Atomistry » Iodine » PDB 4dgh-4hjh » 4e9o
Atomistry »
  Iodine »
    PDB 4dgh-4hjh »
      4e9o »

Iodine in PDB 4e9o: Vaccinia D8L Ectodomain Structure

Protein crystallography data

The structure of Vaccinia D8L Ectodomain Structure, PDB code: 4e9o was solved by M.H.Matho, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.90 / 1.42
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 71.281, 71.281, 44.415, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Vaccinia D8L Ectodomain Structure (pdb code 4e9o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Vaccinia D8L Ectodomain Structure, PDB code: 4e9o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 1 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I301

b:18.7
occ:0.70
 ND2 X:ASN158 3.6 18.1 1.0
N X:TYR155 3.7 16.6 1.0
NZ X:LYS133 3.9 22.5 0.5
CD1 X:TYR130 4.0 17.1 1.0
CG X:LYS133 4.1 16.6 0.5
CA X:PHE154 4.1 17.8 1.0
CD1 X:PHE154 4.2 19.3 1.0
CE X:LYS133 4.3 20.2 0.5
CD2 X:TYR155 4.3 23.7 1.0
CG X:LYS133 4.3 16.7 0.5
C X:PHE154 4.5 18.3 1.0
O X:TYR155 4.5 13.5 1.0
O X:VAL153 4.5 21.1 1.0
CA X:TYR130 4.5 15.3 1.0
CD X:LYS133 4.6 17.7 0.5
CB X:ASN158 4.6 14.2 1.0
CG X:ASN158 4.6 15.3 1.0
CB X:TYR155 4.6 17.3 1.0
CB X:TYR130 4.6 15.8 1.0
CA X:TYR155 4.6 16.5 1.0
CG X:TYR155 4.8 19.5 1.0
CE1 X:PHE154 4.8 20.1 1.0
CG X:TYR130 4.8 15.7 1.0
CE1 X:TYR130 4.9 18.5 1.0
CG X:PHE154 4.9 17.4 1.0
C X:TYR155 4.9 14.8 1.0
CB X:PHE154 5.0 17.6 1.0

Iodine binding site 2 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 2 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I302

b:15.1
occ:0.30
 NZ X:LYS99 3.5 38.9 1.0
CE X:LYS99 4.6 33.7 1.0

Iodine binding site 3 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 3 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I303

b:22.3
occ:0.60
 O X:HOH602 3.0 42.3 1.0
NE2 X:GLN132 3.8 22.0 1.0
OE1 X:GLN132 3.9 17.3 1.0
O X:ASP194 4.0 16.0 1.0
NZ X:LYS127 4.0 25.5 0.5
CB X:ASP194 4.1 16.5 1.0
C X:ASP194 4.1 15.3 1.0
N X:GLN195 4.2 14.3 1.0
CD X:GLN132 4.3 18.4 1.0
CA X:GLN195 4.3 13.7 1.0
CE X:LYS127 4.3 23.8 0.5
CG1 X:VAL135 4.4 15.6 1.0
CG X:GLN195 4.4 14.3 1.0
CG X:LYS198 4.5 21.2 1.0
O X:HOH563 4.5 26.7 1.0
CA X:ASP194 4.8 15.5 1.0
CB X:GLN195 4.9 12.9 1.0
O X:HOH507 4.9 38.9 1.0
CD X:LYS198 5.0 27.5 1.0

Iodine binding site 4 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 4 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I304

b:30.8
occ:0.85
 ND2 X:ASN136 2.7 18.9 0.5
ND2 X:ASN136 3.1 19.1 0.5
O X:HOH508 3.6 30.9 1.0
CD X:LYS133 3.6 20.0 0.5
O X:HOH514 3.7 22.7 1.0
CE X:LYS133 3.8 22.3 0.5
CG X:ASN136 3.9 19.4 0.5
CB X:ASN136 4.0 16.7 0.5
CG X:ASN136 4.0 19.1 0.5
O X:HOH438 4.2 22.8 1.0
CA X:LYS133 4.2 14.4 0.5
CB X:ASN136 4.2 17.4 0.5
CA X:LYS133 4.3 14.4 0.5
CD X:LYS133 4.3 17.7 0.5
CG X:LYS133 4.4 16.7 0.5
O X:GLN132 4.4 15.4 1.0
CE X:LYS133 4.5 20.2 0.5
N X:LYS133 4.6 13.4 1.0
C X:GLN132 4.7 14.4 1.0
CG X:LYS133 4.7 16.6 0.5
NZ X:LYS133 4.8 20.9 0.5
CB X:LYS133 4.8 14.7 0.5
OG X:SER152 4.8 21.3 0.5
OD1 X:ASN136 4.9 21.4 0.5
CG X:GLN132 4.9 16.7 1.0
OG X:SER152 5.0 20.4 0.5

Iodine binding site 5 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 5 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I305

b:24.3
occ:0.55
 O X:HOH594 3.2 50.0 1.0
OG X:SER234 3.5 19.6 1.0
CA X:ASP165 4.0 15.8 1.0
CB X:ASP165 4.0 17.1 1.0
CB X:SER234 4.2 21.4 1.0
C X:SER234 4.3 25.9 1.0
CG X:PRO23 4.4 34.8 1.0
O X:SER234 4.6 28.1 1.0
N X:ASP165 4.6 14.8 1.0
CA X:SER234 4.9 23.4 1.0
O X:LEU164 5.0 14.9 1.0

Iodine binding site 6 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 6 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I306

b:27.6
occ:0.45
 O X:HOH603 1.7 32.2 1.0
I X:IOD312 2.2 27.1 0.3
O X:HOH605 3.6 30.6 1.0
O X:HOH604 3.8 42.8 1.0
N X:GLY50 3.8 17.6 1.0
CB X:GLU30 4.0 24.8 1.0
O X:HOH475 4.1 25.9 1.0
CG X:GLU30 4.2 28.6 1.0
CD2 X:TYR51 4.3 19.4 1.0
CA X:GLY49 4.4 17.2 1.0
CA X:GLY50 4.6 16.6 1.0
C X:GLY49 4.6 15.5 1.0
CE2 X:TYR51 4.7 21.4 1.0
C X:GLY50 4.8 15.8 1.0
O X:HOH592 4.8 36.1 1.0
O X:GLY50 4.9 15.4 1.0

Iodine binding site 7 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 7 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I307

b:34.4
occ:0.55
 I X:IOD310 2.8 28.0 0.4
OH X:TYR104 3.1 32.0 1.0
NZ X:LYS108 3.4 30.9 1.0
OG X:SER177 3.6 19.6 1.0
CE X:LYS108 3.7 29.0 1.0
CG2 X:THR173 3.9 12.0 1.0
CZ X:TYR104 4.1 28.6 1.0
CE2 X:TYR104 4.2 28.3 1.0
OD1 X:ASN175 4.3 16.8 1.0
ND2 X:ASN175 4.3 21.2 1.0
CB X:THR173 4.3 10.2 1.0
CD X:LYS108 4.4 27.5 1.0
OG1 X:THR173 4.4 12.3 1.0
O X:HOH416 4.5 17.9 1.0
CG X:ASN175 4.7 17.9 1.0
I X:IOD309 4.9 25.0 0.3
CG X:LYS108 4.9 24.3 1.0
CB X:SER177 5.0 17.6 1.0

Iodine binding site 8 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 8 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I308

b:16.5
occ:0.30
 CE X:LYS127 3.3 23.8 0.5
CG X:LYS127 3.4 21.1 0.5
CD X:LYS127 3.4 23.8 0.5
CA X:VAL129 3.8 17.6 1.0
CG2 X:VAL129 3.9 23.5 1.0
CB X:GLN132 4.0 14.3 1.0
CG X:GLN132 4.0 16.7 1.0
CB X:VAL129 4.0 19.8 1.0
N X:VAL129 4.3 16.6 1.0
NZ X:LYS127 4.3 25.5 0.5
CB X:LYS127 4.4 21.0 0.5
CB X:LYS127 4.4 20.9 0.5
O X:ASN128 4.5 14.3 1.0
C X:ASN128 4.5 15.6 1.0
CD X:GLN132 4.7 18.4 1.0
O X:LYS127 4.8 20.5 1.0
C X:LYS127 4.8 18.7 1.0
OE1 X:GLN132 4.9 17.3 1.0
C X:VAL129 4.9 17.3 1.0
O X:HOH438 5.0 22.8 1.0

Iodine binding site 9 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 9 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I309

b:25.0
occ:0.35
 O X:HOH488 2.8 36.7 1.0
OG X:SER65 3.4 17.1 0.5
OG X:SER65 3.4 14.4 0.5
NE2 X:HIS67 3.5 16.7 1.0
CB X:SER65 3.9 14.0 0.5
CE1 X:HIS67 3.9 17.2 1.0
NH1 X:ARG44 4.0 33.4 1.0
CD X:ARG44 4.1 23.5 1.0
OH X:TYR104 4.2 32.0 1.0
CB X:SER65 4.3 12.9 0.5
O X:HOH546 4.4 19.6 1.0
I X:IOD310 4.4 28.0 0.4
CZ X:TYR104 4.5 28.6 1.0
CZ X:ARG44 4.6 32.2 1.0
NE X:ARG44 4.7 28.7 1.0
CD2 X:HIS67 4.7 15.9 1.0
CE2 X:TYR104 4.8 28.3 1.0
I X:IOD307 4.9 34.4 0.6
O X:HOH485 4.9 33.0 1.0

Iodine binding site 10 out of 12 in 4e9o

Go back to Iodine Binding Sites List in 4e9o
Iodine binding site 10 out of 12 in the Vaccinia D8L Ectodomain Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Vaccinia D8L Ectodomain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
X:I310

b:28.0
occ:0.40
 I X:IOD307 2.8 34.4 0.6
OH X:TYR104 3.0 32.0 1.0
O X:HOH402 3.3 14.6 1.0
CG2 X:THR173 3.5 12.0 1.0
CE1 X:HIS67 3.8 17.2 1.0
CG2 X:VAL94 4.0 13.4 1.0
CB X:THR173 4.0 10.2 1.0
O X:HOH416 4.0 17.9 1.0
CG1 X:VAL94 4.2 14.8 1.0
CZ X:TYR104 4.3 28.6 1.0
I X:IOD309 4.4 25.0 0.3
CD1 X:ILE116 4.6 14.8 1.0
ND1 X:HIS67 4.6 16.0 1.0
NE2 X:HIS67 4.7 16.7 1.0
CB X:VAL94 4.7 11.7 1.0
OG1 X:THR173 5.0 12.3 1.0

Reference:

M.H.Matho, M.Maybeno, M.R.Benhnia, D.Becker, X.Meng, Y.Xiang, S.Crotty, B.Peters, D.M.Zajonc. Structural and Biochemical Characterization of the Vaccinia Virus Envelope Protein D8 and Its Recognition By the Antibody LA5. J.Virol. V. 86 8050 2012.
ISSN: ISSN 0022-538X
PubMed: 22623786
DOI: 10.1128/JVI.00836-12
Page generated: Sun Aug 11 17:37:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy