Atomistry » Iron » PDB 6nli-6o5y » 6nsy
Atomistry »
  Iron »
    PDB 6nli-6o5y »
      6nsy »

Iron in PDB 6nsy: X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy)

Enzymatic activity of X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy)

All present enzymatic activity of X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy):
1.11.1.6;

Protein crystallography data

The structure of X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy), PDB code: 6nsy was solved by A.Zarate-Romero, E.Rudino-Pinera, V.Stojanoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.60 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.100, 154.500, 160.900, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 20.2

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy) (pdb code 6nsy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy), PDB code: 6nsy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6nsy

Go back to Iron Binding Sites List in 6nsy
Iron binding site 1 out of 4 in the X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:10.7
occ:1.00
FE A:HEM801 0.0 10.7 1.0
NA A:HEM801 2.0 5.0 1.0
NC A:HEM801 2.0 13.2 1.0
NB A:HEM801 2.1 9.0 1.0
ND A:HEM801 2.1 6.0 1.0
OH A:TYR389 2.1 11.1 1.0
O A:HOH1308 2.7 23.2 1.0
C1A A:HEM801 3.0 6.1 1.0
C4A A:HEM801 3.0 6.2 1.0
C1C A:HEM801 3.0 15.2 1.0
C4C A:HEM801 3.0 8.5 1.0
C4B A:HEM801 3.1 9.9 1.0
C1B A:HEM801 3.1 9.1 1.0
C1D A:HEM801 3.1 6.2 1.0
C4D A:HEM801 3.1 7.2 1.0
CZ A:TYR389 3.1 7.7 1.0
CHA A:HEM801 3.4 5.7 1.0
CHC A:HEM801 3.4 7.5 1.0
CHB A:HEM801 3.4 8.3 1.0
CHD A:HEM801 3.4 8.7 1.0
CE2 A:TYR389 3.9 5.6 1.0
CE1 A:TYR389 3.9 5.9 1.0
O A:HOH1051 4.0 10.5 1.0
NE A:ARG385 4.2 7.7 1.0
NH2 A:ARG385 4.2 5.6 1.0
C2A A:HEM801 4.2 6.1 1.0
C3A A:HEM801 4.3 7.2 1.0
C3C A:HEM801 4.3 10.5 1.0
C2C A:HEM801 4.3 10.1 1.0
C3B A:HEM801 4.3 7.3 1.0
C2B A:HEM801 4.3 9.7 1.0
C2D A:HEM801 4.3 7.6 1.0
C3D A:HEM801 4.3 4.1 1.0
CG2 A:VAL101 4.5 4.9 1.0
CZ A:PHE188 4.5 9.0 1.0
NE2 A:HIS102 4.6 8.9 1.0
CZ A:ARG385 4.6 6.5 1.0
CD2 A:HIS102 4.7 4.8 1.0

Iron binding site 2 out of 4 in 6nsy

Go back to Iron Binding Sites List in 6nsy
Iron binding site 2 out of 4 in the X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:8.8
occ:1.00
FE B:HEM801 0.0 8.8 1.0
NA B:HEM801 2.0 11.1 1.0
NB B:HEM801 2.0 13.6 1.0
NC B:HEM801 2.0 6.7 1.0
ND B:HEM801 2.1 9.4 1.0
OH B:TYR389 2.2 9.5 1.0
O B:HOH1286 2.8 19.9 1.0
C4A B:HEM801 3.0 11.3 1.0
C1B B:HEM801 3.0 12.0 1.0
C4B B:HEM801 3.1 9.0 1.0
C1A B:HEM801 3.1 10.2 1.0
C4C B:HEM801 3.1 8.2 1.0
C1C B:HEM801 3.1 8.9 1.0
C1D B:HEM801 3.1 4.4 1.0
C4D B:HEM801 3.1 10.1 1.0
CZ B:TYR389 3.2 9.8 1.0
CHB B:HEM801 3.4 9.7 1.0
CHC B:HEM801 3.4 9.1 1.0
CHD B:HEM801 3.4 4.9 1.0
CHA B:HEM801 3.5 7.3 1.0
CE1 B:TYR389 3.9 7.3 1.0
CE2 B:TYR389 4.0 7.0 1.0
O B:HOH1142 4.1 15.8 1.0
NE B:ARG385 4.2 9.0 1.0
C3A B:HEM801 4.2 6.0 1.0
C2B B:HEM801 4.2 11.2 1.0
C2A B:HEM801 4.3 6.2 1.0
C3B B:HEM801 4.3 10.5 1.0
C3C B:HEM801 4.3 8.4 1.0
C2C B:HEM801 4.3 9.5 1.0
C2D B:HEM801 4.3 11.0 1.0
NH2 B:ARG385 4.3 13.0 1.0
C3D B:HEM801 4.3 4.3 1.0
CZ B:PHE188 4.5 5.2 1.0
CG2 B:VAL101 4.5 3.3 1.0
NE2 B:HIS102 4.5 8.2 1.0
CD2 B:HIS102 4.6 6.9 1.0
CZ B:ARG385 4.7 13.4 1.0

Iron binding site 3 out of 4 in 6nsy

Go back to Iron Binding Sites List in 6nsy
Iron binding site 3 out of 4 in the X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe801

b:8.6
occ:1.00
FE C:HEM801 0.0 8.6 1.0
O C:O811 1.8 8.6 0.6
NA C:HEM801 2.0 10.2 1.0
NC C:HEM801 2.0 6.9 1.0
ND C:HEM801 2.0 5.6 1.0
NB C:HEM801 2.1 7.3 1.0
OH C:TYR389 2.2 6.8 1.0
C4B C:HEM801 3.1 5.9 1.0
C1C C:HEM801 3.1 9.0 1.0
C4A C:HEM801 3.1 8.9 1.0
C1A C:HEM801 3.1 6.6 1.0
C1D C:HEM801 3.1 8.7 1.0
C4C C:HEM801 3.1 7.4 1.0
C1B C:HEM801 3.1 5.7 1.0
C4D C:HEM801 3.1 6.3 1.0
CZ C:TYR389 3.2 11.0 1.0
CHC C:HEM801 3.4 3.2 1.0
CHB C:HEM801 3.4 4.9 1.0
CHA C:HEM801 3.4 5.6 1.0
CHD C:HEM801 3.4 4.1 1.0
O C:HOH902 3.8 10.6 1.0
CE1 C:TYR389 3.9 7.5 1.0
CE2 C:TYR389 4.0 7.6 1.0
NE C:ARG385 4.1 9.1 1.0
NH2 C:ARG385 4.2 3.1 1.0
C3A C:HEM801 4.3 7.2 1.0
C3B C:HEM801 4.3 8.3 1.0
C2C C:HEM801 4.3 14.1 1.0
C2D C:HEM801 4.3 7.9 1.0
C2A C:HEM801 4.3 8.6 1.0
C2B C:HEM801 4.3 10.2 1.0
C3C C:HEM801 4.3 8.2 1.0
C3D C:HEM801 4.3 6.6 1.0
CZ C:PHE188 4.4 7.0 1.0
CG2 C:VAL101 4.4 7.5 1.0
CZ C:ARG385 4.6 8.6 1.0
NE2 C:HIS102 4.7 6.7 1.0
CD2 C:HIS102 4.7 6.5 1.0
CE2 C:PHE188 4.9 11.0 1.0

Iron binding site 4 out of 4 in 6nsy

Go back to Iron Binding Sites List in 6nsy
Iron binding site 4 out of 4 in the X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Reduced Catalase 3 From N.Crassa in Cpd I State (0.263 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe801

b:9.5
occ:1.00
FE D:HEM801 0.0 9.5 1.0
O D:O808 1.8 9.5 0.6
NC D:HEM801 2.0 5.3 1.0
NA D:HEM801 2.1 3.0 1.0
NB D:HEM801 2.1 7.1 1.0
ND D:HEM801 2.1 8.9 1.0
OH D:TYR389 2.2 7.1 1.0
C1C D:HEM801 3.0 12.4 1.0
C4C D:HEM801 3.0 10.5 1.0
C4B D:HEM801 3.0 8.9 1.0
C1D D:HEM801 3.1 7.9 1.0
C1B D:HEM801 3.1 11.0 1.0
C4A D:HEM801 3.1 9.8 1.0
C1A D:HEM801 3.1 6.2 1.0
C4D D:HEM801 3.1 7.5 1.0
CZ D:TYR389 3.2 6.1 1.0
CHC D:HEM801 3.4 10.7 1.0
CHD D:HEM801 3.4 6.2 1.0
CHB D:HEM801 3.5 9.5 1.0
CHA D:HEM801 3.5 5.8 1.0
O D:HOH987 3.9 7.7 1.0
CE1 D:TYR389 3.9 5.6 1.0
CE2 D:TYR389 4.0 6.8 1.0
NE D:ARG385 4.2 6.9 1.0
NH2 D:ARG385 4.2 7.7 1.0
C2C D:HEM801 4.2 17.3 1.0
C3C D:HEM801 4.2 7.7 1.0
C3B D:HEM801 4.2 8.9 1.0
C2B D:HEM801 4.3 14.0 1.0
C2D D:HEM801 4.3 12.2 1.0
C3A D:HEM801 4.3 4.3 1.0
C3D D:HEM801 4.3 8.3 1.0
C2A D:HEM801 4.3 4.9 1.0
CZ D:PHE188 4.5 9.5 1.0
CG2 D:VAL101 4.5 5.8 1.0
CZ D:ARG385 4.6 9.2 1.0
NE2 D:HIS102 4.6 8.0 1.0
CD2 D:HIS102 4.7 6.3 1.0
CE1 D:PHE188 5.0 8.0 1.0

Reference:

A.Zarate-Romero, V.Stojanoff, A.E.Cohen, W.Hansberg, E.Rudino-Pinera. X-Ray Driven Reduction of Cpd I of Catalase-3 From N. Crassa Reveals Differential Sensitivity of Active Sites and Formation of Ferrous State. Arch.Biochem.Biophys. V. 666 107 2019.
ISSN: ESSN 1096-0384
PubMed: 30940570
DOI: 10.1016/J.ABB.2019.03.020
Page generated: Sun Dec 13 16:46:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy