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Iodine in PDB 4oc1: X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid

Enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid

All present enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid, PDB code: 4oc1 was solved by J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.Pomper, J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.396, 130.353, 158.944, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.3

Other elements in 4oc1:

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom
Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid (pdb code 4oc1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid, PDB code: 4oc1:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 4oc1

Go back to Iodine Binding Sites List in 4oc1
Iodine binding site 1 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I818

b:35.9
occ:0.38
 IAG A:2QS818 0.0 35.9 0.4
IAG A:2QS818 1.2 26.7 0.6
CAZ A:2QS818 2.1 36.6 0.4
CAZ A:2QS818 2.9 30.3 0.6
CAI A:2QS818 2.9 37.4 0.4
CAH A:2QS818 3.0 36.6 0.4
N A:ALA535 3.6 20.7 1.0
CG A:ARG534 3.6 21.6 1.0
CA A:ALA535 3.6 20.1 1.0
CAI A:2QS818 3.6 26.0 0.6
N A:ARG536 3.7 20.2 1.0
C A:ALA535 3.7 21.1 1.0
CG A:ARG536 3.7 22.6 1.0
O A:ARG463 3.7 21.5 1.0
C A:ARG534 3.8 19.4 1.0
O A:ARG534 3.9 19.7 1.0
NE A:ARG536 4.0 28.2 1.0
NE A:ARG534 4.0 21.2 1.0
CB A:ARG534 4.1 20.5 1.0
CAH A:2QS818 4.1 28.4 0.6
CB A:ARG536 4.2 21.5 1.0
CD A:ARG534 4.2 21.0 1.0
CAK A:2QS818 4.3 37.2 0.4
CD A:ARG536 4.3 24.5 1.0
C A:ARG463 4.3 21.6 1.0
CAJ A:2QS818 4.3 35.2 0.4
O A:ALA535 4.3 20.2 1.0
CA A:ARG536 4.5 20.9 1.0
CA A:ARG534 4.5 19.0 1.0
CG A:ARG463 4.6 23.5 1.0
N A:ASP465 4.6 21.3 1.0
CZ A:ARG534 4.6 23.7 1.0
CA A:VAL464 4.6 21.4 1.0
CB A:ARG463 4.7 21.7 1.0
CL A:CL817 4.8 24.4 1.0
N A:VAL464 4.8 21.2 1.0
CD A:ARG463 4.8 24.5 1.0
CBA A:2QS818 4.8 36.4 0.4
CZ A:ARG536 4.8 27.1 1.0
O A:HOH921 4.9 29.1 1.0
C A:VAL464 4.9 22.1 1.0
NH2 A:ARG534 5.0 23.2 1.0

Iodine binding site 2 out of 2 in 4oc1

Go back to Iodine Binding Sites List in 4oc1
Iodine binding site 2 out of 2 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I818

b:26.7
occ:0.62
 IAG A:2QS818 0.0 26.7 0.6
IAG A:2QS818 1.2 35.9 0.4
CAZ A:2QS818 1.7 36.6 0.4
CAH A:2QS818 2.2 36.6 0.4
CAZ A:2QS818 2.3 30.3 0.6
CAI A:2QS818 2.9 37.4 0.4
CAI A:2QS818 3.3 26.0 0.6
CAH A:2QS818 3.4 28.4 0.6
CAJ A:2QS818 3.5 35.2 0.4
O A:ARG463 3.6 21.5 1.0
CG A:ARG463 3.7 23.5 1.0
CG A:ARG534 3.8 21.6 1.0
C A:ARG463 3.9 21.6 1.0
CD A:ARG463 4.0 24.5 1.0
N A:ASP465 4.1 21.3 1.0
CAK A:2QS818 4.1 37.2 0.4
N A:VAL464 4.2 21.2 1.0
CB A:ARG463 4.2 21.7 1.0
CA A:VAL464 4.2 21.4 1.0
CG A:ARG536 4.2 22.6 1.0
O A:ARG534 4.2 19.7 1.0
OD1 A:ASP465 4.3 33.4 1.0
C A:VAL464 4.3 22.1 1.0
CBA A:2QS818 4.3 36.4 0.4
CG A:ASP465 4.3 28.7 1.0
NE A:ARG534 4.4 21.2 1.0
NE A:ARG463 4.4 28.3 1.0
CD A:ARG534 4.4 21.0 1.0
C A:ARG534 4.4 19.4 1.0
CA A:ALA535 4.4 20.1 1.0
N A:ARG536 4.4 20.2 1.0
O A:HOH1408 4.4 37.5 1.0
N A:ALA535 4.4 20.7 1.0
C A:ALA535 4.6 21.1 1.0
CB A:ASP465 4.7 21.4 1.0
OD2 A:ASP465 4.7 33.4 1.0
CB A:ARG534 4.7 20.5 1.0
NE A:ARG536 4.7 28.2 1.0
CA A:ARG463 4.7 21.6 1.0
CAK A:2QS818 4.7 26.3 0.6
CD A:ARG536 4.7 24.5 1.0
CAJ A:2QS818 4.7 27.9 0.6
CZ A:ARG534 4.8 23.7 1.0
CA A:ASP465 5.0 20.8 1.0
CB A:ARG536 5.0 21.5 1.0

Reference:

J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.G.Pomper, J.Lubkowski, C.Barinka. Structural Characterization of P1'-Diversified Urea-Based Inhibitors of Glutamate Carboxypeptidase II. Bioorg.Med.Chem.Lett. V. 24 2340 2014.
ISSN: ISSN 0960-894X
PubMed: 24731280
DOI: 10.1016/J.BMCL.2014.03.066
Page generated: Sun Aug 11 18:57:35 2024

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