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Zinc in PDB 4ims: Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine)

Enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine)

All present enzymatic activity of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine):
1.14.13.39;

Protein crystallography data

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine), PDB code: 4ims was solved by H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.845, 110.418, 164.106, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.5

Other elements in 4ims:

The structure of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine) also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine) (pdb code 4ims). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine), PDB code: 4ims:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ims

Go back to Zinc Binding Sites List in 4ims
Zinc binding site 1 out of 3 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn804

b:45.3
occ:1.00
 SG A:CYS331 2.3 45.3 1.0
SG B:CYS326 2.3 49.6 1.0
SG B:CYS331 2.4 45.6 1.0
SG A:CYS326 2.4 52.9 1.0
CB B:CYS331 3.3 50.7 1.0
CB A:CYS331 3.3 45.0 1.0
CB A:CYS326 3.4 55.7 1.0
CB B:CYS326 3.5 53.4 1.0
CA B:CYS331 3.5 49.9 1.0
CA A:CYS331 3.6 48.5 1.0
N B:MET332 3.9 48.7 1.0
N A:MET332 3.9 48.9 1.0
N A:GLY333 4.0 46.6 1.0
N B:GLY333 4.1 48.5 1.0
C B:CYS331 4.2 48.2 1.0
C A:CYS331 4.2 49.0 1.0
CA A:GLY333 4.4 44.6 1.0
CA B:GLY333 4.6 47.0 1.0
CA A:CYS326 4.7 57.9 1.0
N B:CYS331 4.8 52.8 1.0
CA B:CYS326 4.8 55.9 1.0
C A:MET332 4.9 47.6 1.0
N A:CYS331 4.9 52.7 1.0
O B:ILE330 4.9 58.8 1.0
C B:MET332 4.9 48.6 1.0
CA A:MET332 5.0 49.5 1.0

Zinc binding site 2 out of 3 in 4ims

Go back to Zinc Binding Sites List in 4ims
Zinc binding site 2 out of 3 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn805

b:40.1
occ:0.75
 O A:HOH901 2.1 30.2 1.0
OD1 A:ASP600 2.1 44.8 1.0
CL A:CL806 2.1 49.9 1.0
NE2 B:HIS692 2.4 50.4 1.0
CG A:ASP600 2.8 44.0 1.0
OD2 A:ASP600 2.8 44.2 1.0
CD2 B:HIS692 3.2 47.9 1.0
O A:HOH989 3.2 46.5 1.0
CE1 B:HIS692 3.5 44.6 1.0
O A:HOH961 3.7 42.1 1.0
CG A:ARG596 3.8 43.9 1.0
CD A:ARG596 4.2 44.8 1.0
CB A:ASP600 4.2 43.0 1.0
CE2 B:PHE691 4.3 42.4 1.0
CB A:ARG596 4.3 43.8 1.0
CG B:HIS692 4.4 45.4 1.0
ND1 B:HIS692 4.5 46.1 1.0
CA A:ARG596 4.6 44.9 1.0
CD2 B:PHE691 4.6 41.5 1.0
CB B:SER686 4.8 41.2 1.0
O A:HOH916 4.8 37.5 1.0
OG B:SER686 4.8 46.8 1.0
OE1 B:GLU307 4.9 51.9 0.6

Zinc binding site 3 out of 3 in 4ims

Go back to Zinc Binding Sites List in 4ims
Zinc binding site 3 out of 3 in the Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Rat Neuronal Nitric Oxide Synthase Heme Domain in Complex with 6,6'-((5-(3-Aminopropyl)-1,3-Phenylene)Bis(Ethane-2,1-Diyl)) Bis(4-Methylpyridin-2-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn804

b:43.3
occ:0.75
 CL B:CL805 2.1 53.0 1.0
OD1 B:ASP600 2.1 48.3 1.0
O B:HOH901 2.1 31.4 1.0
NE2 A:HIS692 2.4 46.1 1.0
CG B:ASP600 2.8 44.4 1.0
OD2 B:ASP600 2.8 45.1 1.0
CD2 A:HIS692 3.2 44.0 1.0
CE1 A:HIS692 3.5 43.5 1.0
O B:HOH1008 3.8 43.5 1.0
CG B:ARG596 4.0 44.4 1.0
CB B:ASP600 4.2 40.7 1.0
CD B:ARG596 4.3 45.8 1.0
CE2 A:PHE691 4.3 38.6 1.0
CB B:ARG596 4.4 42.6 1.0
CG A:HIS692 4.5 46.0 1.0
ND1 A:HIS692 4.6 45.3 1.0
CD2 A:PHE691 4.7 37.0 1.0
CA B:ARG596 4.7 45.0 1.0
CB A:SER686 4.7 40.6 1.0

Reference:

H.Huang, H.Li, P.Martasek, L.J.Roman, T.L.Poulos, R.B.Silverman. Structure-Guided Design of Selective Inhibitors of Neuronal Nitric Oxide Synthase. J.Med.Chem. V. 56 3024 2013.
ISSN: ISSN 0022-2623
PubMed: 23451760
DOI: 10.1021/JM4000984
Page generated: Sun Oct 27 00:48:10 2024

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