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Nickel in PDB 9gyb: Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli

Enzymatic activity of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli

All present enzymatic activity of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli, PDB code: 9gyb was solved by C.Cavazza, U.Contaldo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.71 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.45, 200.573, 116.37, 90, 111.21, 90
R / Rfree (%) 22.7 / 28.8

Other elements in 9gyb:

The structure of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli also contains other interesting chemical elements:

Sodium (Na) 1 atom
Iron (Fe) 60 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli (pdb code 9gyb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli, PDB code: 9gyb:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 9gyb

Go back to Nickel Binding Sites List in 9gyb
Nickel binding site 1 out of 6 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni702

b:97.6
occ:0.48
 NI A:RQM702 0.0 97.6 0.5
S1 A:RQM702 2.3 80.5 0.5
S4 A:RQM702 2.3 78.2 0.5
FE3 A:RQM702 2.4 95.5 0.5
FE2 A:RQM702 2.6 72.2 0.5
SG A:CYS531 2.9 96.6 1.0
FE1 A:RQM702 3.2 90.2 0.5
FE4 A:RQM702 3.6 76.7 0.5
S3 A:RQM702 3.6 83.9 0.5
NZ A:LYS568 3.8 84.5 1.0
O A:GLY450 3.9 65.5 1.0
CE A:LYS568 4.1 80.2 1.0
S2 A:RQM702 4.2 87.1 0.5
CB A:CYS451 4.2 86.7 1.0
SG A:CYS451 4.3 79.8 1.0
C A:GLY450 4.4 62.5 1.0
CA A:CYS451 4.5 80.3 1.0
CB A:CYS531 4.6 62.8 1.0
N A:CYS451 4.6 73.5 1.0
OG A:SER566 4.7 67.0 1.0
SG A:CYS300 4.9 76.7 1.0
N A:CYS481 4.9 64.0 1.0

Nickel binding site 2 out of 6 in 9gyb

Go back to Nickel Binding Sites List in 9gyb
Nickel binding site 2 out of 6 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni703

b:97.5
occ:0.50
 NI B:RQM703 0.0 97.5 0.5
S1 B:RQM703 2.3 69.6 0.5
S4 B:RQM703 2.3 62.8 0.5
FE3 B:RQM703 2.4 84.6 0.5
FE2 B:RQM703 2.5 76.3 0.5
SG B:CYS531 3.1 86.3 1.0
FE1 B:RQM703 3.3 76.4 0.5
FE4 B:RQM703 3.5 76.3 0.5
S3 B:RQM703 3.7 74.9 0.5
NZ B:LYS568 3.8 74.5 1.0
CB B:CYS531 4.0 75.5 1.0
S2 B:RQM703 4.3 70.9 0.5
SG B:CYS451 4.4 65.5 1.0
C B:GLY450 4.4 67.6 1.0
CB B:CYS451 4.4 86.9 1.0
N B:CYS451 4.5 70.1 1.0
OG B:SER566 4.5 65.5 1.0
CA B:CYS451 4.6 80.7 1.0
O B:GLY450 4.6 71.9 1.0
SG B:CYS300 4.7 76.2 1.0
CA B:GLY450 4.8 73.4 1.0
CE B:LYS568 5.0 64.4 1.0

Nickel binding site 3 out of 6 in 9gyb

Go back to Nickel Binding Sites List in 9gyb
Nickel binding site 3 out of 6 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni703

b:108.4
occ:0.51
 NI C:RQM703 0.0 108.4 0.5
SG C:CYS531 2.0 91.9 1.0
S4 C:RQM703 2.3 71.7 0.5
S1 C:RQM703 2.3 88.6 0.5
FE2 C:RQM703 2.6 83.1 0.5
FE3 C:RQM703 2.9 98.6 0.5
FE1 C:RQM703 3.2 94.2 0.5
S3 C:RQM703 3.3 90.8 0.5
CB C:CYS531 3.5 66.3 1.0
FE4 C:RQM703 3.6 92.9 0.5
SG C:CYS300 3.8 86.1 1.0
NE2 C:HIS265 3.9 83.9 1.0
CE C:LYS568 4.2 72.2 1.0
S2 C:RQM703 4.5 84.7 0.5
CA C:CYS531 4.6 67.3 1.0
CE1 C:HIS265 4.7 78.7 1.0
N C:CYS531 4.7 67.6 1.0
CD2 C:HIS265 4.8 78.6 1.0
NZ C:LYS568 4.9 64.8 1.0
SG C:CYS338 4.9 64.9 1.0
CB C:CYS451 4.9 89.8 1.0

Nickel binding site 4 out of 6 in 9gyb

Go back to Nickel Binding Sites List in 9gyb
Nickel binding site 4 out of 6 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni702

b:107.6
occ:0.50
 NI D:RQM702 0.0 107.6 0.5
SG D:CYS531 2.0 113.2 1.0
S1 D:RQM702 2.3 69.8 0.5
S4 D:RQM702 2.3 73.4 0.5
FE2 D:RQM702 2.6 61.7 0.5
FE3 D:RQM702 2.6 94.2 0.5
FE1 D:RQM702 3.2 84.3 0.5
S3 D:RQM702 3.5 79.3 0.5
CB D:CYS531 3.5 73.6 1.0
FE4 D:RQM702 3.6 93.3 0.5
CE D:LYS568 4.0 92.1 1.0
SG D:CYS300 4.2 70.7 1.0
NE2 D:HIS265 4.3 86.6 1.0
S2 D:RQM702 4.4 79.1 0.5
CD D:LYS568 4.5 79.4 1.0
CA D:CYS531 4.5 70.3 1.0
SG D:CYS451 4.6 82.4 1.0
OG D:SER566 4.7 67.0 1.0
CB D:CYS451 4.7 82.9 1.0
CE1 D:HIS265 5.0 79.3 1.0
O D:GLY450 5.0 60.5 1.0
CB D:LYS568 5.0 55.7 1.0

Nickel binding site 5 out of 6 in 9gyb

Go back to Nickel Binding Sites List in 9gyb
Nickel binding site 5 out of 6 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni703

b:125.1
occ:0.49
 NI E:RQM703 0.0 125.1 0.5
SG E:CYS531 2.0 118.1 1.0
S1 E:RQM703 2.3 113.5 0.5
S4 E:RQM703 2.3 97.2 0.5
FE3 E:RQM703 2.6 115.4 0.5
FE2 E:RQM703 2.6 84.7 0.5
FE1 E:RQM703 3.0 99.4 0.5
S3 E:RQM703 3.3 105.4 0.5
SG E:CYS300 3.4 102.9 1.0
NZ E:LYS568 3.4 93.4 1.0
FE4 E:RQM703 3.4 115.1 0.5
CB E:CYS531 3.5 97.5 1.0
S2 E:RQM703 4.2 105.3 0.5
SG E:CYS451 4.4 109.1 1.0
CA E:CYS531 4.4 97.3 1.0
NE2 E:HIS265 4.5 98.7 1.0
CE1 E:HIS265 4.5 99.4 1.0
N E:CYS531 4.7 101.7 1.0
CA E:GLY480 4.7 97.7 1.0
N E:CYS481 4.7 111.7 1.0
CE E:LYS568 4.7 89.3 1.0
CB E:CYS300 4.8 97.7 1.0

Nickel binding site 6 out of 6 in 9gyb

Go back to Nickel Binding Sites List in 9gyb
Nickel binding site 6 out of 6 in the Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of the Recombinant Codh From Rhodopspirillum Rubrum Produced in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni702

b:118.2
occ:0.49
 NI F:RQM702 0.0 118.2 0.5
NZ F:LYS568 2.0 104.0 1.0
S4 F:RQM702 2.3 92.9 0.5
S1 F:RQM702 2.3 111.6 0.5
FE3 F:RQM702 2.6 97.5 0.5
FE2 F:RQM702 2.6 103.6 0.5
SG F:CYS531 3.0 95.7 1.0
CE F:LYS568 3.2 95.6 1.0
FE1 F:RQM702 3.2 115.1 0.5
S3 F:RQM702 3.6 104.1 0.5
OG F:SER566 3.7 101.2 1.0
FE4 F:RQM702 3.7 114.0 0.5
SG F:CYS338 4.0 102.3 1.0
NE2 F:HIS265 4.2 108.6 1.0
S2 F:RQM702 4.3 106.9 0.5
CD F:LYS568 4.3 88.2 1.0
CE1 F:HIS265 4.4 107.9 1.0
SG F:CYS451 4.4 111.5 1.0
CB F:SER566 4.5 96.3 1.0
CB F:LYS568 4.6 85.9 1.0
CB F:CYS531 4.8 109.2 1.0
CB F:CYS451 4.9 115.5 1.0

Reference:

U.Contaldo, B.Guigliarelli, J.Perard, T.Pichon, A.Le Goff, C.Cavazza. Insights Into the Role of the D-Cluster in [Nife]-Codh From Rhodospirillum Rubrum. Chemistry 03648 2025.
ISSN: ISSN 0947-6539
PubMed: 39912726
DOI: 10.1002/CHEM.202403648
Page generated: Tue Feb 25 11:46:41 2025

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