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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

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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

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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

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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

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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

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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

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