Iron in PDB 8x9e: Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration

Enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration

All present enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration, PDB code: 8x9e was solved by H.H.Lee, Y.Heo, H.J.Yoon, S.M.Kim, S.Y.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.22 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.083, 75.088, 71.14, 90, 111.39, 90
R / Rfree (%) 17.7 / 22.7

Other elements in 8x9e:

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration (pdb code 8x9e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration, PDB code: 8x9e:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 1 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:28.5
occ:1.00
 FE1 A:SF4701 0.0 28.5 1.0
S4 A:SF4701 2.2 30.4 1.0
S3 A:SF4701 2.3 29.1 1.0
S2 A:SF4701 2.3 30.0 1.0
SG A:CYS70 2.4 30.1 1.0
FE2 A:SF4701 2.7 29.1 1.0
FE3 A:SF4701 2.7 30.1 1.0
FE4 A:SF4701 2.8 29.9 1.0
CB A:CYS70 3.4 31.2 1.0
N A:CYS70 3.8 31.4 1.0
S1 A:SF4701 3.9 28.8 1.0
CA A:CYS70 4.2 31.7 1.0
NH2 A:ARG80 4.2 29.3 1.0
CB A:ALA72 4.4 33.3 1.0
O A:HOH830 4.5 30.7 1.0
N A:ILE69 4.5 34.0 1.0
CB A:CYS51 4.6 30.1 1.0
CG A:MET199 4.6 32.2 1.0
C A:GLY68 4.9 33.4 1.0
SG A:CYS56 4.9 32.6 1.0
C A:ILE69 4.9 32.7 1.0
CA A:GLY68 5.0 35.8 1.0
SG A:CYS48 5.0 28.9 1.0

Iron binding site 2 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 2 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:29.1
occ:1.00
 FE2 A:SF4701 0.0 29.1 1.0
S3 A:SF4701 2.3 29.1 1.0
S4 A:SF4701 2.3 30.4 1.0
S1 A:SF4701 2.3 28.8 1.0
SG A:CYS48 2.5 28.9 1.0
FE4 A:SF4701 2.7 29.9 1.0
FE3 A:SF4701 2.7 30.1 1.0
FE1 A:SF4701 2.7 28.5 1.0
CB A:CYS48 3.3 30.9 1.0
NH2 A:ARG80 3.7 29.3 1.0
S2 A:SF4701 3.9 30.0 1.0
N A:HIS50 4.0 28.4 1.0
C A:CYS48 4.1 31.3 1.0
O A:CYS48 4.2 31.7 1.0
CB A:CYS51 4.2 30.1 1.0
CA A:CYS48 4.4 31.6 1.0
N A:ARG49 4.5 30.3 1.0
N A:CYS51 4.5 28.9 1.0
CB A:HIS50 4.5 27.1 1.0
CA A:HIS50 4.6 28.0 1.0
C A:HIS50 4.6 29.1 1.0
SG A:CYS56 4.8 32.6 1.0
CB A:CYS56 4.8 34.2 1.0
CZ A:ARG80 4.9 30.7 1.0
C A:ARG49 4.9 28.6 1.0
CA A:ARG49 4.9 29.6 1.0

Iron binding site 3 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 3 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:30.1
occ:1.00
 FE3 A:SF4701 0.0 30.1 1.0
S2 A:SF4701 2.3 30.0 1.0
S1 A:SF4701 2.3 28.8 1.0
S4 A:SF4701 2.3 30.4 1.0
SG A:CYS56 2.4 32.6 1.0
FE4 A:SF4701 2.7 29.9 1.0
FE2 A:SF4701 2.7 29.1 1.0
FE1 A:SF4701 2.7 28.5 1.0
CB A:CYS56 3.3 34.2 1.0
S3 A:SF4701 3.9 29.1 1.0
N A:ILE69 3.9 34.0 1.0
CB A:ILE69 4.4 31.9 1.0
CA A:GLY54 4.4 31.1 1.0
CA A:CYS56 4.5 34.7 1.0
N A:CYS56 4.5 33.4 1.0
N A:GLY54 4.5 31.1 1.0
CB A:CYS51 4.5 30.1 1.0
CA A:GLY68 4.6 35.8 1.0
O A:CYS48 4.6 31.7 1.0
C A:GLY68 4.7 33.4 1.0
CA A:ILE69 4.7 32.9 1.0
N A:CYS70 4.7 31.4 1.0
CG1 A:ILE69 4.8 32.5 1.0
CD1 A:ILE69 4.8 32.3 1.0
SG A:CYS48 4.9 28.9 1.0
SG A:CYS70 4.9 30.1 1.0
CB A:CYS48 4.9 30.9 1.0

Iron binding site 4 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 4 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:29.9
occ:1.00
 FE4 A:SF4701 0.0 29.9 1.0
CB A:CYS51 2.0 30.1 1.0
S1 A:SF4701 2.2 28.8 1.0
S3 A:SF4701 2.3 29.1 1.0
S2 A:SF4701 2.3 30.0 1.0
FE3 A:SF4701 2.7 30.1 1.0
FE2 A:SF4701 2.7 29.1 1.0
FE1 A:SF4701 2.8 28.5 1.0
SG A:CYS51 3.0 29.9 1.0
CA A:CYS51 3.4 29.9 1.0
N A:CYS51 3.6 28.9 1.0
S4 A:SF4701 3.8 30.4 1.0
C A:CYS51 4.2 30.4 1.0
C A:HIS50 4.3 29.1 1.0
O A:CYS51 4.4 30.6 1.0
N A:GLY54 4.4 31.1 1.0
CG A:MET199 4.4 32.2 1.0
CB A:GLN53 4.6 30.5 1.0
OE1 A:GLN53 4.7 30.3 1.0
O A:HIS50 4.7 28.5 1.0
N A:HIS50 4.8 28.4 1.0
CB A:MET199 4.9 31.8 1.0
SG A:CYS70 4.9 30.1 1.0
N A:GLN53 4.9 31.3 1.0
CA A:GLY54 4.9 31.1 1.0
SG A:CYS56 5.0 32.6 1.0
C A:GLN53 5.0 31.0 1.0
SG A:CYS48 5.0 28.9 1.0

Iron binding site 5 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 5 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:33.9
occ:1.00
 FE1 A:FES702 0.0 33.9 1.0
S2 A:FES702 2.2 34.8 1.0
S1 A:FES702 2.2 37.6 1.0
SG A:CYS47 2.4 33.5 1.0
FE2 A:FES702 2.7 38.5 1.0
CB A:CYS47 3.3 34.2 1.0
CA A:CYS47 4.7 33.6 1.0
CB A:PRO55 4.8 33.6 1.0
CB A:PHE41 4.8 38.2 1.0
CD A:ARG49 4.9 31.5 1.0
SG A:CYS39 5.0 39.4 1.0

Iron binding site 6 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 6 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:38.5
occ:1.00
 FE2 A:FES702 0.0 38.5 1.0
S2 A:FES702 2.2 34.8 1.0
S1 A:FES702 2.2 37.6 1.0
SG A:CYS39 2.5 39.4 1.0
FE1 A:FES702 2.7 33.9 1.0
CB A:CYS39 3.4 41.5 1.0
N A:GLY42 4.1 36.7 1.0
CB A:PHE41 4.1 38.2 1.0
C2 A:EDO705 4.3 43.3 1.0
CD2 A:PHE41 4.4 40.4 1.0
O2 A:EDO705 4.6 43.5 0.5
CA A:GLY42 4.7 35.3 1.0
SG A:CYS47 4.8 33.5 1.0
CG A:PHE41 4.8 39.2 1.0
CA A:CYS39 4.8 39.9 1.0
CB A:CYS47 4.8 34.2 1.0
C A:PHE41 5.0 36.7 1.0
CA A:PHE41 5.0 37.5 1.0

Iron binding site 7 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 7 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:43.1
occ:0.60
 FE1 A:XCC703 0.0 43.1 0.6
SG A:CYS476 2.1 37.9 1.0
FE A:FE704 2.1 43.3 0.4
S3 A:XCC703 2.3 43.8 0.7
S4 A:XCC703 2.3 40.5 0.7
S2 A:XCC703 2.3 44.8 0.7
FE4 A:XCC703 2.6 49.7 0.7
FE3 A:XCC703 2.8 46.1 0.7
CB A:CYS476 3.0 34.5 1.0
FE2 A:XCC703 3.5 48.4 0.7
N A:CYS476 3.6 34.0 1.0
SG A:CYS294 3.8 41.8 0.2
CA A:CYS476 3.9 34.1 1.0
O A:GLY445 4.0 34.0 1.0
NI A:XCC703 4.0 43.6 0.7
CB A:CYS446 4.0 34.5 1.0
CA A:CYS446 4.1 34.8 1.0
S1 A:XCC703 4.1 57.9 0.7
C A:GLY445 4.4 34.1 1.0
SG A:CYS294 4.6 40.1 0.8
N A:CYS446 4.6 34.3 1.0
CB A:SER312 4.6 35.2 1.0
C A:GLY475 4.7 33.3 1.0
SG A:CYS295 4.7 40.2 1.0
OG A:SER312 4.8 34.8 1.0
SG A:CYS333 4.8 50.7 1.0
SG A:CYS446 4.8 35.8 1.0

Iron binding site 8 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 8 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:48.4
occ:0.70
 FE2 A:XCC703 0.0 48.4 0.7
NE2 A:HIS261 2.1 42.1 1.0
S3 A:XCC703 2.3 43.8 0.7
NI A:XCC703 2.6 43.6 0.7
SG A:CYS295 2.8 40.2 1.0
FE4 A:XCC703 3.0 49.7 0.7
CE1 A:HIS261 3.1 42.1 1.0
CD2 A:HIS261 3.1 40.9 1.0
S1 A:XCC703 3.1 57.9 0.7
NZ A:LYS563 3.2 40.5 1.0
S4 A:XCC703 3.3 40.5 0.7
CB A:CYS526 3.5 35.5 1.0
FE1 A:XCC703 3.5 43.1 0.6
CB A:CYS295 3.9 42.1 1.0
FE3 A:XCC703 4.0 46.1 0.7
SG A:CYS294 4.1 41.8 0.2
ND1 A:HIS261 4.2 41.2 1.0
SG A:CYS526 4.2 38.0 1.0
CG A:HIS261 4.2 40.8 1.0
FE A:FE704 4.2 43.3 0.4
O A:HOH906 4.4 36.1 1.0
SG A:CYS333 4.6 50.7 1.0
CE A:LYS563 4.6 37.4 1.0
N A:CYS526 4.7 33.7 1.0
CA A:CYS526 4.7 33.0 1.0
S2 A:XCC703 4.8 44.8 0.7
N A:CYS295 4.9 42.0 1.0
CA A:CYS295 5.0 42.1 1.0

Iron binding site 9 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 9 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:46.1
occ:0.70
 FE3 A:XCC703 0.0 46.1 0.7
S1 A:XCC703 2.2 57.9 0.7
S4 A:XCC703 2.4 40.5 0.7
S2 A:XCC703 2.4 44.8 0.7
SG A:CYS446 2.4 35.8 1.0
FE4 A:XCC703 2.5 49.7 0.7
CB A:CYS446 2.8 34.5 1.0
NI A:XCC703 2.8 43.6 0.7
FE1 A:XCC703 2.8 43.1 0.6
O A:HOH906 3.0 36.1 1.0
CA A:CYS446 3.4 34.8 1.0
N A:CYS446 3.5 34.3 1.0
C A:GLY445 3.7 34.1 1.0
FE2 A:XCC703 4.0 48.4 0.7
S3 A:XCC703 4.0 43.8 0.7
O A:GLY445 4.0 34.0 1.0
SG A:CYS333 4.2 50.7 1.0
FE A:FE704 4.3 43.3 0.4
CE A:MET560 4.3 33.0 1.0
CA A:GLY445 4.3 32.6 1.0
CB A:HIS561 4.3 32.6 1.0
SG A:CYS476 4.8 37.9 1.0
C A:CYS446 4.9 34.2 1.0
CB A:CYS476 4.9 34.5 1.0
N A:HIS561 5.0 30.8 1.0

Iron binding site 10 out of 11 in 8x9e

Go back to Iron Binding Sites List in 8x9e
Iron binding site 10 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in Low Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:49.7
occ:0.70
 FE4 A:XCC703 0.0 49.7 0.7
SG A:CYS333 2.3 50.7 1.0
S3 A:XCC703 2.3 43.8 0.7
S2 A:XCC703 2.3 44.8 0.7
S1 A:XCC703 2.3 57.9 0.7
FE3 A:XCC703 2.5 46.1 0.7
FE1 A:XCC703 2.6 43.1 0.6
FE A:FE704 2.8 43.3 0.4
FE2 A:XCC703 3.0 48.4 0.7
CB A:CYS333 3.3 41.2 1.0
S4 A:XCC703 3.6 40.5 0.7
NI A:XCC703 3.6 43.6 0.7
CE1 A:HIS261 3.7 42.1 1.0
NE2 A:HIS261 3.7 42.1 1.0
SG A:CYS294 3.8 41.8 0.2
NZ A:LYS563 4.2 40.5 1.0
SG A:CYS476 4.5 37.9 1.0
O A:HOH906 4.5 36.1 1.0
CB A:CYS446 4.5 34.5 1.0
CE A:MET560 4.6 33.0 1.0
SG A:CYS446 4.6 35.8 1.0
CA A:CYS333 4.7 37.5 1.0
CB A:HIS561 4.9 32.6 1.0
SG A:CYS294 4.9 40.1 0.8
CE A:LYS563 4.9 37.4 1.0
ND1 A:HIS261 5.0 41.2 1.0

Reference:

S.M.Kim, S.H.Kang, J.Lee, Y.Heo, E.G.Poloniataki, J.Kang, H.J.Yoon, S.Y.Kong, Y.Yun, H.Kim, J.Ryu, H.H.Lee, Y.H.Kim. Identifying A Key Spot For Electron Mediator-Interaction to Tailor Co Dehydrogenase'S Affinity Nat Commun V. 15 2732 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-46909-1
Page generated: Sat Aug 10 19:57:08 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy