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Zinc in PDB 6akx: The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21

Protein crystallography data

The structure of The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21, PDB code: 6akx was solved by Y.Zhu, Q.Zhao, B.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.640, 102.740, 136.870, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21 (pdb code 6akx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21, PDB code: 6akx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6akx

Go back to Zinc Binding Sites List in 6akx
Zinc binding site 1 out of 2 in the The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:53.5
occ:1.00
SG A:CYS1042 2.2 64.3 1.0
SG A:CYS1009 2.2 55.3 1.0
SG A:CYS1039 2.3 56.7 1.0
SG A:CYS1006 2.4 53.3 1.0
CB A:CYS1039 3.2 53.3 1.0
CB A:CYS1009 3.2 51.1 1.0
CB A:CYS1042 3.3 60.3 1.0
CB A:CYS1006 3.3 49.6 1.0
N A:CYS1042 3.5 60.3 1.0
N A:CYS1009 3.7 51.8 1.0
CA A:CYS1042 3.9 59.9 1.0
CA A:CYS1009 4.0 50.4 1.0
CG2 A:VAL1044 4.2 56.1 1.0
CB A:TYR1011 4.5 44.0 1.0
CB A:LEU1041 4.5 61.1 1.0
C A:CYS1042 4.5 62.9 1.0
CB A:VAL1008 4.6 54.4 1.0
C A:LEU1041 4.6 64.6 1.0
CA A:CYS1039 4.7 53.9 1.0
N A:GLY1043 4.7 57.9 1.0
CA A:CYS1006 4.8 49.6 1.0
C A:VAL1008 4.8 56.8 1.0
C A:CYS1009 4.8 50.8 1.0
N A:GLY1010 4.9 43.5 1.0
CA A:LEU1041 4.9 61.0 1.0
N A:LEU1041 5.0 60.9 1.0

Zinc binding site 2 out of 2 in 6akx

Go back to Zinc Binding Sites List in 6akx
Zinc binding site 2 out of 2 in the The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Human Chemokine Receptor CCR5 in Complex with Compound 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:66.8
occ:1.00
SG B:CYS1039 2.2 64.0 1.0
SG B:CYS1006 2.3 53.9 1.0
SG B:CYS1042 2.3 68.3 1.0
SG B:CYS1009 2.3 63.4 1.0
CB B:CYS1039 3.1 60.3 1.0
CB B:CYS1006 3.2 50.4 1.0
CB B:CYS1009 3.5 59.1 1.0
CB B:CYS1042 3.5 64.5 1.0
N B:CYS1042 3.6 64.9 1.0
N B:CYS1009 3.7 59.6 1.0
CA B:CYS1009 4.1 58.6 1.0
CA B:CYS1042 4.1 64.3 1.0
CG2 B:VAL1044 4.2 63.8 1.0
CB B:TYR1011 4.2 50.2 1.0
CB B:VAL1008 4.6 64.0 1.0
CA B:CYS1039 4.6 60.5 1.0
CA B:CYS1006 4.7 51.0 1.0
CB B:LEU1041 4.7 64.8 1.0
C B:CYS1009 4.7 61.1 1.0
C B:LEU1041 4.7 69.5 1.0
N B:TYR1011 4.7 50.3 1.0
N B:GLY1043 4.8 63.9 1.0
C B:CYS1042 4.8 67.9 1.0
C B:VAL1008 4.8 64.1 1.0
N B:GLY1010 4.9 54.7 1.0
N B:LEU1041 4.9 64.7 1.0
CA B:LEU1041 5.0 64.8 1.0

Reference:

P.Peng, H.Chen, Y.Zhu, Z.Wang, J.Li, R.H.Luo, J.Wang, L.Chen, L.M.Yang, H.Jiang, X.Xie, B.Wu, Y.T.Zheng, H.Liu. Structure-Based Design of 1-Heteroaryl-1,3-Propanediamine Derivatives As A Novel Series of Cc-Chemokine Receptor 5 Antagonists. J. Med. Chem. V. 61 9621 2018.
ISSN: ISSN 1520-4804
PubMed: 30234300
DOI: 10.1021/ACS.JMEDCHEM.8B01077
Page generated: Wed Dec 16 11:29:59 2020

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