Atomistry » Iodine » PDB 4xnw-5ax3 » 4ygn
Atomistry »
  Iodine »
    PDB 4xnw-5ax3 »
      4ygn »

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

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