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Zinc in PDB 4gur: Crystal Structure of LSD2-Npac with H3 in Space Group P21

Protein crystallography data

The structure of Crystal Structure of LSD2-Npac with H3 in Space Group P21, PDB code: 4gur was solved by F.Chen, Z.Dong, J.Fang, Y.Yang, Z.Li, Y.Xu, H.Yang, P.Wang, R.Fang, Y.Shi, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.87 / 2.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.243, 89.033, 88.783, 90.00, 103.30, 90.00
R / Rfree (%) 18.8 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of LSD2-Npac with H3 in Space Group P21 (pdb code 4gur). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of LSD2-Npac with H3 in Space Group P21, PDB code: 4gur:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4gur

Go back to Zinc Binding Sites List in 4gur
Zinc binding site 1 out of 3 in the Crystal Structure of LSD2-Npac with H3 in Space Group P21


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 LSD2-Npac with H3 in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:63.3
occ:1.00
NE2 A:HIS90 2.1 53.4 1.0
SG A:CYS58 2.2 73.1 1.0
SG A:CYS53 2.3 84.8 1.0
ND1 A:HIS84 2.4 64.6 1.0
CD2 A:HIS90 3.0 55.7 1.0
CE1 A:HIS90 3.1 49.6 1.0
CB A:CYS58 3.2 83.6 1.0
CB A:CYS53 3.2 73.9 1.0
CE1 A:HIS84 3.3 54.5 1.0
CG A:HIS84 3.4 57.6 1.0
CB A:HIS84 3.7 55.0 1.0
CB A:ALA60 3.9 80.9 1.0
O A:SER86 3.9 51.2 1.0
ND1 A:HIS90 4.2 53.7 1.0
CG A:HIS90 4.2 52.6 1.0
NE2 A:HIS84 4.5 60.1 1.0
CB A:LYS55 4.5 83.0 1.0
CD2 A:HIS84 4.5 56.5 1.0
O A:CYS87 4.6 54.0 1.0
CA A:CYS58 4.6 87.5 1.0
CA A:CYS53 4.6 91.9 1.0
CA A:HIS84 4.7 65.4 1.0
CA A:CYS87 4.8 59.0 1.0
C A:SER86 4.8 57.4 1.0

Zinc binding site 2 out of 3 in 4gur

Go back to Zinc Binding Sites List in 4gur
Zinc binding site 2 out of 3 in the Crystal Structure of LSD2-Npac with H3 in Space Group P21


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 LSD2-Npac with H3 in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:54.7
occ:1.00
SG A:CYS95 2.0 56.7 1.0
SG A:CYS65 2.3 49.4 1.0
SG A:CYS92 2.4 61.2 1.0
SG A:CYS73 2.7 60.7 1.0
CB A:CYS95 2.8 67.4 1.0
CB A:CYS73 3.3 52.8 1.0
CB A:CYS65 3.4 51.5 1.0
CA A:CYS73 3.7 52.7 1.0
CB A:CYS92 3.8 64.0 1.0
N A:SER68 3.9 60.6 1.0
CA A:SER68 4.0 63.1 1.0
CA A:CYS95 4.0 72.0 1.0
N A:CYS95 4.0 59.0 1.0
N A:CYS92 4.1 62.6 1.0
N A:ALA74 4.3 50.4 1.0
CA A:CYS92 4.5 66.8 1.0
O A:CYS92 4.5 61.4 1.0
C A:CYS73 4.5 54.1 1.0
N A:ALA69 4.6 59.7 1.0
CA A:CYS65 4.8 51.0 1.0
C A:SER68 4.8 56.7 1.0
N A:CYS73 4.8 53.9 1.0
C A:CYS92 4.9 66.1 1.0
C A:ALA67 5.0 57.5 1.0
O A:CYS65 5.0 69.1 1.0
CB A:SER68 5.0 65.9 1.0

Zinc binding site 3 out of 3 in 4gur

Go back to Zinc Binding Sites List in 4gur
Zinc binding site 3 out of 3 in the Crystal Structure of LSD2-Npac with H3 in Space Group P21


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 LSD2-Npac with H3 in Space Group P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:55.7
occ:1.00
SG A:CYS147 2.2 53.0 1.0
SG A:CYS185 2.3 57.4 1.0
SG A:CYS169 2.3 60.6 1.0
SG A:CYS142 2.3 54.4 1.0
CB A:CYS185 3.1 57.9 1.0
CB A:CYS142 3.1 43.5 1.0
CB A:CYS147 3.1 61.1 1.0
CB A:CYS169 3.3 53.2 1.0
CA A:CYS185 3.6 59.9 1.0
N A:CYS169 3.8 48.3 1.0
CA A:CYS169 4.2 51.4 1.0
O A:CYS185 4.5 68.6 1.0
N A:CYS185 4.5 65.2 1.0
C A:CYS185 4.6 66.0 1.0
CA A:CYS147 4.6 49.2 1.0
CA A:CYS142 4.6 45.3 1.0
CB A:LYS144 4.6 56.1 1.0
NH1 A:ARG151 4.9 48.3 1.0
N A:ARG148 4.9 55.7 1.0
C A:ARG168 4.9 47.9 1.0
CB A:LYS149 4.9 49.3 1.0
C A:CYS147 5.0 55.2 1.0
N A:LYS149 5.0 51.4 1.0
CD A:LYS144 5.0 65.7 1.0

Reference:

R.Fang, F.Chen, Z.Dong, D.Hu, A.J.Barbera, E.A.Clark, J.Fang, Y.Yang, P.Mei, M.Rutenberg, Z.Li, Y.Zhang, Y.Xu, H.Yang, P.Wang, M.D.Simon, Q.Zhou, J.Li, M.P.Marynick, X.Li, H.Lu, U.B.Kaiser, R.E.Kingston, Y.Xu, Y.G.Shi. LSD2/KDM1B and Its Cofactor Npac/GLYR1 Endow A Structural and Molecular Model For Regulation of H3K4 Demethylation Mol.Cell V. 49 558 2013.
ISSN: ISSN 1097-2765
PubMed: 23260659
DOI: 10.1016/J.MOLCEL.2012.11.019
Page generated: Wed Dec 16 05:20:54 2020

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