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Zinc in PDB 5w8i: Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc

Enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc

All present enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc, PDB code: 5w8i was solved by C.M.Lukacs, J.Abendroth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.840, 80.430, 119.620, 90.00, 117.73, 90.00
R / Rfree (%) 14.9 / 18.8

Other elements in 5w8i:

The structure of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc (pdb code 5w8i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc, PDB code: 5w8i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5w8i

Go back to Zinc Binding Sites List in 5w8i
Zinc binding site 1 out of 5 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


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 Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:23.6
occ:1.00
 N19 A:9YD403 2.0 20.6 1.0
NE2 A:HIS192 2.1 21.5 1.0
O14 A:9YD403 2.1 23.5 1.0
O A:HOH684 2.2 19.3 1.0
O21 A:9YD403 2.3 18.4 1.0
C18 A:9YD403 2.8 20.1 1.0
CD2 A:HIS192 3.0 21.5 1.0
C20 A:9YD403 3.0 19.2 1.0
C15 A:9YD403 3.0 21.6 1.0
CE1 A:HIS192 3.1 22.2 1.0
C12 A:9YD403 3.1 23.7 1.0
N11 A:9YD403 3.4 23.1 1.0
C17 A:9YD403 4.1 20.9 1.0
CG A:HIS192 4.1 20.4 1.0
ND1 A:HIS192 4.1 20.7 1.0
O22 A:9YD403 4.2 18.5 1.0
O A:HOH567 4.3 29.1 1.0
CA A:GLY193 4.3 22.6 1.0
CB A:ALA237 4.4 31.7 1.0
C13 A:9YD403 4.5 25.4 1.0
S16 A:9YD403 4.5 21.1 1.0
NH2 A:ARG168 4.6 16.6 1.0
OD1 A:ASN137 4.7 26.8 1.0
N10 A:9YD403 4.8 22.3 1.0
O A:HOH603 4.8 20.1 1.0
N A:GLY193 4.8 19.9 1.0
O A:HOH517 4.9 29.3 1.0

Zinc binding site 2 out of 5 in 5w8i

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Zinc binding site 2 out of 5 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


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 Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:26.3
occ:1.00
 O6 C:CIT403 2.1 23.7 1.0
O1 C:CIT403 2.1 25.1 1.0
O5 A:CIT404 2.1 25.6 1.0
O7 C:CIT403 2.1 24.6 1.0
O4 A:CIT404 2.2 25.1 1.0
O7 A:CIT404 2.2 23.7 1.0
C6 C:CIT403 2.7 25.4 1.0
C6 A:CIT404 2.7 25.5 1.0
C3 A:CIT404 2.8 25.7 1.0
C3 C:CIT403 3.0 25.4 1.0
C1 C:CIT403 3.1 25.3 1.0
C5 A:CIT404 3.1 24.1 1.0
C4 A:CIT404 3.4 23.8 1.0
C2 C:CIT403 3.5 24.7 1.0
O A:HOH509 3.6 25.1 1.0
O5 C:CIT403 3.8 25.3 1.0
O6 A:CIT404 3.9 24.7 1.0
O A:LEU182 4.1 16.5 1.0
O C:LEU182 4.2 17.0 1.0
C2 A:CIT404 4.2 25.1 1.0
C4 C:CIT403 4.2 26.4 1.0
O3 A:CIT404 4.2 20.4 1.0
O2 C:CIT403 4.3 23.1 1.0
CD2 C:LEU182 4.4 18.1 1.0
CD2 A:LEU182 4.4 18.1 1.0
CE1 A:HIS185 4.5 20.9 1.0
CE1 C:HIS185 4.6 18.6 1.0

Zinc binding site 3 out of 5 in 5w8i

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Zinc binding site 3 out of 5 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:22.6
occ:1.00
 NE2 C:HIS192 2.0 19.2 1.0
N19 C:9YD402 2.0 20.5 1.0
O C:HOH668 2.1 16.9 1.0
O14 C:9YD402 2.1 22.7 1.0
O21 C:9YD402 2.3 17.7 1.0
C18 C:9YD402 2.9 20.5 1.0
CD2 C:HIS192 2.9 19.8 1.0
C20 C:9YD402 3.0 18.8 1.0
CE1 C:HIS192 3.1 19.4 1.0
C15 C:9YD402 3.1 20.7 1.0
C12 C:9YD402 3.1 21.9 1.0
N11 C:9YD402 3.4 21.7 1.0
CG C:HIS192 4.1 19.2 1.0
ND1 C:HIS192 4.1 19.4 1.0
C17 C:9YD402 4.2 21.5 1.0
O22 C:9YD402 4.2 17.8 1.0
CA C:GLY193 4.4 20.6 1.0
C13 C:9YD402 4.4 22.6 1.0
O C:HOH597 4.4 23.7 1.0
CB C:ALA237 4.5 33.1 1.0
NH2 C:ARG168 4.5 17.2 1.0
S16 C:9YD402 4.6 20.9 1.0
OD1 C:ASN137 4.6 27.4 1.0
O C:HOH563 4.7 29.7 1.0
N10 C:9YD402 4.8 20.9 1.0
N C:GLY193 4.9 19.2 1.0

Zinc binding site 4 out of 5 in 5w8i

Go back to Zinc Binding Sites List in 5w8i
Zinc binding site 4 out of 5 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:21.9
occ:1.00
 O5 B:CIT402 2.0 19.5 1.0
O6 D:CIT404 2.1 20.1 1.0
O7 B:CIT402 2.1 20.5 1.0
O4 D:CIT404 2.1 20.3 1.0
O1 B:CIT402 2.1 19.3 1.0
O7 D:CIT404 2.2 18.1 1.0
C6 B:CIT402 2.7 22.1 1.0
C6 D:CIT404 2.7 20.6 1.0
C3 D:CIT404 2.9 20.1 1.0
C3 B:CIT402 3.0 21.8 1.0
C1 B:CIT402 3.1 21.1 1.0
C5 D:CIT404 3.1 20.4 1.0
O D:HOH503 3.4 16.7 1.0
C4 D:CIT404 3.5 19.6 1.0
C2 B:CIT402 3.5 20.7 1.0
O6 B:CIT402 3.8 23.7 1.0
O5 D:CIT404 3.9 21.8 1.0
O D:LEU182 4.1 12.3 1.0
O B:LEU182 4.1 12.0 1.0
C2 D:CIT404 4.2 21.1 1.0
C4 B:CIT402 4.2 22.9 1.0
O3 D:CIT404 4.3 19.8 1.0
O2 B:CIT402 4.3 18.4 1.0
CD2 B:LEU182 4.5 12.0 1.0
CD2 D:LEU182 4.5 13.2 1.0
CE1 B:HIS185 4.5 13.2 1.0
CE1 D:HIS185 4.6 12.4 1.0
NH1 D:ARG170 5.0 10.8 1.0

Zinc binding site 5 out of 5 in 5w8i

Go back to Zinc Binding Sites List in 5w8i
Zinc binding site 5 out of 5 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 23 and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:18.0
occ:1.00
 N19 D:9YD403 2.0 18.0 1.0
NE2 D:HIS192 2.1 14.0 1.0
O D:HOH687 2.1 15.7 1.0
O22 D:9YD403 2.2 13.3 1.0
O14 D:9YD403 2.2 16.1 1.0
C18 D:9YD403 2.9 16.6 1.0
C20 D:9YD403 3.0 15.1 1.0
C15 D:9YD403 3.0 18.5 1.0
CD2 D:HIS192 3.0 13.9 1.0
CE1 D:HIS192 3.1 13.7 1.0
C12 D:9YD403 3.1 18.2 1.0
N11 D:9YD403 3.4 19.2 1.0
O D:HOH621 3.9 27.9 1.0
C17 D:9YD403 4.1 17.1 1.0
ND1 D:HIS192 4.1 13.7 1.0
CG D:HIS192 4.2 13.8 1.0
CB D:ALA237 4.2 29.0 1.0
OD1 D:ASN137 4.2 19.9 1.0
O21 D:9YD403 4.2 14.2 1.0
CA D:GLY193 4.4 14.2 1.0
O D:HOH611 4.4 24.5 1.0
O D:HOH537 4.4 36.7 1.0
C13 D:9YD403 4.4 19.3 1.0
S16 D:9YD403 4.5 18.6 1.0
N10 D:9YD403 4.7 19.5 1.0
NH2 D:ARG168 4.8 11.3 1.0
N D:GLY193 4.9 13.2 1.0

Reference:

G.Rai, K.R.Brimacombe, B.T.Mott, D.J.Urban, X.Hu, S.M.Yang, T.D.Lee, D.M.Cheff, J.Kouznetsova, G.A.Benavides, K.Pohida, E.J.Kuenstner, D.K.Luci, C.M.Lukacs, D.R.Davies, D.M.Dranow, H.Zhu, G.Sulikowski, W.J.Moore, G.M.Stott, A.J.Flint, M.D.Hall, V.M.Darley-Usmar, L.M.Neckers, C.V.Dang, A.G.Waterson, A.Simeonov, A.Jadhav, D.J.Maloney. Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (Ldh). J. Med. Chem. V. 60 9184 2017.
ISSN: ISSN 1520-4804
PubMed: 29120638
DOI: 10.1021/ACS.JMEDCHEM.7B00941
Page generated: Mon Oct 28 13:55:25 2024

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