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Nickel in PDB 1jqk: Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum

Enzymatic activity of Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum

All present enzymatic activity of Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum:
1.2.99.2;

Protein crystallography data

The structure of Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum, PDB code: 1jqk was solved by C.L.Drennan, J.Heo, M.D.Sintchak, E.Schreiter, P.W.Ludden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.600, 200.100, 116.800, 90.00, 111.50, 90.00
R / Rfree (%) 25.7 / 28.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum (pdb code 1jqk). 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 Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum, PDB code: 1jqk:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 1jqk

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Nickel binding site 1 out of 6 in the Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum


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 Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni800

b:68.9
occ:1.00
NI A:WCC800 0.0 68.9 1.0
UNK A:UNX802 1.8 68.2 1.0
SG A:CYS531 2.2 71.1 1.0
S1 A:WCC800 2.2 68.7 1.0
S4 A:WCC800 2.3 66.0 1.0
S3 A:WCC800 2.6 65.9 1.0
FE A:FE2801 2.6 71.8 1.0
FE3 A:WCC800 2.7 68.2 1.0
FE4 A:WCC800 2.8 68.5 1.0
FE1 A:WCC800 2.9 67.4 1.0
S2 A:WCC800 3.9 67.3 1.0
CB A:CYS531 4.0 69.4 1.0
NE2 A:HIS265 4.1 69.4 1.0
SG A:CYS300 4.1 71.3 1.0
SG A:CYS451 4.5 71.9 1.0
SG A:CYS338 4.8 56.4 1.0
CE1 A:HIS265 4.8 70.8 1.0
OG A:SER566 4.8 51.8 1.0
CE A:LYS568 4.9 37.9 1.0
SG A:CYS481 4.9 68.1 1.0
O A:GLY450 4.9 66.7 1.0
NZ A:LYS568 5.0 40.4 1.0

Nickel binding site 2 out of 6 in 1jqk

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Nickel binding site 2 out of 6 in the Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum


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 Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni800

b:70.7
occ:1.00
NI B:WCC800 0.0 70.7 1.0
UNK B:UNX802 1.9 69.0 1.0
SG B:CYS531 2.2 73.3 1.0
S4 B:WCC800 2.3 66.9 1.0
S1 B:WCC800 2.3 65.8 1.0
S3 B:WCC800 2.5 71.6 1.0
FE B:FE2801 2.5 75.3 1.0
FE3 B:WCC800 2.7 67.1 1.0
FE1 B:WCC800 2.8 66.9 1.0
FE4 B:WCC800 2.9 69.5 1.0
S2 B:WCC800 4.0 69.4 1.0
CB B:CYS531 4.0 71.5 1.0
NE2 B:HIS265 4.0 72.8 1.0
SG B:CYS300 4.1 74.1 1.0
SG B:CYS451 4.6 66.7 1.0
SG B:CYS338 4.7 63.2 1.0
CE1 B:HIS265 4.8 74.2 1.0
CE B:LYS568 4.8 50.9 1.0
OG B:SER566 4.9 53.7 1.0
NZ B:LYS568 4.9 49.4 1.0
SG B:CYS481 5.0 67.2 1.0
O B:GLY450 5.0 61.5 1.0

Nickel binding site 3 out of 6 in 1jqk

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Nickel binding site 3 out of 6 in the Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum


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 Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni800

b:41.7
occ:1.00
NI C:WCC800 0.0 41.7 1.0
UNK C:UNX802 1.8 38.6 1.0
S4 C:WCC800 2.2 38.3 1.0
SG C:CYS531 2.2 43.1 1.0
S1 C:WCC800 2.2 37.3 1.0
FE3 C:WCC800 2.6 40.5 1.0
S3 C:WCC800 2.6 41.3 1.0
FE C:FE2801 2.6 44.8 1.0
FE1 C:WCC800 2.9 35.5 1.0
FE4 C:WCC800 2.9 37.9 1.0
S2 C:WCC800 3.9 40.4 1.0
CB C:CYS531 4.0 39.6 1.0
NE2 C:HIS265 4.0 42.2 1.0
SG C:CYS300 4.2 41.1 1.0
SG C:CYS451 4.6 38.6 1.0
SG C:CYS338 4.8 29.9 1.0
OG C:SER566 4.8 34.4 1.0
CE1 C:HIS265 4.8 40.7 1.0
CE C:LYS568 4.9 26.9 1.0
SG C:CYS481 4.9 41.8 1.0
O C:GLY450 4.9 39.1 1.0
NZ C:LYS568 5.0 26.2 1.0

Nickel binding site 4 out of 6 in 1jqk

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Nickel binding site 4 out of 6 in the Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum


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 Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni800

b:49.3
occ:1.00
NI D:WCC800 0.0 49.3 1.0
UNK D:UNX802 1.8 48.2 1.0
S1 D:WCC800 2.2 45.4 1.0
SG D:CYS531 2.2 48.4 1.0
S4 D:WCC800 2.3 45.9 1.0
FE3 D:WCC800 2.6 44.5 1.0
S3 D:WCC800 2.7 43.8 1.0
FE D:FE2801 2.7 46.4 1.0
FE4 D:WCC800 2.9 46.2 1.0
FE1 D:WCC800 2.9 43.3 1.0
CB D:CYS531 3.9 45.6 1.0
S2 D:WCC800 4.0 44.7 1.0
NE2 D:HIS265 4.1 43.7 1.0
SG D:CYS300 4.2 38.5 1.0
SG D:CYS451 4.6 42.2 1.0
OG D:SER566 4.8 38.5 1.0
SG D:CYS338 4.8 38.0 1.0
CE D:LYS568 4.8 32.8 1.0
CE1 D:HIS265 4.9 41.2 1.0
SG D:CYS481 5.0 47.5 1.0
O D:GLY450 5.0 34.2 1.0

Nickel binding site 5 out of 6 in 1jqk

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Nickel binding site 5 out of 6 in the Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum


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 Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni800

b:49.0
occ:1.00
NI E:WCC800 0.0 49.0 1.0
UNK E:UNX802 1.8 46.5 1.0
S1 E:WCC800 2.2 44.1 1.0
SG E:CYS531 2.2 49.4 1.0
S4 E:WCC800 2.2 45.1 1.0
FE E:FE2801 2.6 47.3 1.0
FE3 E:WCC800 2.6 45.8 1.0
S3 E:WCC800 2.6 40.6 1.0
FE4 E:WCC800 2.8 46.2 1.0
FE1 E:WCC800 2.9 43.6 1.0
S2 E:WCC800 3.9 44.0 1.0
CB E:CYS531 4.0 44.9 1.0
NE2 E:HIS265 4.1 46.4 1.0
SG E:CYS300 4.2 42.4 1.0
SG E:CYS451 4.5 41.8 1.0
SG E:CYS338 4.8 41.8 1.0
OG E:SER566 4.8 35.2 1.0
CE E:LYS568 4.9 25.8 1.0
O E:GLY450 4.9 32.0 1.0
CE1 E:HIS265 4.9 48.2 1.0
SG E:CYS481 5.0 44.1 1.0

Nickel binding site 6 out of 6 in 1jqk

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Nickel binding site 6 out of 6 in the Crystal Structure of Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum


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 Carbon Monoxide Dehydrogenase From Rhodospirillum Rubrum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni800

b:48.3
occ:1.00
NI F:WCC800 0.0 48.3 1.0
UNK F:UNX802 1.9 43.0 1.0
SG F:CYS531 2.2 48.7 1.0
S1 F:WCC800 2.3 44.1 1.0
S4 F:WCC800 2.3 41.2 1.0
FE F:FE2801 2.5 45.0 1.0
S3 F:WCC800 2.5 45.9 1.0
FE3 F:WCC800 2.7 45.4 1.0
FE1 F:WCC800 2.8 43.8 1.0
FE4 F:WCC800 2.8 43.5 1.0
S2 F:WCC800 3.9 44.6 1.0
CB F:CYS531 4.0 42.4 1.0
NE2 F:HIS265 4.0 45.5 1.0
SG F:CYS300 4.2 39.2 1.0
SG F:CYS451 4.6 41.0 1.0
SG F:CYS338 4.8 35.5 1.0
CE1 F:HIS265 4.8 44.6 1.0
CE F:LYS568 4.8 17.2 1.0
OG F:SER566 4.9 27.9 1.0
SG F:CYS481 4.9 46.8 1.0
NZ F:LYS568 4.9 20.9 1.0
O F:GLY450 5.0 36.0 1.0

Reference:

C.L.Drennan, J.Heo, M.D.Sintchak, E.Schreiter, P.W.Ludden. Life on Carbon Monoxide: X-Ray Structure of Rhodospirillum Rubrum Ni-Fe-S Carbon Monoxide Dehydrogenase. Proc.Natl.Acad.Sci.Usa V. 98 11973 2001.
ISSN: ISSN 0027-8424
PubMed: 11593006
DOI: 10.1073/PNAS.211429998
Page generated: Fri Sep 25 07:56:07 2020
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