Atomistry » Iron » PDB 1y4r-1yeu » 1y5l
Atomistry »
  Iron »
    PDB 1y4r-1yeu »
      1y5l »

Iron in PDB 1y5l: The Crystal Structure of the Narghi Mutant Nari-H66Y

Enzymatic activity of The Crystal Structure of the Narghi Mutant Nari-H66Y

All present enzymatic activity of The Crystal Structure of the Narghi Mutant Nari-H66Y:
1.7.99.4;

Protein crystallography data

The structure of The Crystal Structure of the Narghi Mutant Nari-H66Y, PDB code: 1y5l was solved by M.G.Bertero, R.A.Rothery, N.Boroumand, M.Palak, F.Blasco, N.Ginet, J.H.Weiner, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.79 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 154.165, 241.903, 139.603, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.7

Other elements in 1y5l:

The structure of The Crystal Structure of the Narghi Mutant Nari-H66Y also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the The Crystal Structure of the Narghi Mutant Nari-H66Y (pdb code 1y5l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the The Crystal Structure of the Narghi Mutant Nari-H66Y, PDB code: 1y5l:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 1 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:21.7
occ:1.00
FE1 A:SF41801 0.0 21.7 1.0
S4 A:SF41801 2.3 21.3 1.0
S2 A:SF41801 2.3 20.6 1.0
S3 A:SF41801 2.3 21.4 1.0
SG A:CYS57 2.3 24.4 1.0
FE4 A:SF41801 2.7 33.0 1.0
FE3 A:SF41801 2.7 24.5 1.0
FE2 A:SF41801 2.7 25.8 1.0
CB A:CYS57 3.3 18.2 1.0
CA A:GLY55 3.8 25.3 1.0
S1 A:SF41801 3.9 21.5 1.0
N A:CYS57 3.9 21.8 1.0
CA A:GLY91 4.1 17.9 1.0
C A:GLY55 4.2 30.2 1.0
CA A:CYS57 4.2 20.3 1.0
N A:SER56 4.3 25.3 1.0
C A:GLY91 4.3 18.5 1.0
N A:GLY91 4.4 21.2 1.0
NE1 A:TRP59 4.5 20.0 1.0
ND1 A:HIS49 4.5 27.8 1.0
N A:CYS92 4.6 19.8 1.0
CG A:PRO262 4.6 15.1 1.0
SG A:CYS53 4.7 34.5 1.0
SG A:CYS92 4.7 25.6 1.0
O A:GLY91 4.8 18.6 1.0
O A:GLY55 4.9 28.2 1.0
N A:GLY55 4.9 28.6 1.0
C A:SER56 4.9 20.5 1.0
CB A:PRO262 4.9 15.6 1.0
CB A:CYS92 5.0 16.7 1.0

Iron binding site 2 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 2 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:25.8
occ:1.00
FE2 A:SF41801 0.0 25.8 1.0
S3 A:SF41801 2.3 21.4 1.0
S4 A:SF41801 2.3 21.3 1.0
S1 A:SF41801 2.3 21.5 1.0
SG A:CYS92 2.3 25.6 1.0
FE4 A:SF41801 2.7 33.0 1.0
FE1 A:SF41801 2.7 21.7 1.0
FE3 A:SF41801 2.7 24.5 1.0
CB A:CYS92 3.3 16.7 1.0
N A:GLY95 3.8 19.9 1.0
S2 A:SF41801 3.9 20.6 1.0
N A:CYS92 3.9 19.8 1.0
CA A:GLY95 4.0 21.0 1.0
CA A:CYS92 4.1 15.7 1.0
C A:GLY91 4.4 18.5 1.0
ND1 A:HIS49 4.5 27.8 1.0
C A:CYS92 4.6 20.4 1.0
O A:CYS92 4.7 17.8 1.0
SG A:CYS53 4.7 34.5 1.0
SG A:CYS57 4.8 24.4 1.0
CB A:ARG94 4.8 17.3 1.0
CA A:GLY91 4.9 17.9 1.0
O A:GLY91 4.9 18.6 1.0
C A:ARG94 4.9 19.3 1.0

Iron binding site 3 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 3 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:24.5
occ:1.00
FE3 A:SF41801 0.0 24.5 1.0
ND1 A:HIS49 2.0 27.8 1.0
S2 A:SF41801 2.3 20.6 1.0
S4 A:SF41801 2.3 21.3 1.0
S1 A:SF41801 2.3 21.5 1.0
FE1 A:SF41801 2.7 21.7 1.0
FE4 A:SF41801 2.7 33.0 1.0
FE2 A:SF41801 2.7 25.8 1.0
CE1 A:HIS49 2.9 25.4 1.0
CG A:HIS49 3.1 24.6 1.0
CB A:HIS49 3.5 20.7 1.0
CA A:GLY95 3.8 21.0 1.0
S3 A:SF41801 3.9 21.4 1.0
NE1 A:TRP59 4.0 20.0 1.0
NE2 A:HIS49 4.1 22.1 1.0
CD2 A:HIS49 4.2 22.4 1.0
OH A:TYR1101 4.4 21.2 1.0
N A:GLY95 4.4 19.9 1.0
SG A:CYS57 4.7 24.4 1.0
SG A:CYS53 4.8 34.5 1.0
SG A:CYS92 4.8 25.6 1.0
CD1 A:TRP59 4.8 20.6 1.0
CE2 A:TRP59 4.8 18.3 1.0
CA A:HIS49 4.8 23.5 1.0
CB A:CYS57 4.9 18.2 1.0
CG1 A:VAL51 4.9 23.5 1.0
N A:HIS49 5.0 23.4 1.0

Iron binding site 4 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 4 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1801

b:33.0
occ:1.00
FE4 A:SF41801 0.0 33.0 1.0
S2 A:SF41801 2.3 20.6 1.0
SG A:CYS53 2.3 34.5 1.0
S3 A:SF41801 2.3 21.4 1.0
S1 A:SF41801 2.3 21.5 1.0
FE1 A:SF41801 2.7 21.7 1.0
FE2 A:SF41801 2.7 25.8 1.0
FE3 A:SF41801 2.7 24.5 1.0
CB A:CYS53 3.4 32.8 1.0
CA A:GLY55 3.8 25.3 1.0
S4 A:SF41801 3.8 21.3 1.0
N A:GLY55 4.1 28.6 1.0
CG1 A:VAL51 4.2 23.5 1.0
N A:SER56 4.4 25.3 1.0
ND1 A:HIS49 4.5 27.8 1.0
C A:GLY55 4.6 30.2 1.0
CA A:CYS53 4.7 30.5 1.0
SG A:CYS57 4.7 24.4 1.0
SG A:CYS92 4.8 25.6 1.0
CB A:HIS49 4.8 20.7 1.0
C A:CYS53 5.0 31.0 1.0

Iron binding site 5 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 5 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1802

b:25.0
occ:1.00
FE1 B:SF41802 0.0 25.0 1.0
S4 B:SF41802 2.3 25.4 1.0
S2 B:SF41802 2.3 23.3 1.0
S3 B:SF41802 2.3 25.2 1.0
SG B:CYS263 2.3 24.2 1.0
FE2 B:SF41802 2.7 26.8 1.0
FE4 B:SF41802 2.7 21.7 1.0
FE3 B:SF41802 2.8 24.8 1.0
CB B:CYS263 3.5 22.1 1.0
CA B:CYS263 3.8 24.7 1.0
S1 B:SF41802 3.9 24.0 1.0
N B:GLY265 4.0 16.3 1.0
N B:VAL264 4.2 19.6 1.0
C B:CYS263 4.2 24.1 1.0
CG1 B:ILE267 4.2 14.3 1.0
CD1 B:ILE267 4.3 18.2 1.0
CG2 B:ILE267 4.4 9.3 1.0
CA B:GLY265 4.5 13.2 1.0
NE B:ARG268 4.7 24.5 1.0
SG B:CYS22 4.8 21.6 1.0
SG B:CYS19 4.8 24.6 1.0
SG B:CYS16 4.9 21.2 1.0
CB B:ILE267 5.0 20.4 1.0
N B:ARG266 5.0 15.8 1.0

Iron binding site 6 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 6 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1802

b:26.8
occ:1.00
FE2 B:SF41802 0.0 26.8 1.0
S3 B:SF41802 2.3 25.2 1.0
S4 B:SF41802 2.3 25.4 1.0
S1 B:SF41802 2.3 24.0 1.0
SG B:CYS22 2.3 21.6 1.0
FE3 B:SF41802 2.7 24.8 1.0
FE1 B:SF41802 2.7 25.0 1.0
FE4 B:SF41802 2.7 21.7 1.0
CB B:CYS22 3.4 14.3 1.0
NH2 B:ARG268 3.9 17.1 1.0
S2 B:SF41802 3.9 23.3 1.0
N B:CYS22 4.0 18.9 1.0
CG2 B:VAL44 4.3 5.9 1.0
CA B:CYS22 4.4 18.7 1.0
N B:HIS20 4.4 24.3 1.0
CB B:PRO181 4.6 16.4 1.0
N B:THR21 4.7 17.7 1.0
NE B:ARG268 4.7 24.5 1.0
CZ B:ARG268 4.7 22.5 1.0
SG B:CYS19 4.7 24.6 1.0
CA B:HIS20 4.7 24.2 1.0
SG B:CYS263 4.8 24.2 1.0
SG B:CYS16 4.8 21.2 1.0
C B:HIS20 4.9 22.6 1.0

Iron binding site 7 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 7 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1802

b:24.8
occ:1.00
FE3 B:SF41802 0.0 24.8 1.0
S4 B:SF41802 2.3 25.4 1.0
S1 B:SF41802 2.3 24.0 1.0
S2 B:SF41802 2.3 23.3 1.0
SG B:CYS19 2.3 24.6 1.0
FE2 B:SF41802 2.7 26.8 1.0
FE4 B:SF41802 2.8 21.7 1.0
FE1 B:SF41802 2.8 25.0 1.0
N B:CYS19 3.6 24.8 1.0
CB B:CYS19 3.7 25.2 1.0
S3 B:SF41802 3.9 25.2 1.0
N B:HIS20 4.0 24.3 1.0
CA B:CYS19 4.0 23.6 1.0
CG1 B:ILE17 4.1 19.9 1.0
C B:CYS19 4.3 26.5 1.0
N B:THR21 4.5 17.7 1.0
N B:GLY265 4.6 16.3 1.0
CD1 B:ILE17 4.6 18.6 1.0
N B:GLY18 4.7 30.8 1.0
N B:VAL264 4.7 19.6 1.0
SG B:CYS22 4.7 21.6 1.0
C B:GLY18 4.8 26.7 1.0
SG B:CYS16 4.8 21.2 1.0
SG B:CYS263 4.9 24.2 1.0
CB B:VAL264 4.9 15.2 1.0
CB B:THR21 4.9 12.5 1.0
CA B:HIS20 4.9 24.2 1.0
N B:ILE17 4.9 25.8 1.0

Iron binding site 8 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 8 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1802

b:21.7
occ:1.00
FE4 B:SF41802 0.0 21.7 1.0
S1 B:SF41802 2.3 24.0 1.0
S3 B:SF41802 2.3 25.2 1.0
S2 B:SF41802 2.3 23.3 1.0
SG B:CYS16 2.3 21.2 1.0
FE1 B:SF41802 2.7 25.0 1.0
FE2 B:SF41802 2.7 26.8 1.0
FE3 B:SF41802 2.8 24.8 1.0
CB B:CYS16 3.6 17.4 1.0
S4 B:SF41802 3.9 25.4 1.0
CA B:CYS16 4.0 20.6 1.0
CD1 B:ILE267 4.1 18.2 1.0
N B:ILE17 4.2 25.8 1.0
N B:GLY18 4.2 30.8 1.0
C B:CYS16 4.5 21.6 1.0
CG B:PRO181 4.6 19.2 1.0
N B:CYS19 4.7 24.8 1.0
CA B:GLY18 4.7 26.7 1.0
CB B:PRO181 4.7 16.4 1.0
SG B:CYS263 4.8 24.2 1.0
SG B:CYS22 4.9 21.6 1.0
CG1 B:ILE267 4.9 14.3 1.0
SG B:CYS19 4.9 24.6 1.0

Iron binding site 9 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 9 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1803

b:18.2
occ:1.00
FE1 B:SF41803 0.0 18.2 1.0
S4 B:SF41803 2.2 17.1 1.0
S2 B:SF41803 2.3 16.9 1.0
S3 B:SF41803 2.3 16.8 1.0
SG B:CYS247 2.3 19.3 1.0
FE3 B:SF41803 2.6 17.1 1.0
FE4 B:SF41803 2.7 15.6 1.0
FE2 B:SF41803 2.7 18.2 1.0
CB B:CYS247 3.5 21.6 1.0
N B:CYS247 3.5 18.0 1.0
S1 B:SF41803 3.8 17.6 1.0
CA B:CYS247 4.0 21.4 1.0
NE1 B:TRP30 4.1 11.2 1.0
C B:PHE246 4.2 14.3 1.0
CB B:THR257 4.2 16.6 1.0
CA B:PHE246 4.4 13.9 1.0
N B:VAL258 4.5 16.0 1.0
CD1 B:TRP30 4.5 15.6 1.0
SG B:CYS259 4.6 22.5 1.0
N B:PHE246 4.6 16.3 1.0
SG B:CYS26 4.8 17.4 1.0
OG1 B:THR257 4.8 23.4 1.0
SG B:CYS244 4.8 18.1 1.0
CG2 B:THR257 4.9 14.2 1.0
N B:CYS259 4.9 17.5 1.0
CD1 B:ILE245 4.9 34.5 1.0
CA B:THR257 5.0 17.8 1.0

Iron binding site 10 out of 20 in 1y5l

Go back to Iron Binding Sites List in 1y5l
Iron binding site 10 out of 20 in the The Crystal Structure of the Narghi Mutant Nari-H66Y


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Crystal Structure of the Narghi Mutant Nari-H66Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1803

b:18.2
occ:1.00
FE2 B:SF41803 0.0 18.2 1.0
S1 B:SF41803 2.2 17.6 1.0
S3 B:SF41803 2.3 16.8 1.0
S4 B:SF41803 2.3 17.1 1.0
SG B:CYS244 2.3 18.1 1.0
FE4 B:SF41803 2.6 15.6 1.0
FE3 B:SF41803 2.7 17.1 1.0
FE1 B:SF41803 2.7 18.2 1.0
CB B:CYS244 3.4 18.2 1.0
S2 B:SF41803 3.8 16.9 1.0
N B:PHE246 3.9 16.3 1.0
CA B:CYS244 4.0 16.9 1.0
CA B:PHE246 4.1 13.9 1.0
N B:ILE245 4.2 12.0 1.0
C B:CYS244 4.4 12.6 1.0
CD1 B:LEU183 4.4 18.1 1.0
N B:CYS247 4.6 18.0 1.0
CB B:LEU183 4.6 20.8 1.0
C B:PHE246 4.7 14.3 1.0
CB B:PHE41 4.8 13.4 1.0
SG B:CYS26 4.8 17.4 1.0
SG B:CYS259 4.8 22.5 1.0
SG B:CYS247 4.9 19.3 1.0
C B:ILE245 4.9 15.2 1.0

Reference:

M.G.Bertero, R.A.Rothery, N.Boroumand, M.Palak, F.Blasco, N.Ginet, J.H.Weiner, N.C.J.Strynadka. Structural and Biochemical Characterization of A Quinol Binding Site of Escherichia Coli Nitrate Reductase A J.Biol.Chem. V. 280 14836 2005.
ISSN: ISSN 0021-9258
PubMed: 15615728
DOI: 10.1074/JBC.M410457200
Page generated: Wed Jul 16 22:24:53 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy