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Zinc in PDB 4kjv: Crystal Structure of Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone Inhibitor.

Protein crystallography data

The structure of Crystal Structure of Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone Inhibitor., PDB code: 4kjv was solved by C.M.Lukacs, C.A.Janson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.13 / 1.70
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 74.196, 74.196, 108.564, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone Inhibitor. (pdb code 4kjv). 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 Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone Inhibitor., PDB code: 4kjv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4kjv

Go back to Zinc Binding Sites List in 4kjv
Zinc binding site 1 out of 2 in the Crystal Structure of Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone 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 Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:24.3
occ:1.00
NE2 A:HIS220 2.1 19.8 1.0
SG A:CYS227 2.3 21.7 1.0
SG A:CYS200 2.3 20.9 1.0
SG A:CYS203 2.4 22.2 1.0
CE1 A:HIS220 2.9 20.6 1.0
CB A:CYS200 3.0 20.8 1.0
CB A:CYS227 3.2 22.6 1.0
CB A:CYS203 3.2 20.8 1.0
CD2 A:HIS220 3.3 22.0 1.0
N A:CYS203 3.6 20.8 1.0
CA A:CYS203 4.0 21.3 1.0
ND1 A:HIS220 4.1 20.1 1.0
CG A:HIS220 4.3 21.2 1.0
CA A:CYS227 4.5 21.8 1.0
CA A:CYS200 4.5 20.5 1.0
CB A:ALA202 4.5 21.2 1.0
CG2 A:VAL230 4.6 23.9 1.0
CB A:PHE224 4.7 24.1 1.0
C A:ALA202 4.7 21.5 1.0
CB A:PHE229 4.8 25.0 1.0
C A:CYS203 4.8 24.9 1.0
N A:GLY204 4.8 23.5 1.0
N A:ALA202 5.0 21.1 1.0

Zinc binding site 2 out of 2 in 4kjv

Go back to Zinc Binding Sites List in 4kjv
Zinc binding site 2 out of 2 in the Crystal Structure of Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone 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 Xiap-BIR2 with A Bound Spirocyclic Benzoxazepinone Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:25.6
occ:1.00
NE2 C:HIS220 2.2 23.6 1.0
SG C:CYS227 2.3 23.8 1.0
SG C:CYS203 2.3 23.1 1.0
SG C:CYS200 2.4 23.8 1.0
CE1 C:HIS220 2.9 23.9 1.0
CB C:CYS200 3.0 22.3 1.0
CB C:CYS227 3.2 22.0 1.0
CB C:CYS203 3.2 23.2 1.0
CD2 C:HIS220 3.4 23.8 1.0
N C:CYS203 3.6 23.0 1.0
CA C:CYS203 4.0 21.6 1.0
ND1 C:HIS220 4.1 24.8 1.0
CG C:HIS220 4.4 23.3 1.0
CA C:CYS200 4.4 21.5 1.0
CB C:ALA202 4.5 26.1 1.0
CG2 C:VAL230 4.6 30.4 1.0
CA C:CYS227 4.6 23.4 1.0
C C:ALA202 4.6 23.0 1.0
CB C:PHE224 4.8 24.7 1.0
CB C:PHE229 4.8 25.4 1.0
C C:CYS203 4.8 21.6 1.0
N C:GLY204 4.9 21.1 1.0
CA C:ALA202 4.9 24.2 1.0
N C:ALA202 5.0 24.2 1.0
C C:CYS200 5.0 23.2 1.0

Reference:

R.F.Kester, A.F.Donnell, Y.Lou, S.W.Remiszewski, L.J.Lombardo, S.Chen, N.T.Le, J.Lo, J.A.Moliterni, X.Han, J.H.Hogg, W.Liang, C.Michoud, K.C.Rupert, S.Mischke, K.Le, M.Weisel, C.A.Janson, C.M.Lukacs, A.J.Fretland, K.Hong, A.Polonskaia, L.Gao, S.Li, D.S.Solis, D.Aguilar, C.Tardell, M.Dvorozniak, S.Tannu, E.C.Lee, A.D.Schutt, B.Goggin. Optimization of Benzodiazepinones As Selective Inhibitors of the X-Linked Inhibitor of Apoptosis Protein (Xiap) Second Baculovirus Iap Repeat (BIR2) Domain. J.Med.Chem. V. 56 7788 2013.
ISSN: ISSN 0022-2623
PubMed: 24093940
DOI: 10.1021/JM400732V
Page generated: Wed Dec 16 05:29:24 2020

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