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Iodine in PDB 4ygn: Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein

Enzymatic activity of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein

All present enzymatic activity of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein:
4.2.1.1;

Protein crystallography data

The structure of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein, PDB code: 4ygn was solved by J.M.Fox, K.Kang, W.Sherman, A.Heroux, G.M.Sastry, M.Baghbanzadeh, M.R.Lockett, G.M.Whitesides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.23
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.341, 41.336, 72.837, 90.00, 104.57, 90.00
R / Rfree (%) 17.5 / 20.9

Other elements in 4ygn:

The structure of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein (pdb code 4ygn). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein, PDB code: 4ygn:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 4ygn

Go back to Iodine Binding Sites List in 4ygn
Iodine binding site 1 out of 5 in the Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:17.1
occ:0.40
 I A:IOD306 1.7 30.3 0.5
I A:IOD303 3.7 26.6 0.3
ZN A:ZN301 3.8 7.8 1.0
N A:THR199 4.0 7.7 1.0
CD2 A:LEU198 4.1 19.9 1.0
CA A:LEU198 4.1 8.1 1.0
O A:HOH501 4.2 17.4 1.0
CZ2 A:TRP209 4.2 9.8 1.0
CG2 A:VAL143 4.2 9.5 1.0
CH2 A:TRP209 4.3 8.8 1.0
ND1 A:HIS119 4.3 8.1 1.0
CE1 A:HIS94 4.3 8.7 1.0
CG2 A:VAL121 4.4 9.4 1.0
NE2 A:HIS94 4.5 8.4 1.0
OG1 A:THR199 4.6 8.9 1.0
CG1 A:VAL143 4.6 8.0 1.0
CB A:LEU198 4.6 10.7 1.0
C A:LEU198 4.6 7.8 1.0
CG A:HIS119 4.9 7.3 1.0
CB A:VAL143 4.9 7.9 1.0
CB A:HIS119 5.0 7.7 1.0
CE1 A:HIS119 5.0 7.0 1.0
CG A:LEU198 5.0 14.8 1.0

Iodine binding site 2 out of 5 in 4ygn

Go back to Iodine Binding Sites List in 4ygn
Iodine binding site 2 out of 5 in the Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:26.6
occ:0.30
 NE2 A:GLN92 3.5 15.5 1.0
O A:HOH501 3.5 17.4 1.0
I A:IOD302 3.7 17.1 0.4
CG2 A:VAL121 4.0 9.4 1.0
CD2 A:LEU198 4.1 19.9 1.0
CE1 A:HIS94 4.2 8.7 1.0
I A:IOD306 4.3 30.3 0.5
CG1 A:VAL121 4.5 9.7 1.0
CD A:GLN92 4.7 12.8 1.0
O A:HOH526 4.8 21.1 1.0
ND1 A:HIS94 4.8 8.3 1.0
OG1 A:THR200 4.8 12.0 1.0
CB A:VAL121 4.9 8.0 1.0
CZ A:PHE131 5.0 13.1 1.0

Iodine binding site 3 out of 5 in 4ygn

Go back to Iodine Binding Sites List in 4ygn
Iodine binding site 3 out of 5 in the Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:15.0
occ:0.50
 CD A:PRO202 3.9 13.8 1.0
CG A:PRO202 4.0 14.5 1.0
CE2 A:PHE131 4.2 14.1 1.0
CG2 A:VAL135 4.3 11.0 1.0
CD1 A:LEU198 4.4 17.3 1.0
CG1 A:VAL135 4.5 13.2 1.0
CD1 A:LEU204 4.6 14.8 1.0
CZ A:PHE131 4.7 13.1 1.0
CB A:VAL135 4.7 12.2 1.0

Iodine binding site 4 out of 5 in 4ygn

Go back to Iodine Binding Sites List in 4ygn
Iodine binding site 4 out of 5 in the Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:14.0
occ:0.50
 O A:HOH479 3.6 14.5 1.0
NE2 A:GLN249 3.7 12.6 1.0
CG A:PRO247 3.8 13.2 0.5
CD A:PRO247 4.1 11.2 0.5
CA A:GLU14 4.2 12.2 1.0
C A:PRO13 4.2 9.6 1.0
N A:GLU14 4.2 11.7 1.0
CB A:PRO13 4.2 11.6 1.0
O A:PRO13 4.3 10.4 1.0
CB A:PRO247 4.4 9.6 0.5
CD A:PRO247 4.5 9.3 0.5
CB A:GLU14 4.5 14.9 1.0
CG A:PRO247 4.5 8.6 0.5
OE1 A:GLN249 4.6 14.8 1.0
CD A:GLN249 4.6 13.1 1.0
CA A:PRO13 4.8 11.2 1.0
CB A:PRO247 4.9 11.0 0.5

Iodine binding site 5 out of 5 in 4ygn

Go back to Iodine Binding Sites List in 4ygn
Iodine binding site 5 out of 5 in the Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Nai--Interactions Between Hofmeister Anions and the Binding Pocket of A Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:30.3
occ:0.50
 I A:IOD302 1.7 17.1 0.4
ZN A:ZN301 2.4 7.8 1.0
OG1 A:THR199 3.2 8.9 1.0
O A:HOH501 3.3 17.4 1.0
ND1 A:HIS119 3.4 8.1 1.0
NE2 A:HIS94 3.6 8.4 1.0
N A:THR199 3.7 7.7 1.0
CE1 A:HIS94 3.9 8.7 1.0
CE1 A:HIS119 4.0 7.0 1.0
CB A:THR199 4.1 7.5 1.0
NE2 A:HIS96 4.2 6.6 1.0
I A:IOD303 4.3 26.6 0.3
CG2 A:THR199 4.3 9.8 1.0
CG A:HIS119 4.3 7.3 1.0
CA A:THR199 4.4 8.0 1.0
CH2 A:TRP209 4.5 8.8 1.0
CZ2 A:TRP209 4.6 9.8 1.0
C A:LEU198 4.7 7.8 1.0
CB A:HIS119 4.7 7.7 1.0
OE1 A:GLU106 4.7 9.2 1.0
CE1 A:HIS96 4.7 9.2 1.0
CA A:LEU198 4.7 8.1 1.0
N A:THR200 4.8 8.9 1.0
CD2 A:HIS94 4.9 8.4 1.0
C A:THR199 4.9 7.4 1.0
OG1 A:THR200 4.9 12.0 1.0

Reference:

J.M.Fox, K.Kang, W.Sherman, A.Heroux, M.Sastry, M.Baghbanzadeh, M.R.Lockett, G.M.Whitesides. Interactions Between Hofmeister Anions and the Binding Pocket of A Protein. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25738615
DOI: 10.1021/JACS.5B00187
Page generated: Sun Aug 11 20:24:29 2024

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