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Iodine in PDB 4op1: Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate

Protein crystallography data

The structure of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate, PDB code: 4op1 was solved by S.R.Jordan, S.Chmait, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.39
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 149.180, 149.180, 132.105, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 26.8

Other elements in 4op1:

The structure of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iodine atom in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate (pdb code 4op1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 28 binding sites of Iodine where determined in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate, PDB code: 4op1:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 1 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I703

b:64.3
occ:0.95
N A:PHE472 3.6 54.3 1.0
CB A:TYR468 3.8 72.2 1.0
CD2 A:TYR468 3.9 67.1 1.0
N A:ILE473 3.9 50.6 1.0
N A:TYR468 4.0 82.1 1.0
CB A:PHE472 4.2 51.8 1.0
CB A:PHE466 4.2 0.9 1.0
OE1 A:GLU467 4.3 96.5 1.0
CA A:PHE472 4.3 52.5 1.0
CG A:TYR468 4.3 69.1 1.0
N A:GLU467 4.4 0.8 1.0
C A:ASN471 4.4 60.8 1.0
CD1 A:LEU275 4.5 40.8 1.0
CA A:TYR468 4.5 75.6 1.0
CB A:ILE473 4.5 62.5 1.0
CA A:ASN471 4.6 69.2 1.0
C A:PHE472 4.6 49.5 1.0
CA A:PHE466 4.6 0.0 1.0
CG2 A:ILE473 4.6 63.1 1.0
CD2 A:PHE472 4.7 52.6 1.0
ND2 A:ASN471 4.7 71.5 1.0
O A:TYR468 4.7 82.3 1.0
CA A:ILE473 4.8 52.8 1.0
CE2 A:TYR468 4.9 66.6 1.0
CD2 A:LEU275 4.9 39.6 1.0
CG A:PHE472 5.0 54.5 1.0

Iodine binding site 2 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 2 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I704

b:60.1
occ:1.00
CD2 A:LEU506 4.0 51.9 1.0
CA A:CYS598 4.2 59.1 1.0
CG2 A:VAL601 4.2 54.3 1.0
CB A:LEU506 4.3 45.3 1.0
CB A:VAL601 4.4 54.2 1.0
CB A:ASP507 4.5 36.9 1.0
CG1 A:VAL597 4.5 57.0 1.0
N A:CYS598 4.6 59.9 1.0
CG1 A:VAL601 4.6 57.7 1.0
O A:VAL597 4.7 57.1 1.0
CG A:LEU506 4.7 50.8 1.0
CD2 A:LEU501 4.8 55.0 1.0
CB A:CYS598 4.8 67.5 1.0
C A:VAL597 4.8 57.9 1.0
N A:ASP507 4.9 43.2 1.0
SG A:CYS598 4.9 78.2 1.0
O A:LYS499 4.9 63.3 1.0

Iodine binding site 3 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 3 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I705

b:46.1
occ:0.65
NH1 A:ARG73 3.6 39.1 1.0
O A:HOH810 3.8 40.3 1.0
CA A:GLY250 3.9 29.5 1.0
N A:GLY250 4.1 29.4 1.0
CG2 A:ILE30 4.2 36.9 1.0
CB A:ALA248 4.5 29.5 1.0
CD1 A:ILE30 4.5 38.4 1.0
CG1 A:ILE30 4.7 37.1 1.0
CD A:PRO251 4.7 33.0 1.0
CZ A:ARG73 4.8 39.2 1.0

Iodine binding site 4 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 4 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I706

b:82.4
occ:0.90
N A:ALA46 3.6 58.4 1.0
CD2 A:LEU496 3.9 52.1 1.0
CB A:ALA46 4.1 62.4 1.0
CB A:ASP45 4.1 63.5 1.0
CA A:ASP45 4.1 64.5 1.0
CD1 A:LEU496 4.3 56.9 1.0
C A:ASP45 4.3 60.1 1.0
CG A:LYS318 4.3 69.6 1.0
CA A:ALA46 4.4 63.9 1.0
CD A:LYS318 4.7 75.8 1.0
NZ A:LYS318 4.7 77.8 1.0
CG A:LEU496 4.7 55.6 1.0

Iodine binding site 5 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 5 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I707

b:55.7
occ:0.70
OG1 A:THR298 3.2 38.8 1.0
CG1 A:ILE295 4.0 38.0 1.0
CG1 A:ILE473 4.1 61.6 1.0
O A:GLU294 4.2 42.1 1.0
CA A:ILE295 4.2 38.0 1.0
C A:GLU294 4.2 42.6 1.0
CB A:THR298 4.3 39.7 1.0
N A:ILE295 4.3 38.6 1.0
CB A:GLU294 4.3 48.2 1.0
CD1 A:ILE473 4.4 68.0 1.0
CD1 A:LEU464 4.5 78.5 1.0
OE2 A:GLU294 4.6 68.1 1.0
CB A:ILE295 4.7 40.6 1.0
CG2 A:THR298 4.7 38.2 1.0
NZ A:LYS279 4.9 63.2 1.0
CA A:GLU294 4.9 44.5 1.0

Iodine binding site 6 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 6 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I708

b:77.3
occ:0.85
N A:GLY151 3.5 34.8 1.0
CA A:ARG149 3.8 44.6 1.0
C A:ARG149 3.8 43.0 1.0
CA A:GLY151 3.9 35.6 1.0
N A:GLU150 4.1 37.4 1.0
O A:ARG149 4.2 42.8 1.0
CB A:ARG149 4.3 46.4 1.0
C A:GLY151 4.5 38.0 1.0
CG2 A:THR152 4.6 43.6 1.0
N A:THR152 4.6 38.8 1.0
C A:GLU150 4.7 36.1 1.0
I A:IOD715 4.8 76.3 0.4
CG A:ARG149 4.9 50.4 1.0
O A:HOH840 4.9 41.0 1.0
CA A:GLU150 4.9 38.0 1.0
NE2 A:HIS565 5.0 46.1 1.0

Iodine binding site 7 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 7 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I709

b:94.2
occ:0.70
N A:GLY3 3.5 66.0 1.0
CG A:ARG6 3.6 45.2 1.0
CA A:GLY3 3.8 65.5 1.0
N A:LYS5 3.8 53.1 1.0
C A:GLY3 3.8 65.1 1.0
N A:THR4 3.9 60.8 1.0
N A:ARG6 4.1 47.5 1.0
CB A:LYS5 4.1 65.0 1.0
CD A:ARG6 4.3 42.0 1.0
CB A:ALA554 4.3 34.7 1.0
CA A:LYS5 4.4 59.3 1.0
O A:GLY3 4.4 60.5 1.0
CA A:ALA554 4.4 36.7 1.0
C A:THR4 4.6 54.1 1.0
C A:LYS5 4.6 53.2 1.0
O A:ALA554 4.7 30.5 1.0
C A:PRO2 4.7 71.7 1.0
O A:MET1 4.7 81.3 1.0
CB A:ARG6 4.8 42.8 1.0
CA A:THR4 4.8 58.1 1.0
CA A:PRO2 4.9 77.1 1.0

Iodine binding site 8 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 8 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I710

b:63.4
occ:0.50
CG A:GLU25 3.7 62.8 1.0
OE2 A:GLU25 3.7 79.4 1.0
N A:SER34 3.7 37.0 1.0
CD A:GLU25 3.8 73.2 1.0
NH2 A:ARG525 3.9 71.6 1.0
CG A:LYS33 4.0 38.0 1.0
CA A:LYS33 4.1 38.1 1.0
CB A:LYS33 4.1 38.9 1.0
C11 A:2UW701 4.3 41.6 1.0
C A:LYS33 4.5 38.9 1.0
CD A:LYS33 4.5 35.5 1.0
OE1 A:GLU25 4.5 69.1 1.0
CG1 A:VAL28 4.5 39.0 1.0
CB A:SER34 4.5 40.6 1.0
CB A:VAL28 4.6 39.1 1.0
CA A:SER34 4.7 41.3 1.0
O A:SER34 4.7 42.0 1.0
CG2 A:VAL28 4.7 40.6 1.0
O1 A:2UW701 4.8 44.5 1.0

Iodine binding site 9 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 9 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I711

b:94.9
occ:0.50
NZ A:LYS531 3.1 37.7 1.0
O A:THR4 3.1 43.7 1.0
CE A:LYS531 3.5 39.4 1.0
O A:PHE7 3.5 35.5 1.0
C A:PHE7 3.6 31.9 1.0
N A:GLN8 3.8 33.0 1.0
CB A:PHE7 3.8 33.7 1.0
CA A:GLN8 3.9 41.0 1.0
C A:THR4 3.9 54.1 1.0
CA A:THR4 3.9 58.1 1.0
CA A:PHE7 4.2 32.7 1.0
CG2 A:THR4 4.3 61.5 1.0
CB A:THR4 4.6 59.4 1.0
O A:GLY3 4.6 60.5 1.0
N A:PHE7 4.6 36.6 1.0
OG1 A:THR4 4.7 65.2 1.0
C A:GLN8 4.9 37.1 1.0
CB A:GLN8 4.9 48.2 1.0
CD A:LYS531 4.9 41.7 1.0

Iodine binding site 10 out of 28 in 4op1

Go back to Iodine Binding Sites List in 4op1
Iodine binding site 10 out of 28 in the Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Gkrp Bound to AMG0556 and Sorbitol-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I712

b:70.2
occ:0.50
OD1 A:ASN196 3.1 59.3 1.0
I B:IOD714 3.7 66.7 0.5
CA A:CYS193 3.9 34.8 1.0
CG A:ASN196 4.2 45.6 1.0
CH2 A:TRP222 4.2 33.9 1.0
CB A:CYS193 4.2 39.6 1.0
CB A:ASN196 4.5 46.8 1.0
CZ2 A:TRP222 4.6 32.4 1.0
N A:CYS193 4.6 32.9 1.0
SG A:CYS193 4.7 54.8 1.0
CD1 A:ILE160 4.9 36.0 1.0

Reference:

N.Tamayo, M.H.Norman, M.D.Bartberger, Y.Bo, J.Chen, R.Cupples, C.Fotsch, C.Hale, F-T Hong, S.R.Jordan, L.Liu, D.J.Lloyd, C.Moyer, N.Nishimura, G.Sivits, S.Tadesse, G.Van, K.C.Yang, D.J.St. Jean. Small Molecule Disruptors of the Glucokinase- Glucokinase Regulatory Protein Interaction:5. New Aryl Sulfones Series, Optimization Through Conformational Analysis J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
Page generated: Sun Dec 13 19:35:51 2020

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