Atomistry » Nickel » PDB 2w94-2zpl » 2z8y
Atomistry »
  Nickel »
    PDB 2w94-2zpl »
      2z8y »

Nickel in PDB 2z8y: Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica

Enzymatic activity of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica

All present enzymatic activity of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica:
1.2.7.4; 1.2.99.2; 2.3.1.169;

Protein crystallography data

The structure of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica, PDB code: 2z8y was solved by T.I.Doukov, L.C.Blasiak, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 2.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.540, 136.600, 141.750, 101.29, 109.22, 103.91
R / Rfree (%) 17.8 / 25

Other elements in 2z8y:

The structure of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica also contains other interesting chemical elements:

Xenon (Xe) 42 atoms
Iron (Fe) 56 atoms
Copper (Cu) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica (pdb code 2z8y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica, PDB code: 2z8y:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 1 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni800

b:57.1
occ:1.00
 NI A:XCC800 0.0 57.1 1.0
SG A:CYS550 2.2 36.4 1.0
S4 A:XCC800 2.4 56.7 1.0
S1 A:XCC800 2.4 51.5 1.0
FE2 A:XCC800 2.9 37.6 1.0
FE3 A:XCC800 3.1 50.5 1.0
CB A:CYS550 3.3 22.9 1.0
FE1 A:XCC800 3.7 42.9 1.0
S3 A:XCC800 4.1 44.6 1.0
FE4 A:XCC800 4.2 48.5 1.0
NZ A:LYS587 4.3 17.4 1.0
OG A:SER585 4.3 9.9 1.0
O A:HOH1012 4.3 21.5 1.0
SG A:CYS317 4.4 23.7 1.0
S2 A:XCC800 4.4 49.0 1.0
NE2 A:HIS283 4.6 24.4 1.0
CA A:CYS550 4.6 21.0 1.0
CA A:GLY469 4.7 25.4 1.0
CB A:LYS587 4.9 12.9 1.0
CE A:LYS587 4.9 20.1 1.0
C A:GLY469 4.9 24.6 1.0
SG A:CYS470 4.9 27.1 1.0
CD A:LYS587 5.0 19.2 1.0

Nickel binding site 2 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 2 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni800

b:54.6
occ:1.00
 NI B:XCC800 0.0 54.6 1.0
SG B:CYS550 2.2 36.2 1.0
S4 B:XCC800 2.4 57.9 1.0
S1 B:XCC800 2.4 52.6 1.0
CB B:CYS550 3.0 19.3 1.0
FE2 B:XCC800 3.1 37.4 1.0
FE3 B:XCC800 3.2 52.7 1.0
NZ B:LYS587 3.7 17.4 1.0
FE1 B:XCC800 3.8 40.5 1.0
O B:HOH1023 4.1 20.2 1.0
S3 B:XCC800 4.3 45.5 1.0
FE4 B:XCC800 4.3 52.7 1.0
S2 B:XCC800 4.3 52.6 1.0
OG B:SER585 4.4 13.5 1.0
CA B:CYS550 4.4 19.6 1.0
CB B:LYS587 4.4 14.8 1.0
CE B:LYS587 4.5 18.1 1.0
NE2 B:HIS283 4.6 26.4 1.0
SG B:CYS317 4.6 19.6 1.0
CD B:LYS587 4.7 19.8 1.0
CD1 B:ILE591 4.7 12.8 1.0
CA B:GLY469 4.8 28.0 1.0

Nickel binding site 3 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 3 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni800

b:66.2
occ:1.00
 NI C:XCC800 0.0 66.2 1.0
SG C:CYS550 1.8 42.9 1.0
S4 C:XCC800 2.3 64.4 1.0
S1 C:XCC800 2.4 66.1 1.0
FE2 C:XCC800 3.2 40.0 1.0
FE3 C:XCC800 3.3 61.2 1.0
CB C:CYS550 3.4 27.0 1.0
O C:HOH1021 3.7 24.3 1.0
FE1 C:XCC800 4.1 53.2 1.0
FE4 C:XCC800 4.2 54.3 1.0
CA C:GLY469 4.3 27.3 1.0
CA C:CYS550 4.4 25.8 1.0
OG C:SER585 4.4 21.8 1.0
NZ C:LYS587 4.4 22.9 1.0
SG C:CYS317 4.5 27.1 1.0
S3 C:XCC800 4.5 52.5 1.0
S2 C:XCC800 4.6 59.5 1.0
SG C:CYS470 4.7 31.3 1.0
CB C:LYS587 4.8 21.4 1.0
N C:GLY469 4.8 26.5 1.0
CD1 C:ILE591 4.9 8.8 1.0
C C:GLY469 4.9 27.1 1.0
N C:CYS550 4.9 23.7 1.0
CE C:LYS587 4.9 27.2 1.0
CA C:GLY499 5.0 21.0 1.0
NE2 C:HIS283 5.0 24.9 1.0

Nickel binding site 4 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 4 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni800

b:69.2
occ:1.00
 NI D:XCC800 0.0 69.2 1.0
SG D:CYS550 2.1 39.0 1.0
S4 D:XCC800 2.4 69.2 1.0
S1 D:XCC800 2.4 66.6 1.0
FE2 D:XCC800 3.1 52.5 1.0
FE3 D:XCC800 3.2 61.9 1.0
CB D:CYS550 3.5 25.8 1.0
FE1 D:XCC800 3.7 57.0 1.0
O D:HOH1013 4.0 20.7 1.0
FE4 D:XCC800 4.2 61.3 1.0
S3 D:XCC800 4.2 57.0 1.0
NZ D:LYS587 4.5 25.0 1.0
CB D:LYS587 4.5 22.3 1.0
S2 D:XCC800 4.5 61.8 1.0
CD D:LYS587 4.5 23.0 1.0
SG D:CYS317 4.5 33.4 1.0
OG D:SER585 4.5 21.6 1.0
NE2 D:HIS283 4.6 32.8 1.0
CA D:CYS550 4.7 24.2 1.0
SG D:CYS470 4.8 32.6 1.0
CA D:GLY469 4.8 30.7 1.0
CE D:LYS587 4.9 27.3 1.0

Nickel binding site 5 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 5 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ni951

b:18.4
occ:1.00
 N M:CYS597 1.9 16.9 1.0
N M:GLY596 1.9 16.5 1.0
SG M:CYS597 2.1 20.9 1.0
SG M:CYS595 2.2 20.2 1.0
C M:GLY596 2.7 16.8 1.0
CA M:GLY596 2.7 16.5 1.0
CA M:CYS597 2.9 19.0 1.0
C M:CYS595 3.0 17.1 1.0
CU M:CU1950 3.0 30.4 1.0
CB M:CYS595 3.0 17.6 1.0
CB M:CYS597 3.1 18.6 1.0
CA M:CYS595 3.4 17.5 1.0
N M:PHE598 3.6 19.9 1.0
N M:CYS595 3.6 17.6 1.0
C M:CYS597 3.7 19.4 1.0
XE M:XE1008 3.8 31.0 0.8
O M:GLY596 3.9 18.3 1.0
CD1 M:LEU527 4.0 14.4 1.0
O M:CYS595 4.0 18.7 1.0
CD2 M:PHE598 4.4 23.9 1.0
CE2 M:PHE598 4.7 22.9 1.0
O M:CYS597 4.7 21.0 1.0
S3 M:SF4900 4.8 20.6 1.0
C M:SER594 4.9 18.6 1.0
CA M:PHE598 4.9 19.4 1.0
SG M:CYS509 4.9 21.9 1.0

Nickel binding site 6 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 6 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ni951

b:18.0
occ:1.00
 N N:CYS597 1.9 17.5 1.0
N N:GLY596 2.1 17.8 1.0
SG N:CYS597 2.1 18.9 1.0
SG N:CYS595 2.2 22.5 1.0
C N:GLY596 2.8 17.3 1.0
CA N:GLY596 2.8 17.7 1.0
CU N:CU1950 2.9 28.3 1.0
CA N:CYS597 3.0 16.2 1.0
CB N:CYS597 3.0 16.5 1.0
CB N:CYS595 3.1 20.7 1.0
C N:CYS595 3.2 19.8 1.0
CA N:CYS595 3.5 20.6 1.0
N N:PHE598 3.7 14.8 1.0
C N:CYS597 3.7 16.1 1.0
N N:CYS595 3.8 20.2 1.0
XE N:XE1009 3.8 34.8 0.7
CD1 N:LEU527 3.9 14.6 1.0
O N:GLY596 4.0 16.7 1.0
O N:CYS595 4.3 23.1 1.0
CD2 N:PHE598 4.3 16.3 1.0
O N:CYS597 4.7 16.9 1.0
CE2 N:PHE598 4.7 14.1 1.0
S3 N:SF4900 4.8 17.4 1.0
CA N:PHE598 4.9 15.6 1.0
C N:SER594 4.9 20.7 1.0
SG N:CYS509 5.0 17.6 1.0

Nickel binding site 7 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 7 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ni951

b:76.0
occ:1.00
 N O:CYS597 1.9 59.0 1.0
N O:GLY596 2.4 60.8 1.0
SG O:CYS597 2.5 55.8 1.0
SG O:CYS595 2.6 62.8 1.0
CU O:CU1950 2.7 88.5 1.0
CA O:CYS597 2.7 57.2 1.0
C O:GLY596 2.9 59.6 1.0
CB O:CYS597 3.0 57.0 1.0
N O:PHE598 3.1 55.9 1.0
CA O:GLY596 3.2 59.9 1.0
C O:CYS597 3.2 56.3 1.0
C O:CYS595 3.3 59.9 1.0
CD1 O:LEU527 3.3 53.9 1.0
CB O:CYS595 3.4 57.9 1.0
CA O:CYS595 3.5 59.1 1.0
N O:CYS595 3.6 58.3 1.0
O O:GLY596 4.0 59.8 1.0
CA O:PHE598 4.2 56.3 1.0
O O:CYS597 4.2 56.0 1.0
SG O:CYS509 4.3 46.3 1.0
CD2 O:PHE598 4.4 57.3 1.0
O O:CYS595 4.5 60.6 1.0
XE O:XE1009 4.5 42.3 0.4
CB O:PHE598 4.6 56.5 1.0
CG O:PHE598 4.6 57.5 1.0
S3 O:SF4900 4.6 60.0 1.0
CG O:LEU527 4.7 55.3 1.0
C O:SER594 4.7 58.3 1.0

Nickel binding site 8 out of 8 in 2z8y

Go back to Nickel Binding Sites List in 2z8y
Nickel binding site 8 out of 8 in the Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Xenon-Bound Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase(Codh/Acs) From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ni951

b:44.5
occ:1.00
 SG P:CYS595 2.0 41.3 1.0
N P:CYS597 2.0 34.6 1.0
SG P:CYS597 2.1 37.6 1.0
N P:GLY596 2.2 37.4 1.0
CB P:CYS597 2.8 32.9 1.0
C P:GLY596 2.9 34.2 1.0
CU P:CU1950 2.9 52.6 1.0
CA P:CYS597 2.9 33.6 1.0
CA P:GLY596 3.0 35.2 1.0
CB P:CYS595 3.1 39.9 1.0
C P:CYS595 3.2 38.4 1.0
XE P:XE1009 3.5 31.9 0.5
CA P:CYS595 3.6 39.8 1.0
C P:CYS597 3.8 32.8 1.0
N P:PHE598 3.9 31.4 1.0
N P:CYS595 4.0 39.8 1.0
CD1 P:LEU527 4.1 36.9 1.0
O P:GLY596 4.1 33.9 1.0
O P:CYS595 4.3 39.2 1.0
CD2 P:PHE598 4.7 23.4 1.0
O P:CYS597 4.8 33.8 1.0
S3 P:SF4900 4.8 33.5 1.0
SG P:CYS509 4.8 30.9 1.0
CE2 P:PHE598 4.9 27.7 1.0
CE1 P:PHE229 5.0 30.9 1.0
CD1 P:PHE229 5.0 30.7 1.0

Reference:

T.I.Doukov, L.C.Blasiak, J.Seravalli, S.W.Ragsdale, C.L.Drennan. Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase Biochemistry V. 47 3474 2008.
ISSN: ISSN 0006-2960
PubMed: 18293927
DOI: 10.1021/BI702386T
Page generated: Wed Dec 16 01:20:52 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