CB A:LYS217 4.8 22.6 1.0
N A:HIS219 4.8 20.7 1.0
NZ A:LYS217 4.8 45.6 1.0
C A:GLN218 4.8 20.8 1.0
CB A:HIS219 4.9 18.8 1.0

Iodine binding site 8 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 8 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1655

b:47.3
occ:0.71
O A:HOH2021 2.5 9.6 0.3
H A:GLU47 2.8 23.5 1.0
HG21 A:ILE63 3.3 21.9 1.0
HB2 A:GLU47 3.5 28.4 1.0
HA A:PRO46 3.5 23.1 1.0
O A:HOH2028 3.6 46.4 1.0
N A:GLU47 3.6 22.8 1.0
HB3 A:PRO46 3.6 23.3 1.0
HB2 A:HIS50 3.7 24.1 1.0
HG22 A:ILE63 3.7 21.9 1.0
CG2 A:ILE63 4.0 23.1 1.0
HD2 A:PRO64 4.0 24.3 1.0
CG A:HIS50 4.1 32.8 1.0
CA A:PRO46 4.1 22.5 1.0
HB3 A:HIS50 4.2 24.1 1.0
CB A:GLU47 4.2 29.6 1.0
HB3 A:GLU47 4.2 28.4 1.0
CB A:HIS50 4.2 23.9 1.0
CD2 A:HIS50 4.2 42.4 1.0
CB A:PRO46 4.3 24.4 1.0
HD2 A:HIS50 4.4 40.4 1.0
C A:PRO46 4.4 23.8 1.0
HG12 A:ILE63 4.5 19.5 1.0
HB2 A:PRO46 4.5 23.3 1.0
ND1 A:HIS50 4.5 39.2 1.0
CA A:GLU47 4.5 24.9 1.0
HG23 A:ILE63 4.5 21.9 1.0
HE3 A:LYS66 4.5 36.8 1.0
HD12 A:ILE63 4.6 18.5 1.0
NE2 A:HIS50 4.7 45.1 1.0
HG2 A:PRO64 4.8 27.1 1.0
CE1 A:HIS50 4.9 41.5 1.0
O A:GLU47 5.0 20.8 1.0
HA A:ILE63 5.0 21.0 1.0
CD A:PRO64 5.0 25.2 1.0

Iodine binding site 9 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 9 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1656

b:45.8
occ:0.67
HE A:ARG640 3.1 33.3 1.0
HG2 A:GLN227 3.1 31.7 1.0
HB2 A:PRO226 3.3 23.8 1.0
HG23 A:VAL642 3.4 33.0 1.0
O B:HOH2047 3.4 28.0 1.0
HB2 B:SER220 3.5 24.1 1.0
HG3 A:GLN227 3.8 31.7 1.0
CG A:GLN227 3.9 32.4 1.0
HH21 A:ARG640 3.9 32.3 1.0
NE2 A:GLN227 3.9 35.3 1.0
NE A:ARG640 3.9 35.1 1.0
OG B:SER220 4.0 33.9 1.0
HG2 A:PRO226 4.1 23.1 1.0
CB A:PRO226 4.1 23.4 1.0
CG2 A:VAL642 4.2 34.6 1.0
CB B:SER220 4.2 23.9 1.0
HG21 A:VAL642 4.3 33.0 1.0
HD3 A:ARG640 4.3 30.2 1.0
HB3 A:PRO226 4.3 23.8 1.0
HG22 A:VAL642 4.4 33.0 1.0
CD A:GLN227 4.4 39.9 1.0
NH2 A:ARG640 4.5 32.9 1.0
HB3 B:SER220 4.6 24.1 1.0
CG A:PRO226 4.6 22.0 1.0
HB3 A:ARG640 4.6 22.7 1.0
HB2 A:ARG640 4.6 22.7 1.0
CZ A:ARG640 4.6 35.2 1.0
CD A:ARG640 4.7 29.7 1.0
H B:SER220 4.8 20.6 1.0
HG12 A:VAL642 4.8 31.2 1.0
HD2 A:PRO226 4.9 20.8 1.0
H A:GLN227 4.9 23.5 1.0

Iodine binding site 10 out of 176 in 1w2z

Go back to Iodine Binding Sites List in 1w2z
Iodine binding site 10 out of 176 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1657

b:49.0
occ:0.67
HE2 A:TYR550 3.2 16.5 1.0
HB3 A:ALA579 3.3 15.1 1.0
HH2 A:TRP553 3.5 15.1 1.0
ND2 A:ASN549 3.6 11.9 1.0
HB2 A:ASN549 3.8 14.7 1.0
HB2 A:ALA579 3.9 15.1 1.0
HB3 A:ASN549 3.9 14.7 1.0
CB A:ALA579 4.0 15.7 1.0
CE2 A:TYR550 4.0 16.0 1.0
CB A:ASN549 4.2 14.2 1.0
CH2 A:TRP553 4.3 16.5 1.0
HA A:ALA579 4.4 14.6 1.0
CG A:ASN549 4.4 14.8 1.0
HZ3 A:TRP553 4.5 14.1 1.0
HB2 A:ALA546 4.6 9.4 1.0
HD2 A:TYR550 4.6 16.9 1.0
OE2 A:GLU537 4.7 48.4 1.0
HB1 A:ALA579 4.7 15.1 1.0
NZ A:LYS496 4.7 18.4 1.0
CA A:ALA579 4.8 15.0 1.0
OH A:TYR550 4.8 20.1 1.0
HD3 A:LYS496 4.8 19.1 1.0
CD2 A:TYR550 4.8 17.9 1.0
CZ3 A:TRP553 4.8 14.6 1.0
CZ A:TYR550 4.9 18.2 1.0

Reference:

A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss. Using Xenon As A Probe For Dioxygen-Binding Sites in Copper Amine Oxidases. J.Mol.Biol. V. 344 599 2004.
ISSN: ISSN 0022-2836
PubMed: 15533431
DOI: 10.1016/J.JMB.2004.09.075
Page generated: Sun Dec 13 19:21:53 2020

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