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Zinc in PDB 3kmc: Crystal Structure of Catalytic Domain of Tace with Tartrate-Based Inhibitor

Enzymatic activity of Crystal Structure of Catalytic Domain of Tace with Tartrate-Based Inhibitor

All present enzymatic activity of Crystal Structure of Catalytic Domain of Tace with Tartrate-Based Inhibitor:
3.4.24.86;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Tace with Tartrate-Based Inhibitor, PDB code: 3kmc was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.16 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.313, 76.103, 103.768, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Tace with Tartrate-Based Inhibitor (pdb code 3kmc). 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 Tace with Tartrate-Based Inhibitor, PDB code: 3kmc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3kmc

Go back to Zinc Binding Sites List in 3kmc
Zinc binding site 1 out of 2 in the Crystal Structure of Catalytic Domain of Tace with Tartrate-Based Inhibitor


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 Tace with Tartrate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:24.2
occ:1.00
NE2 A:HIS415 2.0 23.2 1.0
NE2 A:HIS405 2.1 21.9 1.0
NE2 A:HIS409 2.1 21.8 1.0
O4 A:INN485 2.1 24.3 1.0
O A:INN485 2.2 25.4 1.0
O A:HOH493 2.2 30.9 1.0
C A:INN485 2.8 25.9 1.0
CE1 A:HIS415 2.9 23.4 1.0
CD2 A:HIS405 3.0 22.4 1.0
CD2 A:HIS409 3.0 22.2 1.0
N A:INN485 3.0 26.8 1.0
CD2 A:HIS415 3.0 23.5 1.0
CE1 A:HIS405 3.1 21.5 1.0
CE1 A:HIS409 3.2 22.1 1.0
O A:HOH490 3.9 24.6 1.0
ND1 A:HIS415 4.1 24.5 1.0
CG A:HIS415 4.1 23.1 1.0
CG A:HIS405 4.2 21.2 1.0
CG A:HIS409 4.2 21.1 1.0
C0 A:INN485 4.2 27.3 1.0
ND1 A:HIS405 4.2 22.4 1.0
ND1 A:HIS409 4.3 22.2 1.0
O A:HOH167 4.4 20.9 1.0
OE1 A:GLU406 4.5 21.8 1.0
O A:HOH495 4.6 40.0 1.0
CA A:INN485 4.6 32.9 1.0
OE2 A:GLU406 4.6 21.2 1.0
CB A:INN485 4.7 29.9 1.0
CE A:MET435 4.8 18.9 1.0
CD A:GLU406 5.0 19.2 1.0

Zinc binding site 2 out of 2 in 3kmc

Go back to Zinc Binding Sites List in 3kmc
Zinc binding site 2 out of 2 in the Crystal Structure of Catalytic Domain of Tace with Tartrate-Based Inhibitor


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 Tace with Tartrate-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:24.0
occ:1.00
NE2 B:HIS415 2.1 24.9 1.0
O21 B:403485 2.1 29.3 1.0
NE2 B:HIS405 2.1 23.4 1.0
NE2 B:HIS409 2.1 24.0 1.0
O22 B:403485 2.3 30.1 1.0
O10 B:403485 2.4 39.4 1.0
C1 B:403485 2.8 34.6 1.0
C2 B:403485 2.9 38.8 1.0
CD2 B:HIS405 3.0 23.8 1.0
CD2 B:HIS415 3.0 24.6 1.0
CE1 B:HIS415 3.0 24.8 1.0
CD2 B:HIS409 3.1 24.5 1.0
C3 B:403485 3.1 32.6 1.0
CE1 B:HIS409 3.2 23.7 1.0
CE1 B:HIS405 3.2 23.0 1.0
O B:HOH562 4.0 31.5 1.0
N20 B:403485 4.1 31.4 1.0
C6 B:403485 4.1 33.4 1.0
CG B:HIS415 4.2 23.5 1.0
ND1 B:HIS415 4.2 25.4 1.0
CG B:HIS405 4.2 21.0 1.0
CG B:HIS409 4.2 23.2 1.0
N4 B:403485 4.2 39.1 1.0
ND1 B:HIS405 4.3 23.5 1.0
ND1 B:HIS409 4.3 24.4 1.0
O B:HOH553 4.4 41.5 1.0
OE2 B:GLU406 4.5 20.2 1.0
O B:HOH566 4.6 39.0 1.0
OE1 B:GLU406 4.6 22.0 1.0
CE B:MET435 4.8 20.9 1.0
CD B:GLU406 4.9 25.4 1.0

Reference:

K.E.Rosner, Z.Guo, P.Orth, G.W.Shipps, D.B.Belanger, T.Y.Chan, P.J.Curran, C.Dai, Y.Deng, V.M.Girijavallabhan, L.Hong, B.J.Lavey, J.F.Lee, D.Li, Z.Liu, J.Popovici-Muller, P.C.Ting, H.Vaccaro, L.Wang, T.Wang, W.Yu, G.Zhou, X.Niu, J.Sun, J.A.Kozlowski, D.J.Lundell, V.Madison, B.Mckittrick, J.J.Piwinski, N.Y.Shih, M.Arshad Siddiqui, C.O.Strickland. The Discovery of Novel Tartrate-Based Tnf-Alpha Converting Enzyme (Tace) Inhibitors. Bioorg.Med.Chem.Lett. V. 20 1189 2009.
ISSN: ISSN 0960-894X
PubMed: 20022498
DOI: 10.1016/J.BMCL.2009.12.004
Page generated: Sat Sep 26 11:11:37 2020
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