Atomistry » Nickel » PDB 6lv5-6r3z » 6n95
Atomistry »
  Nickel »
    PDB 6lv5-6r3z »
      6n95 »

Nickel in PDB 6n95: Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa

Protein crystallography data

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa, PDB code: 6n95 was solved by L.M.Stunkard, A.D.Dixon, T.J.Huth, J.R.Lohman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.927, 114.421, 193.430, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.2

Other elements in 6n95:

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa also contains other interesting chemical elements:

Potassium (K) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa (pdb code 6n95). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa, PDB code: 6n95:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6n95

Go back to Nickel Binding Sites List in 6n95
Nickel binding site 1 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:41.8
occ:1.00
NE2 B:HIS220 2.0 41.9 1.0
NE2 A:HIS220 2.0 35.7 1.0
NE2 C:HIS220 2.2 34.4 1.0
O C:HOH557 2.4 44.8 1.0
O B:HOH571 2.5 48.7 1.0
CE1 B:HIS220 2.9 45.3 1.0
CE1 C:HIS220 3.0 38.6 1.0
CE1 A:HIS220 3.0 41.9 1.0
CD2 A:HIS220 3.1 34.1 1.0
CD2 B:HIS220 3.1 36.1 1.0
CD2 C:HIS220 3.2 37.4 1.0
ND1 B:HIS220 4.0 40.1 1.0
ND1 C:HIS220 4.1 40.3 1.0
ND1 A:HIS220 4.1 38.3 1.0
CG B:HIS220 4.1 31.0 1.0
CG A:HIS220 4.2 28.0 1.0
CG C:HIS220 4.2 30.0 1.0
O A:HOH634 4.5 58.7 1.0
O B:HOH543 4.7 33.2 1.0
O B:HOH558 4.7 36.6 1.0
O A:HOH553 4.8 37.0 1.0
O C:HOH670 4.9 45.3 1.0
O C:HOH464 4.9 36.7 1.0
O C:HOH440 5.0 33.8 1.0
O A:HOH570 5.0 36.8 1.0

Nickel binding site 2 out of 2 in 6n95

Go back to Nickel Binding Sites List in 6n95
Nickel binding site 2 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:39.5
occ:1.00
NE2 D:HIS220 2.1 34.6 1.0
NE2 E:HIS220 2.1 35.1 1.0
NE2 F:HIS220 2.1 37.8 1.0
O F:HOH608 2.4 43.7 1.0
CE1 D:HIS220 2.9 39.5 1.0
CE1 E:HIS220 3.0 40.6 1.0
CE1 F:HIS220 3.0 45.4 1.0
CD2 E:HIS220 3.2 32.1 1.0
CD2 F:HIS220 3.2 34.2 1.0
CD2 D:HIS220 3.2 38.1 1.0
ND1 D:HIS220 4.0 43.0 1.0
ND1 E:HIS220 4.1 39.4 1.0
ND1 F:HIS220 4.2 42.2 1.0
CG E:HIS220 4.2 29.8 1.0
CG D:HIS220 4.2 31.3 1.0
CG F:HIS220 4.3 28.9 1.0
O E:HOH658 4.8 42.9 1.0
O E:HOH499 4.8 37.5 1.0
O D:HOH504 4.8 39.5 1.0
O F:HOH615 4.9 53.6 1.0
O F:HOH552 4.9 31.4 1.0
O E:HOH653 4.9 42.9 1.0

Reference:

L.M.Stunkard, A.D.Dixon, T.J.Huth, J.R.Lohman. Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-Coa Decarboxylase Structure-Function Studies. J. Am. Chem. Soc. V. 141 5121 2019.
ISSN: ESSN 1520-5126
PubMed: 30869886
DOI: 10.1021/JACS.9B00650
Page generated: Wed Dec 16 01:52:52 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