Zinc in PDB 6ok1: LTP2-CHSH2(DUF35) Aldolase

Protein crystallography data

The structure of LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1 was solved by M.S.Kimber, E.Mallette, R.Aggett, S.Y.K.Seah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.83 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.680, 110.560, 120.140, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 16.8

Other elements in 6ok1:

The structure of LTP2-CHSH2(DUF35) Aldolase also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the LTP2-CHSH2(DUF35) Aldolase (pdb code 6ok1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ok1

Go back to Zinc Binding Sites List in 6ok1
Zinc binding site 1 out of 2 in the LTP2-CHSH2(DUF35) Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:27.8
occ:1.00
SG B:CYS215 2.3 27.9 1.0
SG B:CYS229 2.3 28.3 1.0
SG B:CYS212 2.3 26.6 1.0
SG B:CYS226 2.4 24.4 1.0
H B:CYS215 3.0 34.0 1.0
HB2 B:CYS212 3.1 27.2 1.0
CB B:CYS212 3.1 22.6 1.0
HB3 B:CYS226 3.1 29.5 1.0
HB3 B:CYS212 3.1 27.2 1.0
HB3 B:CYS215 3.1 36.6 1.0
CB B:CYS226 3.2 24.5 1.0
HB3 B:CYS229 3.2 38.7 1.0
HB2 B:CYS226 3.2 29.5 1.0
CB B:CYS215 3.3 30.5 1.0
H B:CYS229 3.3 32.0 1.0
CB B:CYS229 3.4 32.2 1.0
HB3 B:ALA214 3.7 34.4 1.0
HB2 B:HIS228 3.7 30.8 1.0
N B:CYS215 3.7 28.4 1.0
HB3 B:SER231 3.8 34.1 1.0
N B:CYS229 3.8 26.6 1.0
CA B:CYS215 4.1 25.1 1.0
H B:SER231 4.1 32.4 1.0
HB2 B:CYS215 4.1 36.6 1.0
CA B:CYS229 4.1 31.4 1.0
HB2 B:CYS229 4.1 38.7 1.0
H B:THR217 4.3 31.3 1.0
HB B:THR217 4.3 34.1 1.0
H B:HIS228 4.4 32.0 1.0
H B:GLY230 4.5 31.5 1.0
H B:ALA214 4.5 36.9 1.0
HB2 B:SER231 4.6 34.1 1.0
CA B:CYS212 4.6 23.0 1.0
CB B:ALA214 4.6 28.7 1.0
CA B:CYS226 4.6 23.3 1.0
CB B:SER231 4.6 28.4 1.0
H B:LYS216 4.6 31.3 1.0
CB B:HIS228 4.6 25.7 1.0
HG1 B:THR217 4.7 34.7 1.0
C B:CYS215 4.7 32.4 1.0
C B:CYS229 4.8 33.5 1.0
C B:HIS228 4.8 35.1 1.0
C B:ALA214 4.8 32.2 1.0
N B:GLY230 4.8 26.2 1.0
HA B:CYS212 4.9 27.6 1.0
O B:HOH575 4.9 23.3 1.0
HA B:CYS215 4.9 30.2 1.0
N B:SER231 4.9 26.9 1.0
HD2 B:HIS228 4.9 82.1 1.0
N B:LYS216 4.9 26.1 1.0
HA B:CYS226 4.9 28.0 1.0
HB1 B:ALA214 5.0 34.4 1.0
HA B:CYS229 5.0 37.7 1.0

Zinc binding site 2 out of 2 in 6ok1

Go back to Zinc Binding Sites List in 6ok1
Zinc binding site 2 out of 2 in the LTP2-CHSH2(DUF35) Aldolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:36.2
occ:1.00
SG D:CYS229 2.3 40.7 1.0
SG D:CYS215 2.4 40.4 1.0
SG D:CYS212 2.4 36.4 1.0
SG D:CYS226 2.4 34.9 1.0
H D:CYS215 3.0 49.0 1.0
HB3 D:CYS229 3.0 54.2 1.0
HB3 D:CYS226 3.1 38.2 1.0
CB D:CYS226 3.2 31.8 1.0
H D:CYS229 3.2 46.9 1.0
HB3 D:CYS215 3.2 55.4 1.0
CB D:CYS229 3.2 45.2 1.0
HB2 D:CYS226 3.2 38.2 1.0
CB D:CYS212 3.3 33.4 1.0
HB2 D:CYS212 3.3 40.1 1.0
HB3 D:CYS212 3.3 40.1 1.0
CB D:CYS215 3.4 46.2 1.0
HB3 D:ALA214 3.6 61.2 1.0
HB2 D:HIS228 3.7 46.8 1.0
N D:CYS215 3.7 40.8 1.0
N D:CYS229 3.7 39.1 1.0
HB3 D:SER231 3.8 45.7 1.0
H D:SER231 4.0 41.8 1.0
CA D:CYS229 4.0 34.8 1.0
HB2 D:CYS229 4.0 54.2 1.0
CA D:CYS215 4.1 43.8 1.0
HB2 D:CYS215 4.2 55.4 1.0
H D:THR217 4.4 47.2 1.0
H D:ALA214 4.5 52.4 1.0
H D:HIS228 4.5 37.5 1.0
CB D:ALA214 4.5 51.0 1.0
H D:GLY230 4.5 43.2 1.0
HB D:THR217 4.5 43.5 1.0
CA D:CYS226 4.6 31.3 1.0
C D:CYS229 4.6 43.9 1.0
CB D:SER231 4.6 38.1 1.0
CB D:HIS228 4.6 39.0 1.0
HB2 D:SER231 4.6 45.7 1.0
H D:LYS216 4.7 53.4 1.0
C D:HIS228 4.7 43.2 1.0
CA D:CYS212 4.7 39.0 1.0
N D:GLY230 4.8 36.0 1.0
HG1 D:THR217 4.8 49.7 1.0
N D:SER231 4.8 34.8 1.0
C D:ALA214 4.8 55.1 1.0
C D:CYS215 4.8 40.6 1.0
HB1 D:ALA214 4.8 61.2 1.0
HA D:CYS229 4.9 41.7 1.0
HD2 D:HIS228 4.9 99.7 1.0
O D:HOH537 4.9 32.6 1.0
HA D:CYS215 4.9 52.5 1.0
HA D:CYS226 5.0 37.6 1.0
N D:LYS216 5.0 44.5 1.0

Reference:

R.Aggett, E.Mallette, S.E.Gilbert, M.A.Vachon, K.L.Schroeter, M.S.Kimber, S.Y.K.Seah. The Steroid Side-Chain-Cleaving Aldolase LTP2-CHSH2DUF35IS A Thiolase Superfamily Member with A Radically Repurposed Active Site. J.Biol.Chem. V. 294 11934 2019.
ISSN: ESSN 1083-351X
PubMed: 31209106
DOI: 10.1074/JBC.RA119.008889
Page generated: Wed Dec 16 12:26:44 2020

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