Atomistry » Nickel » PDB 3qsi-3tsn » 3s2x
Atomistry »
  Nickel »
    PDB 3qsi-3tsn »
      3s2x »

Nickel in PDB 3s2x: Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain

Enzymatic activity of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain

All present enzymatic activity of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain:
2.3.1.169;

Protein crystallography data

The structure of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain, PDB code: 3s2x was solved by P.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.60 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 129.040, 129.040, 46.030, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 26.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain (pdb code 3s2x). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain, PDB code: 3s2x:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3s2x

Go back to Nickel Binding Sites List in 3s2x
Nickel binding site 1 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni200

b:61.9
occ:1.00
N A:CYS4 1.9 55.2 1.0
SG A:CYS2 2.2 57.8 1.0
N A:GLY3 2.2 59.0 1.0
SG A:CYS4 2.4 57.1 1.0
CA A:CYS4 2.8 53.8 1.0
CB A:CYS4 2.8 54.2 1.0
C A:GLY3 2.9 57.6 1.0
CB A:CYS2 2.9 59.1 1.0
CA A:GLY3 3.1 57.9 1.0
C A:CYS2 3.2 59.4 1.0
N A:PHE5 3.4 51.7 1.0
CA A:CYS2 3.5 60.4 1.0
C A:CYS4 3.5 53.0 1.0
NI A:NI201 3.6 66.8 1.0
N A:CYS2 3.8 62.2 1.0
O A:HOH139 3.8 46.0 1.0
O A:GLY3 4.0 58.4 1.0
CD1 A:PHE5 4.1 53.8 1.0
O A:CYS2 4.4 61.3 1.0
CE1 A:PHE5 4.6 54.4 1.0
O A:CYS4 4.6 53.0 1.0
CA A:PHE5 4.6 51.8 1.0
CG A:PHE5 4.9 53.2 1.0
CB A:PHE5 4.9 51.8 1.0
C A:SER1 5.0 63.2 1.0

Nickel binding site 2 out of 4 in 3s2x

Go back to Nickel Binding Sites List in 3s2x
Nickel binding site 2 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:66.8
occ:1.00
N A:CYS2 2.1 62.2 1.0
N A:SER1 2.2 61.1 1.0
SG A:CYS2 2.4 57.8 1.0
O A:HOH139 2.7 46.0 1.0
CA A:SER1 2.8 62.9 1.0
C A:SER1 2.8 63.2 1.0
CA A:CYS2 3.2 60.4 1.0
CB A:CYS2 3.4 59.1 1.0
CD1 A:PHE5 3.5 53.8 1.0
NI A:NI200 3.6 61.9 1.0
O A:SER1 4.0 64.4 1.0
C A:CYS2 4.1 59.4 1.0
N A:GLY3 4.1 59.0 1.0
CB A:SER1 4.2 63.5 1.0
CE1 A:PHE5 4.2 54.4 1.0
O A:GLY53 4.4 53.6 1.0
CG A:PHE5 4.4 53.2 1.0
CB A:PHE5 4.5 51.8 1.0
SG A:CYS4 4.7 57.1 1.0
N A:PHE5 4.8 51.7 1.0
OG A:SER1 4.9 64.3 1.0
C A:GLY53 5.0 54.1 1.0

Nickel binding site 3 out of 4 in 3s2x

Go back to Nickel Binding Sites List in 3s2x
Nickel binding site 3 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni202

b:61.6
occ:1.00
N B:CYS4 2.1 57.3 1.0
SG B:CYS2 2.2 60.5 1.0
SG B:CYS4 2.4 61.2 1.0
N B:GLY3 2.4 59.8 1.0
CB B:CYS4 2.9 56.1 1.0
CA B:CYS4 2.9 56.0 1.0
CB B:CYS2 3.0 60.8 1.0
C B:GLY3 3.1 58.0 1.0
CA B:GLY3 3.3 58.4 1.0
C B:CYS2 3.3 61.2 1.0
N B:PHE5 3.4 53.4 1.0
NI B:NI203 3.4 70.9 1.0
CA B:CYS2 3.4 62.0 1.0
C B:CYS4 3.6 54.4 1.0
N B:CYS2 3.6 65.0 1.0
CD1 B:PHE5 4.0 53.9 1.0
O B:GLY3 4.2 57.2 1.0
O B:CYS2 4.4 61.4 1.0
CE1 B:PHE5 4.6 54.2 1.0
CA B:PHE5 4.7 53.7 1.0
O B:CYS4 4.7 52.8 1.0
CG B:PHE5 4.9 53.3 1.0
C B:SER1 4.9 66.4 1.0

Nickel binding site 4 out of 4 in 3s2x

Go back to Nickel Binding Sites List in 3s2x
Nickel binding site 4 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni203

b:70.9
occ:1.00
N B:SER1 2.1 66.4 1.0
N B:CYS2 2.2 65.0 1.0
SG B:CYS2 2.4 60.5 1.0
CA B:SER1 2.9 66.5 1.0
C B:SER1 2.9 66.4 1.0
CA B:CYS2 3.3 62.0 1.0
CB B:CYS2 3.3 60.8 1.0
CD1 B:PHE5 3.4 53.9 1.0
NI B:NI202 3.4 61.6 1.0
O B:SER1 4.0 68.2 1.0
CE1 B:PHE5 4.1 54.2 1.0
N B:GLY3 4.1 59.8 1.0
C B:CYS2 4.2 61.2 1.0
CB B:SER1 4.3 68.2 1.0
CG B:PHE5 4.4 53.3 1.0
CB B:PHE5 4.5 53.2 1.0
O B:GLY53 4.5 48.1 1.0
SG B:CYS4 4.5 61.2 1.0
N B:PHE5 4.7 53.4 1.0

Reference:

Y.Liu, F.Wang, P.Li, X.Tan. Insights Into the Mechanistic Role of the [Fe(4) S(4) ] Cubane in the A-Cluster {[Fe(4) S(4) ]-(Sr)-[Ni(P) Ni(D) ]} of Acetyl-Coenzyme A Synthase. Chembiochem V. 12 1417 2011.
ISSN: ISSN 1439-4227
PubMed: 21626638
DOI: 10.1002/CBIC.201100101
Page generated: Wed Dec 16 01:27:37 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