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Iodine in PDB 1jwg: Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide

Protein crystallography data

The structure of Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide, PDB code: 1jwg was solved by T.Shiba, H.Takatsu, T.Nogi, N.Matsugaki, M.Kawasaki, N.Igarashi, M.Suzuki, R.Kato, T.Earnest, K.Nakayama, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.146, 65.770, 101.426, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide (pdb code 1jwg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide, PDB code: 1jwg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 1jwg

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Iodine binding site 1 out of 6 in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I148

b:32.8
occ:1.00
O A:HOH167 3.5 29.1 1.0
NZ A:LYS110 3.6 40.0 1.0
CD A:LYS110 4.2 32.9 1.0
CE A:LYS110 4.2 33.6 1.0
CZ3 A:TRP61 4.2 26.1 1.0
CG2 A:ILE64 4.3 24.6 1.0
CE3 A:TRP61 4.4 25.4 1.0

Iodine binding site 2 out of 6 in 1jwg

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Iodine binding site 2 out of 6 in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I149

b:64.8
occ:1.00
NE2 A:GLN59 3.0 29.1 1.0
CD A:PRO58 3.8 27.5 1.0
CD A:GLN59 4.1 29.1 1.0
CG A:PRO58 4.1 28.9 1.0
CG A:GLN59 4.2 27.1 1.0
OG A:SER57 4.3 24.6 1.0
CB A:PRO58 4.8 28.2 1.0
N A:PRO58 4.9 26.7 1.0
OE2 A:GLU62 4.9 32.8 1.0
N A:GLN59 5.0 24.8 1.0

Iodine binding site 3 out of 6 in 1jwg

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Iodine binding site 3 out of 6 in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I148

b:63.6
occ:1.00
CA B:GLU39 3.4 51.4 1.0
CB B:GLU39 3.4 51.9 1.0
N A:LYS79 3.5 32.5 1.0
N B:GLU39 3.5 48.9 1.0
N A:ARG80 3.6 31.4 1.0
O B:GLU35 3.7 32.1 1.0
O B:HOH184 3.7 50.2 1.0
NE A:ARG80 3.8 47.1 1.0
C B:ASN38 3.9 47.0 1.0
CA A:GLY78 4.0 33.4 1.0
C A:GLY78 4.0 32.9 1.0
O B:ASN38 4.1 47.4 1.0
NH2 A:ARG80 4.1 51.2 1.0
CB A:ARG80 4.1 32.5 1.0
OD1 B:ASN38 4.3 51.9 1.0
CA A:LYS79 4.3 32.6 1.0
CB A:LYS79 4.4 33.2 1.0
CZ A:ARG80 4.4 49.3 1.0
CG A:ARG80 4.4 37.7 1.0
C A:LYS79 4.5 32.2 1.0
CA A:ARG80 4.5 32.1 1.0
O B:GLN36 4.6 35.0 1.0
OD1 A:ASN38 4.6 47.4 1.0
CG B:ASN38 4.6 49.5 1.0
CG B:GLU39 4.7 55.2 1.0
CA B:ASN38 4.7 45.5 1.0
CD A:ARG80 4.7 42.4 1.0
N B:ASN38 4.8 42.1 1.0
C B:GLU39 4.8 52.5 1.0
C B:GLU35 4.8 32.8 1.0
C B:GLN36 4.9 34.6 1.0
CA B:GLN36 4.9 34.0 1.0
CB B:ASN38 4.9 46.0 1.0
O A:GLY78 5.0 32.0 1.0

Iodine binding site 4 out of 6 in 1jwg

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Iodine binding site 4 out of 6 in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I149

b:58.6
occ:1.00
NZ B:LYS96 3.5 40.2 1.0
O B:HOH197 3.7 44.2 1.0
CE B:LYS96 3.8 40.8 1.0
CD B:LYS96 4.0 38.1 1.0
O B:HOH161 4.2 64.1 1.0
CD1 B:TYR102 4.3 44.5 1.0
CE1 B:TYR102 4.3 43.7 1.0
O B:HOH185 4.5 56.4 1.0
CG B:LYS96 5.0 36.1 1.0

Iodine binding site 5 out of 6 in 1jwg

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Iodine binding site 5 out of 6 in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I150

b:50.4
occ:1.00
NE2 B:GLN59 3.3 32.9 1.0
CD B:PRO58 3.8 30.6 1.0
CG B:GLN59 4.1 34.0 1.0
CG B:PRO58 4.2 34.1 1.0
CD B:GLN59 4.2 32.7 1.0
OG B:SER57 4.4 30.2 1.0
CB B:PRO58 4.6 31.9 1.0
N B:PRO58 4.8 31.0 1.0
OE1 B:GLU62 4.9 32.8 1.0
N B:GLN59 5.0 31.0 1.0

Iodine binding site 6 out of 6 in 1jwg

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Iodine binding site 6 out of 6 in the Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Vhs Domain of Human GGA1 Complexed with Cation-Independent M6PR C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I151

b:57.9
occ:1.00
O B:HOH199 3.2 32.5 1.0
CB B:ARG80 3.5 47.4 1.0
N B:PHE81 3.6 44.6 1.0
N B:GLY78 3.8 41.0 1.0
ND2 B:ASN38 3.8 50.2 1.0
CB B:ASN38 4.0 46.0 1.0
N B:ARG80 4.0 46.3 1.0
CB B:PHE81 4.1 42.6 1.0
O B:GLY78 4.1 43.0 1.0
CA B:ARG80 4.1 46.7 1.0
CG B:ASN38 4.1 49.5 1.0
C B:GLY78 4.2 43.8 1.0
CA B:GLY78 4.2 42.8 1.0
CD1 B:LEU37 4.2 33.2 1.0
SG A:CYS77 4.3 38.8 1.0
C B:ARG80 4.3 45.9 1.0
CB B:CYS77 4.4 40.0 1.0
CA B:PHE81 4.5 43.4 1.0
CG B:ARG80 4.7 50.6 1.0
N B:LYS79 4.7 45.1 1.0
C B:CYS77 4.8 40.4 1.0
CG B:PRO44 4.9 41.5 1.0
C B:LYS79 4.9 46.0 1.0
CA B:CYS77 5.0 39.7 1.0

Reference:

T.Shiba, H.Takatsu, T.Nogi, N.Matsugaki, M.Kawasaki, N.Igarashi, M.Suzuki, R.Kato, T.Earnest, K.Nakayama, S.Wakatsuki. Structural Basis For Recognition of Acidic-Cluster Dileucine Sequence By GGA1. Nature V. 415 937 2002.
ISSN: ISSN 0028-0836
PubMed: 11859376
DOI: 10.1038/415937A
Page generated: Sun Dec 13 19:20:07 2020

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