Atomistry » Zinc » PDB 4n3v-4ngp » 4n7s
Atomistry »
  Zinc »
    PDB 4n3v-4ngp »
      4n7s »

Zinc in PDB 4n7s: Crystal Structure of TSE3-TSI3 Complex with Zinc Ion

Protein crystallography data

The structure of Crystal Structure of TSE3-TSI3 Complex with Zinc Ion, PDB code: 4n7s was solved by G.J.Shang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.80 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.196, 93.254, 171.790, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.6

Other elements in 4n7s:

The structure of Crystal Structure of TSE3-TSI3 Complex with Zinc Ion also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion (pdb code 4n7s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion, PDB code: 4n7s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4n7s

Go back to Zinc Binding Sites List in 4n7s
Zinc binding site 1 out of 7 in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion


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 TSE3-TSI3 Complex with Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:53.0
occ:1.00
 O A:HOH652 2.2 46.7 1.0
OE2 A:GLU25 2.2 46.4 1.0
O A:HOH675 2.3 43.0 1.0
O A:HOH893 2.4 54.4 1.0
O A:HOH861 2.6 57.2 1.0
CD A:GLU25 2.9 40.0 1.0
OE1 A:GLU25 2.9 40.5 1.0
O A:LEU11 4.1 36.0 1.0
OD2 A:ASP18 4.1 55.7 1.0
O A:SER13 4.1 34.4 1.0
O A:GLN20 4.3 52.5 1.0
CG A:GLU25 4.3 41.1 1.0
OD1 A:ASP18 4.4 57.1 1.0
CG A:ASP18 4.7 51.7 1.0
O A:SER10 4.9 34.6 1.0
C A:LEU11 5.0 30.1 1.0

Zinc binding site 2 out of 7 in 4n7s

Go back to Zinc Binding Sites List in 4n7s
Zinc binding site 2 out of 7 in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion


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 TSE3-TSI3 Complex with Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:36.4
occ:1.00
 O A:HOH892 2.1 22.9 1.0
OE2 A:GLU258 2.1 26.1 1.0
OD1 A:ASP262 2.1 27.0 1.0
OE2 B:GLU126 2.2 41.3 1.0
OE1 B:GLU126 2.7 30.5 1.0
CD B:GLU126 2.7 39.3 1.0
CG A:ASP262 2.8 28.2 1.0
OD2 A:ASP262 2.9 23.5 1.0
CD A:GLU258 3.0 24.2 1.0
CG A:GLU258 3.2 22.8 1.0
OE1 A:GLN280 3.4 26.0 1.0
O A:SER275 3.8 22.1 1.0
NZ A:LYS261 3.9 38.2 1.0
O A:HOH742 4.0 35.9 1.0
OE1 A:GLU258 4.2 27.0 1.0
CG B:GLU126 4.2 32.4 1.0
CA A:CA511 4.2 25.1 1.0
O A:HOH658 4.2 26.3 1.0
CB A:ASP262 4.3 22.7 1.0
CD A:GLN280 4.4 22.3 1.0
O A:GLU258 4.4 21.9 1.0
NE2 A:GLN254 4.5 21.5 1.0
OE1 A:GLN254 4.6 21.2 1.0
CB A:GLU258 4.7 19.3 1.0
NE2 A:GLN280 4.7 25.0 1.0
CE A:LYS261 4.7 35.2 1.0
CB A:SER275 4.8 22.2 1.0
C A:SER275 4.8 20.1 1.0
CA A:ASP262 4.9 23.1 1.0
N A:SER275 4.9 24.7 1.0
CD A:GLN254 5.0 24.2 1.0

Zinc binding site 3 out of 7 in 4n7s

Go back to Zinc Binding Sites List in 4n7s
Zinc binding site 3 out of 7 in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion


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 TSE3-TSI3 Complex with Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:49.2
occ:1.00
 O A:ARG379 2.3 30.3 1.0
O A:ASN384 2.4 35.1 1.0
OD1 A:ASP382 2.6 32.8 1.0
O A:HOH643 2.6 31.5 1.0
OE1 A:GLU375 2.6 28.0 1.0
OE2 A:GLU375 2.6 28.7 1.0
OG A:SER378 2.7 24.7 1.0
CD A:GLU375 2.9 29.3 1.0
C A:ARG379 3.5 27.5 1.0
CG A:ASP382 3.5 35.8 1.0
C A:ASN384 3.5 38.3 1.0
OD2 A:ASP382 3.7 30.1 1.0
CB A:SER378 3.8 28.2 1.0
N A:ARG379 4.0 31.4 1.0
C A:SER378 4.2 29.1 1.0
N A:ASN384 4.2 34.5 1.0
CA A:ARG379 4.2 30.4 1.0
O A:HOH810 4.3 44.5 1.0
CA A:ASN384 4.3 32.7 1.0
N A:TRP381 4.4 31.4 1.0
CG A:GLU375 4.4 28.9 1.0
N A:PRO380 4.5 29.5 1.0
CB A:ASN384 4.5 35.1 1.0
N A:ASP382 4.5 35.2 1.0
CA A:PRO380 4.5 30.5 1.0
O A:SER378 4.5 28.0 1.0
N A:LEU385 4.6 33.6 1.0
O A:SER374 4.6 25.0 1.0
CA A:SER378 4.6 24.2 1.0
CB A:ARG379 4.6 30.0 1.0
O A:HOH686 4.7 37.5 1.0
CA A:GLU375 4.7 26.5 1.0
CA A:LEU385 4.8 35.0 1.0
C A:PRO380 4.8 34.7 1.0
OG A:SER374 4.8 27.6 1.0
CB A:ASP382 4.8 29.5 1.0
CB A:GLU375 4.9 28.3 1.0

Zinc binding site 4 out of 7 in 4n7s

Go back to Zinc Binding Sites List in 4n7s
Zinc binding site 4 out of 7 in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion


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 TSE3-TSI3 Complex with Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:74.2
occ:1.00
 O B:HOH312 2.4 46.3 1.0
O B:HOH322 2.5 50.9 1.0
OE2 B:GLU49 2.5 55.1 1.0
OE1 B:GLU49 2.7 44.9 1.0
CD B:GLU49 2.9 52.1 1.0
O B:HOH340 4.0 49.5 1.0
CB B:ASN32 4.3 42.2 1.0
CG B:GLU49 4.4 48.6 1.0
ND2 B:ASN32 4.4 38.6 1.0
O B:ALA48 4.7 43.7 1.0
O3 B:GOL207 4.8 59.2 1.0
CG B:ASN32 4.9 44.0 1.0

Zinc binding site 5 out of 7 in 4n7s

Go back to Zinc Binding Sites List in 4n7s
Zinc binding site 5 out of 7 in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion


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 TSE3-TSI3 Complex with Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:33.4
occ:1.00
 O C:HOH739 2.0 34.9 1.0
O C:HOH605 2.1 33.5 1.0
O C:HOH601 2.1 28.2 1.0
O C:HOH602 2.2 27.3 1.0
OE2 C:GLU25 2.3 36.3 1.0
OE1 C:GLU25 2.4 32.0 1.0
CD C:GLU25 2.7 36.6 1.0
OD2 C:ASP18 3.8 32.1 1.0
OD1 C:ASP18 4.1 33.2 1.0
O C:LEU11 4.1 29.3 1.0
CG C:GLU25 4.2 33.2 1.0
O C:SER13 4.2 26.7 1.0
O C:HOH727 4.2 39.9 1.0
O C:GLN20 4.3 28.9 1.0
O C:HOH703 4.3 48.3 1.0
CG C:ASP18 4.4 33.2 1.0
CA C:VAL21 4.7 29.2 1.0
N C:THR22 4.7 24.0 1.0
CG2 C:THR22 4.8 42.9 1.0
CB C:GLU25 5.0 32.2 1.0

Zinc binding site 6 out of 7 in 4n7s

Go back to Zinc Binding Sites List in 4n7s
Zinc binding site 6 out of 7 in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion


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 TSE3-TSI3 Complex with Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:47.8
occ:1.00
 O C:HOH746 1.7 36.1 1.0
OE2 C:GLU258 2.1 34.9 1.0
OE1 D:GLU126 2.3 50.7 1.0
OD1 C:ASP262 2.4 44.9 1.0
OE2 D:GLU126 2.6 46.1 1.0
CD D:GLU126 2.8 43.8 1.0
OD2 C:ASP262 2.9 35.5 1.0
CG C:ASP262 2.9 42.5 1.0
CD C:GLU258 3.2 37.5 1.0
OE1 C:GLN280 3.3 42.1 1.0
CG C:GLU258 3.5 36.2 1.0
NZ C:LYS261 3.8 47.7 1.0
O C:SER275 3.8 37.8 1.0
O C:HOH628 4.1 43.1 1.0
CA C:CA512 4.2 36.4 1.0
CG D:GLU126 4.2 46.6 1.0
OE1 C:GLU258 4.3 37.3 1.0
CD C:GLN280 4.3 39.8 1.0
CB C:ASP262 4.3 38.4 1.0
NE2 C:GLN254 4.3 36.1 1.0
CE C:LYS261 4.5 41.9 1.0
NE2 C:GLN280 4.5 35.8 1.0
O C:GLU258 4.6 37.8 1.0
CB C:SER275 4.7 39.1 1.0
C C:SER275 4.7 34.3 1.0
OE1 C:GLN254 4.8 32.5 1.0
N C:SER275 4.8 35.1 1.0
CB C:GLU258 4.9 33.7 1.0
CA C:ASP262 4.9 33.6 1.0
CB D:GLU126 4.9 41.0 1.0

Zinc binding site 7 out of 7 in 4n7s

Go back to Zinc Binding Sites List in 4n7s
Zinc binding site 7 out of 7 in the Crystal Structure of TSE3-TSI3 Complex with Zinc Ion


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 TSE3-TSI3 Complex with Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:67.9
occ:1.00
 O C:ARG379 2.3 49.4 1.0
O C:ASN384 2.4 51.7 1.0
O C:HOH631 2.6 45.8 1.0
OE1 C:GLU375 2.6 45.8 1.0
OD1 C:ASP382 2.6 50.5 1.0
OG C:SER378 2.6 41.0 1.0
OE2 C:GLU375 2.7 40.6 1.0
CD C:GLU375 2.9 41.7 1.0
C C:ARG379 3.4 48.5 1.0
CG C:ASP382 3.5 46.1 1.0
C C:ASN384 3.6 51.9 1.0
CB C:SER378 3.7 41.4 1.0
OD2 C:ASP382 3.9 54.3 1.0
N C:ARG379 3.9 42.3 1.0
C C:SER378 4.1 42.3 1.0
CA C:ARG379 4.2 47.3 1.0
N C:ASN384 4.2 54.6 1.0
N C:TRP381 4.3 53.1 1.0
CA C:ASN384 4.4 56.2 1.0
N C:ASP382 4.4 49.1 1.0
CG C:GLU375 4.4 44.4 1.0
CB C:ARG379 4.5 49.5 1.0
N C:PRO380 4.5 46.0 1.0
O C:SER378 4.5 41.6 1.0
N C:LEU385 4.6 52.7 1.0
O C:SER374 4.6 44.1 1.0
CA C:SER378 4.6 41.5 1.0
O C:HOH666 4.6 50.1 1.0
CB C:ASN384 4.6 56.8 1.0
CA C:PRO380 4.6 45.7 1.0
CA C:LEU385 4.7 45.8 1.0
CA C:GLU375 4.7 42.3 1.0
OG C:SER374 4.7 41.4 1.0
CB C:ASP382 4.8 49.5 1.0
C C:PRO380 4.8 49.2 1.0
N C:ASP383 4.9 55.2 1.0
CB C:GLU375 4.9 42.7 1.0
OE2 D:GLU103 4.9 46.0 1.0

Reference:

D.Lu, G.Shang, H.Zhang, Q.Yu, X.Cong, J.Yuan, F.He, C.Zhu, Y.Zhao, K.Yin, Y.Chen, J.Hu, X.Zhang, Z.Yuan, S.Xu, W.Hu, H.Cang, L.Gu. Structural Insights Into the T6SS Effector Protein TSE3 and the TSE3-TSI3 Complex From Pseudomonas Aeruginosa Reveal A Calcium-Dependent Membrane-Binding Mechanism Mol.Microbiol. V. 92 1092 2014.
ISSN: ISSN 0950-382X
PubMed: 24724564
DOI: 10.1111/MMI.12616
Page generated: Sun Oct 27 03:01:49 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy