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Nickel in PDB 1ru3: Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans

Protein crystallography data

The structure of Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans, PDB code: 1ru3 was solved by V.Svetlitchnyi, H.Dobbek, W.Meyer-Klaucke, T.Meins, B.Thiele, P.Rmer, R.Huber, O.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 200.310, 200.310, 169.410, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 27.4

Other elements in 1ru3:

The structure of Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans (pdb code 1ru3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans, PDB code: 1ru3:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1ru3

Go back to Nickel Binding Sites List in 1ru3
Nickel binding site 1 out of 2 in the Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans


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 Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni734

b:53.5
occ:1.00
SG A:CYS600 2.2 40.3 1.0
SG A:CYS512 2.2 45.8 1.0
SG A:CYS598 2.3 41.0 1.0
FE4 A:SF4733 2.7 46.4 1.0
O A:HOH736 2.7 46.1 1.0
S1 A:SF4733 2.9 48.1 1.0
NI A:NI735 3.0 39.3 1.0
CB A:CYS600 3.4 33.4 1.0
CB A:CYS512 3.4 41.6 1.0
CB A:CYS598 3.5 36.7 1.0
CZ A:PHE515 3.8 36.0 1.0
CE1 A:PHE515 4.2 52.1 1.0
N A:CYS600 4.2 28.7 1.0
S2 A:SF4733 4.4 47.5 1.0
CA A:CYS600 4.4 33.9 1.0
FE3 A:SF4733 4.5 48.8 1.0
CB A:CYS531 4.6 32.5 1.0
N A:GLY599 4.6 26.0 1.0
S3 A:SF4733 4.6 46.6 1.0
FE2 A:SF4733 4.7 47.7 1.0
CA A:CYS512 4.8 38.5 1.0
CA A:CYS598 4.8 38.5 1.0
CE2 A:PHE515 4.9 46.9 1.0
CD1 A:LEU530 4.9 46.6 1.0

Nickel binding site 2 out of 2 in 1ru3

Go back to Nickel Binding Sites List in 1ru3
Nickel binding site 2 out of 2 in the Crystal Structure of the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans


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 Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni735

b:39.3
occ:1.00
N A:CYS600 1.9 28.7 1.0
N A:GLY599 1.9 26.0 1.0
SG A:CYS600 2.1 40.3 1.0
SG A:CYS598 2.1 41.0 1.0
C A:GLY599 2.7 31.1 1.0
CA A:GLY599 2.8 26.5 1.0
CB A:CYS598 2.9 36.7 1.0
CA A:CYS600 2.9 33.9 1.0
CB A:CYS600 2.9 33.4 1.0
C A:CYS598 2.9 31.0 1.0
NI A:NI734 3.0 53.5 1.0
CA A:CYS598 3.2 38.5 1.0
N A:CYS598 3.5 39.9 1.0
N A:PHE601 3.6 42.2 1.0
C A:CYS600 3.6 51.7 1.0
CD1 A:LEU530 3.8 46.6 1.0
CZ A:PHE515 3.8 36.0 1.0
O A:GLY599 3.9 41.1 1.0
O A:CYS598 4.1 39.2 1.0
CE2 A:PHE515 4.2 46.9 1.0
S1 A:SF4733 4.6 48.1 1.0
O A:CYS600 4.7 39.0 1.0
C A:SER597 4.8 45.5 1.0
SG A:CYS512 4.8 45.8 1.0
CD2 A:PHE601 4.8 36.3 1.0
CA A:PHE601 4.9 45.6 1.0

Reference:

V.Svetlitchnyi, H.Dobbek, W.Meyer-Klaucke, T.Meins, B.Thiele, P.Rmer, R.Huber, O.Meyer. A Functional Ni-Ni-[4FE-4S] Cluster in the Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans Proc.Natl.Acad.Sci.Usa V. 101 446 2004.
ISSN: ISSN 0027-8424
PubMed: 14699043
DOI: 10.1073/PNAS.0304262101
Page generated: Wed Dec 16 01:15:09 2020

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