Zinc in PDB 6ktq: Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa

Enzymatic activity of Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa

All present enzymatic activity of Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa:
2.3.3.14;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa, PDB code: 6ktq was solved by T.Suzuki, T.Tomita, T.Kuzuyama, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 125.71 / 1.98
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.693, 114.693, 125.713, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa (pdb code 6ktq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa, PDB code: 6ktq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ktq

Go back to Zinc Binding Sites List in 6ktq
Zinc binding site 1 out of 2 in the Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:30.6
occ:0.30
 OE1 A:GLU20 2.2 31.7 1.0
O5 A:AKG402 2.2 53.2 1.0
NE2 A:HIS205 2.2 32.6 1.0
NE2 A:HIS207 2.3 27.4 1.0
O A:HOH631 2.4 29.7 1.0
O1 A:AKG402 2.5 60.0 1.0
C2 A:AKG402 2.8 60.4 1.0
C1 A:AKG402 3.0 58.9 1.0
CD A:GLU20 3.1 28.2 1.0
CD2 A:HIS205 3.1 33.7 1.0
CE1 A:HIS205 3.2 32.6 1.0
CD2 A:HIS207 3.2 27.1 1.0
CE1 A:HIS207 3.3 27.2 1.0
OE2 A:GLU20 3.4 27.2 1.0
O A:HOH625 3.9 29.4 1.0
C3 A:AKG402 4.1 54.8 1.0
O2 A:AKG402 4.3 61.6 1.0
CG A:HIS205 4.3 31.8 1.0
ND1 A:HIS205 4.3 33.1 1.0
C4 A:AKG402 4.3 48.2 1.0
CG2 A:ILE241 4.3 23.7 1.0
CG A:GLU20 4.3 26.2 1.0
ND1 A:HIS207 4.4 27.8 1.0
CG A:HIS207 4.4 25.4 1.0
NH1 A:ARG19 4.5 33.9 1.0
NH2 A:ARG19 4.5 33.9 1.0

Zinc binding site 2 out of 2 in 6ktq

Go back to Zinc Binding Sites List in 6ktq
Zinc binding site 2 out of 2 in the Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Catalytic Domain of Homocitrate Synthase From Sulfolobus Acidocaldarius (Sahcs(Dram)) in Complex with Alpha- Ketoglutarate/ZN2+/Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:35.8
occ:0.30
 OE1 B:GLU20 2.1 35.5 1.0
NE2 B:HIS205 2.2 39.0 1.0
O2 B:AKG404 2.3 66.6 1.0
NE2 B:HIS207 2.3 38.4 1.0
O B:HOH603 2.4 40.2 1.0
O5 B:AKG404 2.8 79.1 1.0
CD B:GLU20 3.0 29.4 1.0
CD2 B:HIS205 3.0 38.5 1.0
C1 B:AKG404 3.1 70.6 1.0
C2 B:AKG404 3.1 72.7 1.0
CE1 B:HIS205 3.3 40.1 1.0
CE1 B:HIS207 3.3 37.0 1.0
CD2 B:HIS207 3.3 33.7 1.0
OE2 B:GLU20 3.4 29.2 1.0
O B:HOH613 4.0 30.8 1.0
CG B:GLU20 4.2 26.7 1.0
CG B:HIS205 4.2 35.8 1.0
C3 B:AKG404 4.2 63.7 1.0
C4 B:AKG404 4.2 57.5 1.0
O1 B:AKG404 4.3 67.3 1.0
CG2 B:ILE241 4.3 27.2 1.0
ND1 B:HIS205 4.3 39.1 1.0
NH1 B:ARG19 4.3 46.2 1.0
ND1 B:HIS207 4.4 36.9 1.0
CG B:HIS207 4.4 34.1 1.0
NH2 B:ARG19 4.6 44.8 1.0
CB B:GLU20 4.9 27.0 1.0
CZ B:ARG19 5.0 44.0 1.0

Reference:

T.Suzuki, T.Tomita, K.Hirayama, M.Suzuki, T.Kuzuyama, M.Nishiyama. Involvement of Subdomain II in the Recognition of Acetyl-Coa Revealed By the Crystal Structure of Homocitrate Synthase From Sulfolobus Acidocaldarius. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32897601
DOI: 10.1111/FEBS.15527
Page generated: Wed Dec 16 12:10:00 2020

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