Atomistry » Zinc » PDB 7cq4-7d3x » 7d2t
Atomistry »
  Zinc »
    PDB 7cq4-7d3x »
      7d2t »

Zinc in PDB 7d2t: Crystal Structure of RSU1/PINCH1_LIM45C Complex

Protein crystallography data

The structure of Crystal Structure of RSU1/PINCH1_LIM45C Complex, PDB code: 7d2t was solved by H.Yang, Z.Wei, C.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 114.624, 51.293, 119.626, 90, 101.55, 90
R / Rfree (%) 17 / 19.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RSU1/PINCH1_LIM45C Complex (pdb code 7d2t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of RSU1/PINCH1_LIM45C Complex, PDB code: 7d2t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 1 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C 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 RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:41.2
occ:1.00
 SG B:CYS303 2.3 38.2 1.0
SG B:CYS300 2.3 44.8 1.0
SG B:CYS278 2.3 36.0 1.0
SG B:CYS281 2.4 46.9 1.0
CB B:CYS278 3.2 36.2 1.0
CB B:CYS281 3.2 40.4 1.0
CB B:CYS303 3.3 44.3 1.0
CB B:CYS300 3.4 47.1 1.0
OG1 B:THR280 3.8 41.1 1.0
N B:CYS281 3.8 37.1 1.0
N B:CYS300 4.0 37.9 1.0
CA B:CYS281 4.1 40.7 1.0
CA B:CYS300 4.2 40.8 1.0
O B:HOH539 4.3 52.3 1.0
N B:CYS303 4.3 40.5 1.0
CA B:CYS303 4.4 41.4 1.0
C B:THR280 4.6 35.6 1.0
CA B:CYS278 4.6 38.6 1.0
O B:CYS300 4.7 38.8 1.0
C B:CYS281 4.8 40.0 1.0
C B:CYS300 4.8 41.9 1.0
CB B:THR280 4.9 36.6 1.0

Zinc binding site 2 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 2 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C 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 RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:49.5
occ:1.00
 SG B:CYS255 2.3 47.1 1.0
SG B:CYS275 2.3 49.1 1.0
SG B:CYS252 2.4 44.7 1.0
SG B:CYS272 2.5 50.2 1.0
CB B:CYS252 3.0 43.6 1.0
CB B:CYS272 3.2 48.0 1.0
CB B:CYS275 3.3 46.1 1.0
CB B:CYS255 3.3 47.4 1.0
N B:CYS272 3.9 43.0 1.0
N B:CYS255 3.9 47.3 1.0
CA B:CYS272 4.1 47.1 1.0
CA B:CYS255 4.2 48.2 1.0
CA B:CYS252 4.5 41.9 1.0
CA B:CYS275 4.7 46.3 1.0
CB B:HIS254 4.8 48.4 1.0
C B:CYS255 5.0 48.6 1.0

Zinc binding site 3 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 3 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C 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 RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:68.9
occ:1.00
 ND1 B:HIS243 2.2 78.4 1.0
SG B:CYS240 2.3 73.8 1.0
SG B:CYS222 2.4 90.9 1.0
SG B:CYS219 2.4 64.3 1.0
CE1 B:HIS243 3.1 79.0 1.0
CG B:HIS243 3.1 74.2 1.0
CB B:CYS219 3.2 71.2 1.0
CB B:CYS240 3.3 65.5 1.0
CB B:HIS243 3.5 70.6 1.0
CB B:CYS222 3.6 91.5 1.0
N B:CYS222 3.7 86.0 1.0
N B:CYS240 3.9 73.7 1.0
O B:CYS222 4.1 96.5 1.0
CA B:CYS222 4.1 91.5 1.0
NE2 B:HIS243 4.2 77.4 1.0
CA B:CYS240 4.2 71.4 1.0
CD2 B:HIS243 4.2 75.0 1.0
CB B:LYS221 4.3 73.8 1.0
C B:CYS222 4.6 95.5 1.0
CA B:CYS219 4.7 73.0 1.0
CA B:HIS243 4.7 67.7 1.0
N B:HIS243 4.8 65.9 1.0
C B:LYS221 4.8 86.4 1.0
C B:CYS240 4.9 64.0 1.0
O B:CYS240 4.9 61.4 1.0
OG1 B:THR242 4.9 81.6 1.0
CA B:LYS221 4.9 78.7 1.0
N B:LYS221 5.0 74.5 1.0

Zinc binding site 4 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 4 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C 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 RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:95.8
occ:1.00
 ND1 B:HIS216 2.1 104.7 1.0
ND1 B:HIS213 2.3 106.0 1.0
SG B:CYS196 2.4 122.8 1.0
SG B:CYS193 2.4 96.5 1.0
CE1 B:HIS216 2.9 108.1 1.0
CB B:CYS193 3.0 97.3 1.0
CG B:HIS216 3.1 99.4 1.0
CG B:HIS213 3.2 104.1 1.0
CB B:HIS213 3.3 100.3 1.0
CE1 B:HIS213 3.4 107.7 1.0
CB B:HIS216 3.5 94.4 1.0
CB B:CYS196 3.5 114.0 1.0
NE2 B:HIS216 4.0 106.3 1.0
N B:HIS213 4.0 96.6 1.0
CD2 B:HIS216 4.1 101.2 1.0
N B:CYS196 4.2 109.9 1.0
CA B:HIS213 4.3 95.3 1.0
CD2 B:HIS213 4.4 106.1 1.0
CA B:CYS196 4.4 114.2 1.0
CA B:CYS193 4.5 96.9 1.0
NE2 B:HIS213 4.5 108.2 1.0
CA B:HIS216 5.0 93.3 1.0

Zinc binding site 5 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 5 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:40.0
occ:1.00
 SG D:CYS303 2.3 39.1 1.0
SG D:CYS278 2.3 39.8 1.0
SG D:CYS300 2.4 40.9 1.0
SG D:CYS281 2.4 45.8 1.0
CB D:CYS278 3.1 44.7 1.0
CB D:CYS303 3.2 35.5 1.0
CB D:CYS281 3.3 40.3 1.0
CB D:CYS300 3.4 37.7 1.0
OG1 D:THR280 3.7 41.2 1.0
N D:CYS281 3.8 38.6 1.0
N D:CYS300 4.0 37.0 1.0
CA D:CYS281 4.2 40.4 1.0
CA D:CYS300 4.2 38.2 1.0
CA D:CYS303 4.3 39.5 1.0
N D:CYS303 4.3 41.5 1.0
CG2 D:THR283 4.3 42.9 0.5
O D:HOH535 4.5 51.4 1.0
CA D:CYS278 4.6 43.0 1.0
C D:THR280 4.6 39.2 1.0
O D:CYS300 4.6 42.9 1.0
C D:CYS300 4.8 40.6 1.0
C D:CYS281 4.8 41.3 1.0
CB D:THR280 4.9 36.5 1.0
N D:THR280 4.9 37.5 1.0
N D:ASN282 5.0 44.5 1.0

Zinc binding site 6 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 6 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:64.7
occ:1.00
 ND1 D:HIS243 2.1 76.2 1.0
SG D:CYS240 2.3 60.1 1.0
SG D:CYS219 2.4 63.9 1.0
SG D:CYS222 2.4 76.5 1.0
CE1 D:HIS243 3.1 79.9 1.0
CG D:HIS243 3.1 72.3 1.0
CB D:CYS219 3.2 62.6 1.0
CB D:CYS240 3.4 59.2 1.0
CB D:HIS243 3.5 65.8 1.0
CB D:CYS222 3.6 75.2 1.0
N D:CYS222 3.7 74.6 1.0
N D:CYS240 3.9 57.5 1.0
CA D:CYS222 4.1 78.4 1.0
NE2 D:HIS243 4.2 81.6 1.0
O D:CYS222 4.2 90.5 1.0
CA D:CYS240 4.2 57.0 1.0
CD2 D:HIS243 4.2 77.6 1.0
CB D:LYS221 4.4 68.3 1.0
C D:CYS222 4.6 84.7 1.0
CA D:CYS219 4.7 65.2 1.0
N D:HIS243 4.7 63.7 1.0
CA D:HIS243 4.7 66.3 1.0
OG1 D:THR242 4.8 76.8 1.0
C D:LYS221 4.8 78.2 1.0
C D:CYS240 4.9 56.5 1.0
O D:CYS240 4.9 54.9 1.0
CA D:LYS221 5.0 72.2 1.0
N D:LYS221 5.0 70.6 1.0

Zinc binding site 7 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 7 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:51.6
occ:1.00
 SG D:CYS275 2.3 51.5 1.0
SG D:CYS255 2.3 53.1 1.0
SG D:CYS272 2.4 62.7 1.0
SG D:CYS252 2.5 48.2 1.0
CB D:CYS252 3.1 44.8 1.0
CB D:CYS272 3.2 56.1 1.0
CB D:CYS275 3.2 49.2 1.0
CB D:CYS255 3.4 54.1 1.0
N D:CYS272 3.9 52.5 1.0
N D:CYS255 3.9 48.6 1.0
CA D:CYS272 4.2 54.2 1.0
CA D:CYS255 4.2 51.0 1.0
CA D:CYS252 4.6 43.9 1.0
CA D:CYS275 4.7 50.1 1.0
NH1 D:ARG257 4.8 68.6 1.0
CB D:HIS254 4.9 53.0 1.0
C D:CYS255 5.0 47.7 1.0

Zinc binding site 8 out of 8 in 7d2t

Go back to Zinc Binding Sites List in 7d2t
Zinc binding site 8 out of 8 in the Crystal Structure of RSU1/PINCH1_LIM45C Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of RSU1/PINCH1_LIM45C Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:75.3
occ:1.00
 ND1 D:HIS216 2.1 84.8 1.0
ND1 D:HIS213 2.2 82.4 1.0
SG D:CYS193 2.3 80.1 1.0
SG D:CYS196 2.4 86.1 1.0
CB D:CYS193 2.9 78.2 1.0
CG D:HIS216 3.0 83.1 1.0
CE1 D:HIS216 3.1 86.6 1.0
CE1 D:HIS213 3.1 84.7 1.0
CG D:HIS213 3.2 79.3 1.0
CB D:HIS216 3.3 80.2 1.0
CB D:CYS196 3.3 90.8 1.0
CB D:HIS213 3.6 76.6 1.0
N D:CYS196 3.8 88.8 1.0
N D:HIS213 4.1 72.7 1.0
CA D:CYS196 4.1 91.2 1.0
NE2 D:HIS216 4.2 85.9 1.0
CD2 D:HIS216 4.2 83.8 1.0
NE2 D:HIS213 4.2 84.0 1.0
CD2 D:HIS213 4.3 80.7 1.0
CA D:CYS193 4.4 78.8 1.0
CA D:HIS213 4.4 75.5 1.0
CB D:ALA195 4.6 86.8 1.0
C D:ALA195 4.7 89.8 1.0
CA D:HIS216 4.8 79.2 1.0
C D:CYS196 4.9 92.0 1.0
N D:ALA195 4.9 83.4 1.0
C D:CYS193 5.0 80.9 1.0
CA D:ALA195 5.0 86.7 1.0

Reference:

H.Yang, L.Lin, K.Sun, T.Zhang, W.Chen, L.Li, Y.Xie, C.Wu, Z.Wei, C.Yu. Complex Structures of RSU1 and PINCH1 Reveal A Regulatory Mechanism of the Ilk/Pinch/Parvin Complex For F-Actin Dynamics. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 33587032
DOI: 10.7554/ELIFE.64395
Page generated: Tue Oct 29 18:37:22 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy