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 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy