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Zinc in PDB 6b4h: Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex

Protein crystallography data

The structure of Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex, PDB code: 6b4h was solved by D.H.Lin, A.R.Correia, S.W.Cai, F.M.Huber, C.A.Jette, A.Hoelz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.85 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.160, 73.276, 117.665, 90.00, 94.20, 90.00
R / Rfree (%) 19.3 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex (pdb code 6b4h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex, PDB code: 6b4h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6b4h

Go back to Zinc Binding Sites List in 6b4h
Zinc binding site 1 out of 4 in the Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex


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 Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:41.1
occ:0.90
O25 A:IHP601 1.9 38.6 1.0
O46 A:IHP602 1.9 34.0 1.0
O26 A:IHP601 2.0 47.1 1.0
O21 A:IHP602 2.1 54.0 1.0
H46 A:IHP602 2.4 40.8 1.0
O16 A:IHP601 2.8 37.4 1.0
P6 A:IHP601 2.9 37.1 1.0
O16 A:IHP602 3.1 39.0 1.0
P6 A:IHP602 3.1 45.1 1.0
P5 A:IHP601 3.2 41.9 1.0
P1 A:IHP602 3.2 50.6 1.0
O11 A:IHP602 3.6 49.5 1.0
H31 A:IHP602 3.7 62.0 1.0
H1 A:IHP602 3.7 64.1 1.0
O15 A:IHP601 3.7 47.3 1.0
H5 A:IHP601 3.7 48.1 1.0
O31 A:IHP602 3.8 51.6 1.0
O36 A:IHP601 3.8 41.8 1.0
O36 A:IHP602 3.8 46.8 1.0
O35 A:IHP601 3.8 50.1 1.0
H35 A:IHP601 3.8 60.1 1.0
O A:HOH716 3.8 56.0 1.0
C6 A:IHP601 4.0 39.6 1.0
C1 A:IHP602 4.0 53.4 1.0
C5 A:IHP601 4.0 40.1 1.0
O46 A:IHP601 4.1 35.5 1.0
C6 A:IHP602 4.2 48.2 1.0
O26 A:IHP602 4.3 45.1 1.0
ZN A:ZN606 4.4 39.8 1.0
O45 A:IHP601 4.4 43.3 1.0
H46 A:IHP601 4.4 42.5 1.0
H6 A:IHP601 4.5 47.6 1.0
O A:HOH833 4.5 61.2 1.0
O41 A:IHP602 4.6 60.6 1.0
H36 A:IHP601 4.7 50.2 1.0
H36 A:IHP602 4.7 56.1 1.0
H6 A:IHP602 4.8 57.9 1.0
H5 A:IHP602 4.9 55.0 1.0
H1 A:IHP601 5.0 43.5 1.0

Zinc binding site 2 out of 4 in 6b4h

Go back to Zinc Binding Sites List in 6b4h
Zinc binding site 2 out of 4 in the Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex


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 Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:39.8
occ:1.00
H36 A:IHP601 1.8 50.2 1.0
O45 A:IHP602 1.9 48.7 1.0
O36 A:IHP601 1.9 41.8 1.0
H36 A:IHP602 2.0 56.1 1.0
O36 A:IHP602 2.0 46.8 1.0
O21 A:IHP601 2.1 40.6 1.0
H45 A:IHP602 2.2 58.5 1.0
O16 A:IHP602 3.0 39.0 1.0
P6 A:IHP602 3.1 45.1 1.0
P6 A:IHP601 3.1 37.1 1.0
P1 A:IHP601 3.2 41.7 1.0
P5 A:IHP602 3.2 47.9 1.0
O16 A:IHP601 3.2 37.4 1.0
H35 A:IHP602 3.4 54.5 1.0
O11 A:IHP601 3.5 41.7 1.0
H41 A:IHP601 3.6 45.0 1.0
O15 A:IHP602 3.6 55.6 1.0
H1 A:IHP601 3.7 43.5 1.0
O35 A:IHP602 3.7 45.4 1.0
O41 A:IHP601 3.7 37.5 1.0
O46 A:IHP602 3.9 34.0 1.0
O26 A:IHP601 4.0 47.1 1.0
H5 A:IHP602 4.0 55.0 1.0
C1 A:IHP601 4.0 36.3 1.0
C5 A:IHP602 4.2 45.8 1.0
C6 A:IHP602 4.2 48.2 1.0
O46 A:IHP601 4.2 35.5 1.0
O26 A:IHP602 4.2 45.1 1.0
C6 A:IHP601 4.2 39.6 1.0
HZ1 A:LYS327 4.3 42.7 1.0
O25 A:IHP602 4.4 57.0 1.0
ZN A:ZN605 4.4 41.1 0.9
O31 A:IHP601 4.5 37.3 1.0
H6 A:IHP602 4.6 57.9 1.0
H31 A:IHP601 4.7 44.8 1.0
H6 A:IHP601 4.8 47.6 1.0
H46 A:IHP602 4.8 40.8 1.0
HZ2 A:LYS327 4.8 42.7 1.0
HH12 A:ARG253 4.9 0.1 1.0

Zinc binding site 3 out of 4 in 6b4h

Go back to Zinc Binding Sites List in 6b4h
Zinc binding site 3 out of 4 in the Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex


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 Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn605

b:33.6
occ:0.82
H34 C:IHP601 1.8 43.4 1.0
H46 C:IHP602 1.8 48.5 1.0
O34 C:IHP601 1.8 36.2 1.0
H35 C:IHP602 1.8 51.0 1.0
O43 C:IHP601 1.9 38.2 1.0
O35 C:IHP602 1.9 42.5 1.0
O46 C:IHP602 2.0 40.4 1.0
H43 C:IHP601 2.2 45.8 1.0
O16 C:IHP602 3.0 45.7 1.0
P4 C:IHP601 3.1 37.3 1.0
P6 C:IHP602 3.1 44.2 1.0
P3 C:IHP601 3.2 38.2 1.0
O14 C:IHP601 3.2 33.0 1.0
P5 C:IHP602 3.2 43.5 1.0
O C:HOH703 3.4 57.0 1.0
O13 C:IHP601 3.5 35.8 1.0
O15 C:IHP602 3.5 56.8 1.0
H33 C:IHP601 3.6 45.3 1.0
H3 C:IHP601 3.6 42.0 1.0
O C:HOH710 3.7 41.0 1.0
O33 C:IHP601 3.7 37.8 1.0
O45 C:IHP602 3.8 45.1 1.0
O44 C:IHP601 3.8 45.2 1.0
O36 C:IHP602 3.9 38.1 1.0
H5 C:IHP602 4.0 65.6 1.0
C3 C:IHP601 4.0 35.0 1.0
H45 C:IHP602 4.1 54.1 1.0
C5 C:IHP602 4.1 54.7 1.0
C6 C:IHP602 4.1 51.5 1.0
O24 C:IHP601 4.2 37.8 1.0
C4 C:IHP601 4.2 37.4 1.0
O26 C:IHP602 4.3 47.7 1.0
O23 C:IHP601 4.3 34.6 1.0
HZ3 C:LYS327 4.3 41.5 1.0
O25 C:IHP602 4.4 51.8 1.0
ZN C:ZN606 4.4 41.8 1.0
H6 C:IHP602 4.6 61.9 1.0
H44 C:IHP601 4.7 54.3 1.0
H36 C:IHP602 4.8 45.7 1.0
O C:HOH746 4.8 54.1 1.0
H4 C:IHP601 4.8 44.9 1.0
HZ1 C:LYS327 4.8 41.5 1.0
HG C:SER331 4.9 66.3 1.0
O C:HOH755 4.9 55.4 1.0

Zinc binding site 4 out of 4 in 6b4h

Go back to Zinc Binding Sites List in 6b4h
Zinc binding site 4 out of 4 in the Crystal Structure of Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex


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 Chaetomium Thermophilum GLE1 Ctd-NUP42 Gbm-IP6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn606

b:41.8
occ:0.98
H44 C:IHP601 1.8 54.3 1.0
O25 C:IHP601 1.9 40.6 1.0
O44 C:IHP601 2.0 45.2 1.0
O36 C:IHP602 2.1 38.1 1.0
H36 C:IHP602 2.1 45.7 1.0
O21 C:IHP602 2.1 52.5 1.0
O14 C:IHP601 2.8 33.0 1.0
P4 C:IHP601 3.0 37.3 1.0
O16 C:IHP602 3.1 45.7 1.0
P5 C:IHP601 3.1 45.9 1.0
P6 C:IHP602 3.2 44.2 1.0
P1 C:IHP602 3.3 54.7 1.0
O15 C:IHP601 3.7 48.7 1.0
O11 C:IHP602 3.7 58.0 1.0
H5 C:IHP601 3.7 44.5 1.0
O35 C:IHP601 3.7 47.7 1.0
O31 C:IHP602 3.7 52.3 1.0
H1 C:IHP602 3.7 73.4 1.0
O34 C:IHP601 3.8 36.2 1.0
H34 C:IHP601 3.9 43.4 1.0
H46 C:IHP602 3.9 48.5 1.0
O46 C:IHP602 3.9 40.4 1.0
C4 C:IHP601 4.0 37.4 1.0
C5 C:IHP601 4.0 37.1 1.0
O C:HOH755 4.1 55.4 1.0
C1 C:IHP602 4.1 61.2 1.0
O24 C:IHP601 4.1 37.8 1.0
C6 C:IHP602 4.2 51.5 1.0
O26 C:IHP602 4.3 47.7 1.0
O45 C:IHP601 4.4 51.0 1.0
ZN C:ZN605 4.4 33.6 0.8
H4 C:IHP601 4.5 44.9 1.0
O41 C:IHP602 4.6 83.2 1.0
H31 C:IHP602 4.6 62.8 1.0
H35 C:IHP601 4.7 57.3 1.0
H6 C:IHP602 4.8 61.9 1.0
H3 C:IHP601 5.0 42.0 1.0
H5 C:IHP602 5.0 65.6 1.0

Reference:

D.H.Lin, A.R.Correia, S.W.Cai, F.M.Huber, C.A.Jette, A.Hoelz. Structural and Functional Analysis of Mrna Export Regulation By the Nuclear Pore Complex. Nat Commun V. 9 2319 2018.
ISSN: ESSN 2041-1723
PubMed: 29899397
DOI: 10.1038/S41467-018-04459-3
Page generated: Wed Dec 16 11:31:25 2020

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