Iron in PDB 8x9g: Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv

Enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv

All present enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv, PDB code: 8x9g 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) 35.32 / 3.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.613, 75.437, 72.176, 90, 111.85, 90
R / Rfree (%) 22.9 / 27.2

Other elements in 8x9g:

The structure of Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv (pdb code 8x9g). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv, PDB code: 8x9g:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 8x9g

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Iron binding site 1 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:36.0
occ:1.00
 FE1 A:SF4701 0.0 36.0 1.0
S2 A:SF4701 2.3 45.8 1.0
S3 A:SF4701 2.3 54.8 1.0
S4 A:SF4701 2.3 46.9 1.0
SG A:CYS70 2.6 45.6 1.0
FE4 A:SF4701 2.7 49.6 1.0
FE3 A:SF4701 2.7 43.4 1.0
FE2 A:SF4701 2.7 49.5 1.0
CB A:CYS70 3.5 46.4 1.0
S1 A:SF4701 3.9 52.7 1.0
N A:CYS70 4.1 45.1 1.0
CG A:MET199 4.3 49.1 1.0
CA A:CYS70 4.4 47.7 1.0
CB A:CYS51 4.4 56.0 1.0
NH2 A:ARG80 4.6 48.4 1.0
SG A:CYS56 4.6 49.5 1.0
SG A:CYS51 4.6 52.1 1.0
N A:ILE69 4.9 44.8 1.0
CB A:MET199 5.0 47.8 1.0

Iron binding site 2 out of 10 in 8x9g

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Iron binding site 2 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:49.5
occ:1.00
 FE2 A:SF4701 0.0 49.5 1.0
S1 A:SF4701 2.3 52.7 1.0
S3 A:SF4701 2.3 54.8 1.0
S4 A:SF4701 2.3 46.9 1.0
FE3 A:SF4701 2.7 43.4 1.0
FE4 A:SF4701 2.7 49.6 1.0
FE1 A:SF4701 2.7 36.0 1.0
SG A:CYS48 2.8 57.2 1.0
CB A:CYS48 3.6 55.2 1.0
N A:HIS50 3.8 55.9 1.0
S2 A:SF4701 3.9 45.8 1.0
NH2 A:ARG80 3.9 48.4 1.0
CB A:CYS51 4.1 56.0 1.0
CB A:HIS50 4.2 54.9 1.0
N A:CYS51 4.3 48.5 1.0
CA A:HIS50 4.3 57.9 1.0
C A:HIS50 4.3 54.3 1.0
C A:CYS48 4.4 56.5 1.0
O A:CYS48 4.5 53.9 1.0
N A:ARG49 4.6 57.2 1.0
CA A:CYS48 4.7 56.7 1.0
SG A:CYS56 4.7 49.5 1.0
C A:ARG49 4.7 56.1 1.0
CG A:HIS50 4.7 55.5 1.0
CZ A:ARG80 4.7 51.0 1.0
CA A:CYS51 4.8 53.5 1.0
O A:HIS50 4.9 54.7 1.0
CA A:ARG49 4.9 56.0 1.0
NH1 A:ARG80 4.9 53.5 1.0
SG A:CYS70 5.0 45.6 1.0

Iron binding site 3 out of 10 in 8x9g

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Iron binding site 3 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:43.4
occ:1.00
 FE3 A:SF4701 0.0 43.4 1.0
SG A:CYS56 2.1 49.5 1.0
S4 A:SF4701 2.3 46.9 1.0
S2 A:SF4701 2.3 45.8 1.0
S1 A:SF4701 2.3 52.7 1.0
FE2 A:SF4701 2.7 49.5 1.0
FE1 A:SF4701 2.7 36.0 1.0
FE4 A:SF4701 2.7 49.6 1.0
CB A:CYS56 2.9 45.0 1.0
S3 A:SF4701 3.9 54.8 1.0
CA A:CYS56 4.2 54.1 1.0
N A:ILE69 4.3 44.8 1.0
N A:CYS56 4.4 55.4 1.0
O A:CYS48 4.5 53.9 1.0
CB A:CYS48 4.5 55.2 1.0
SG A:CYS70 4.5 45.6 1.0
O A:GLY54 4.6 53.0 1.0
CA A:GLY68 4.7 43.9 1.0
SG A:CYS48 4.8 57.2 1.0
CB A:CYS51 4.8 56.0 1.0
CB A:ILE69 4.9 38.0 1.0
C A:CYS48 5.0 56.5 1.0
C A:GLY68 5.0 43.3 1.0

Iron binding site 4 out of 10 in 8x9g

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Iron binding site 4 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:49.6
occ:1.00
 FE4 A:SF4701 0.0 49.6 1.0
CB A:CYS51 2.1 56.0 1.0
S3 A:SF4701 2.3 54.8 1.0
S1 A:SF4701 2.3 52.7 1.0
S2 A:SF4701 2.3 45.8 1.0
FE1 A:SF4701 2.7 36.0 1.0
FE2 A:SF4701 2.7 49.5 1.0
FE3 A:SF4701 2.7 43.4 1.0
SG A:CYS51 3.0 52.1 1.0
CA A:CYS51 3.5 53.5 1.0
N A:CYS51 3.8 48.5 1.0
S4 A:SF4701 3.9 46.9 1.0
SG A:CYS56 3.9 49.5 1.0
O A:GLY54 4.0 53.0 1.0
CB A:GLN53 4.1 46.9 1.0
C A:CYS51 4.2 51.7 1.0
O A:CYS51 4.4 49.9 1.0
C A:HIS50 4.5 54.3 1.0
N A:GLN53 4.5 52.3 1.0
C A:GLN53 4.6 47.2 1.0
CA A:GLN53 4.6 50.4 1.0
N A:GLY54 4.8 52.4 1.0
N A:HIS50 4.9 55.9 1.0
O A:HIS50 4.9 54.7 1.0
O A:GLN53 4.9 43.5 1.0
N A:LEU52 5.0 53.2 1.0

Iron binding site 5 out of 10 in 8x9g

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Iron binding site 5 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:49.0
occ:1.00
 FE1 A:FES702 0.0 49.0 1.0
SG A:CYS47 2.1 56.7 1.0
S2 A:FES702 2.2 63.1 1.0
S1 A:FES702 2.2 68.2 1.0
FE2 A:FES702 2.7 77.1 1.0
CB A:CYS47 3.1 51.5 1.0
CA A:CYS47 4.5 54.5 1.0
CB A:PHE41 4.8 62.3 1.0
CD A:ARG49 4.8 59.1 1.0
N A:GLY42 4.9 51.1 1.0
SG A:CYS39 4.9 60.2 1.0

Iron binding site 6 out of 10 in 8x9g

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Iron binding site 6 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:77.1
occ:1.00
 FE2 A:FES702 0.0 77.1 1.0
S2 A:FES702 2.2 63.1 1.0
S1 A:FES702 2.2 68.2 1.0
SG A:CYS39 2.5 60.2 1.0
FE1 A:FES702 2.7 49.0 1.0
CB A:CYS39 3.2 57.5 1.0
N A:GLY42 4.0 51.1 1.0
CB A:PHE41 4.3 62.3 1.0
CA A:GLY42 4.4 54.6 1.0
SG A:CYS47 4.6 56.7 1.0
CA A:CYS39 4.7 57.8 1.0
C1 A:PGE704 4.7 56.4 1.0
CD2 A:PHE41 4.8 62.7 1.0
CB A:CYS47 4.9 51.5 1.0
C A:PHE41 4.9 53.0 1.0

Iron binding site 7 out of 10 in 8x9g

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Iron binding site 7 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:51.8
occ:0.80
 FE1 A:XCC703 0.0 51.8 0.8
S3 A:XCC703 2.3 51.0 0.8
S4 A:XCC703 2.3 50.9 0.8
S2 A:XCC703 2.3 51.1 0.8
SG A:CYS476 2.4 73.4 1.0
FE4 A:XCC703 2.7 53.4 0.8
FE3 A:XCC703 2.9 51.6 0.8
CB A:CYS476 3.2 68.3 1.0
FE2 A:XCC703 3.6 52.7 0.8
N A:CYS476 3.9 62.5 1.0
CA A:CYS476 4.1 62.1 1.0
SG A:CYS295 4.1 82.2 1.0
SG A:CYS294 4.1 69.1 1.0
S1 A:XCC703 4.1 51.2 0.8
NI A:XCC703 4.2 53.5 0.8
CB A:SER312 4.3 63.3 1.0
CA A:CYS446 4.4 68.8 1.0
SG A:CYS526 4.5 90.2 1.0
CB A:CYS446 4.7 72.9 1.0
SG A:CYS333 4.7 85.5 1.0
CB A:CYS333 4.8 74.8 1.0
C A:GLY475 4.9 61.2 1.0
OG A:SER312 4.9 62.9 1.0
SG A:CYS446 5.0 74.7 1.0
O A:GLY445 5.0 64.7 1.0
NE2 A:HIS261 5.0 74.5 1.0

Iron binding site 8 out of 10 in 8x9g

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Iron binding site 8 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:52.7
occ:0.80
 FE2 A:XCC703 0.0 52.7 0.8
S3 A:XCC703 2.3 51.0 0.8
NE2 A:HIS261 2.3 74.5 1.0
SG A:CYS295 2.3 82.2 1.0
SG A:CYS526 2.4 90.2 1.0
CD2 A:HIS261 3.1 71.9 1.0
FE4 A:XCC703 3.1 53.4 0.8
NZ A:LYS563 3.1 70.3 1.0
NI A:XCC703 3.2 53.5 0.8
CE1 A:HIS261 3.4 74.1 1.0
CB A:CYS526 3.4 68.3 1.0
S4 A:XCC703 3.4 50.9 0.8
CB A:CYS295 3.5 60.6 1.0
S1 A:XCC703 3.5 51.2 0.8
FE1 A:XCC703 3.6 51.8 0.8
CG A:HIS261 4.3 67.5 1.0
FE3 A:XCC703 4.3 51.6 0.8
ND1 A:HIS261 4.4 70.5 1.0
N A:CYS526 4.5 61.4 1.0
CE A:LYS563 4.5 61.0 1.0
CA A:CYS526 4.5 60.8 1.0
N A:CYS295 4.7 64.7 1.0
CA A:CYS295 4.7 61.5 1.0
SG A:CYS333 4.8 85.5 1.0
S2 A:XCC703 5.0 51.1 0.8

Iron binding site 9 out of 10 in 8x9g

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Iron binding site 9 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:51.6
occ:0.80
 FE3 A:XCC703 0.0 51.6 0.8
SG A:CYS446 2.2 74.7 1.0
S1 A:XCC703 2.3 51.2 0.8
S4 A:XCC703 2.3 50.9 0.8
S2 A:XCC703 2.4 51.1 0.8
FE4 A:XCC703 2.7 53.4 0.8
CB A:CYS446 2.7 72.9 1.0
NI A:XCC703 2.8 53.5 0.8
FE1 A:XCC703 2.9 51.8 0.8
CA A:CYS446 3.1 68.8 1.0
N A:CYS446 3.6 66.6 1.0
SG A:CYS333 4.0 85.5 1.0
C A:GLY445 4.1 65.1 1.0
S3 A:XCC703 4.2 51.0 0.8
FE2 A:XCC703 4.3 52.7 0.8
CB A:HIS561 4.5 55.8 1.0
C A:CYS446 4.5 63.0 1.0
O A:GLY445 4.5 64.7 1.0
CE A:MET560 4.6 60.2 1.0
SG A:CYS526 4.6 90.2 1.0
CB A:CYS476 4.6 68.3 1.0
SG A:CYS476 4.6 73.4 1.0
N A:ASN447 4.9 60.4 1.0
N A:HIS561 4.9 56.6 1.0
CA A:GLY445 5.0 57.6 1.0

Iron binding site 10 out of 10 in 8x9g

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Iron binding site 10 out of 10 in the Crystal Structure of Co Dehydrogenase Mutant in Complex with Bv


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 in Complex with Bv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:53.4
occ:0.80
 FE4 A:XCC703 0.0 53.4 0.8
SG A:CYS333 2.2 85.5 1.0
S3 A:XCC703 2.3 51.0 0.8
S2 A:XCC703 2.4 51.1 0.8
S1 A:XCC703 2.4 51.2 0.8
FE3 A:XCC703 2.7 51.6 0.8
FE1 A:XCC703 2.7 51.8 0.8
CB A:CYS333 2.9 74.8 1.0
FE2 A:XCC703 3.1 52.7 0.8
S4 A:XCC703 3.5 50.9 0.8
NE2 A:HIS261 3.5 74.5 1.0
CE1 A:HIS261 3.7 74.1 1.0
NI A:XCC703 3.7 53.5 0.8
NZ A:LYS563 3.9 70.3 1.0
CA A:CYS333 4.3 64.2 1.0
SG A:CYS446 4.5 74.7 1.0
CE A:LYS563 4.6 61.0 1.0
SG A:CYS294 4.6 69.1 1.0
SG A:CYS526 4.7 90.2 1.0
SG A:CYS295 4.8 82.2 1.0
ND1 A:HIS561 4.8 51.0 1.0
N A:CYS333 4.8 63.8 1.0
CD2 A:HIS261 4.9 71.9 1.0
SG A:CYS476 4.9 73.4 1.0
ND1 A:HIS261 5.0 70.5 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 19:57:17 2024

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