Atomistry » Zinc » PDB 3i4m-3iet » 3iel
Atomistry »
  Zinc »
    PDB 3i4m-3iet »
      3iel »

Zinc in PDB 3iel: Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump

Protein crystallography data

The structure of Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump, PDB code: 3iel was solved by H.Ishikawa, N.Nakagawa, S.Kuramitsu, S.Yokoyama, R.Masui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.238, 146.677, 120.349, 90.00, 110.11, 90.00
R / Rfree (%) 22.2 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump (pdb code 3iel). 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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump, PDB code: 3iel:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 1 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn468

b:74.8
occ:1.00
OD1 A:ASP162 2.3 39.8 1.0
NE2 A:HIS400 2.4 37.7 1.0
OD2 A:ASP63 2.6 45.4 1.0
NE2 A:HIS64 3.1 36.3 1.0
CG A:ASP162 3.1 37.8 1.0
O A:HOH472 3.2 44.3 1.0
CE1 A:HIS400 3.3 36.7 1.0
OD2 A:ASP162 3.3 41.5 1.0
CD2 A:HIS400 3.3 35.7 1.0
CD2 A:HIS64 3.3 34.2 1.0
ZN A:ZN469 3.3 95.2 1.0
CG A:ASP63 3.4 41.1 1.0
OD1 A:ASP63 3.6 43.1 1.0
O A:HOH549 3.7 35.4 1.0
CE1 A:HIS64 4.2 36.9 1.0
NE2 A:HIS59 4.2 37.0 1.0
O A:VAL12 4.3 39.1 1.0
ND1 A:HIS400 4.3 35.9 1.0
CE1 A:HIS59 4.4 36.0 1.0
CG A:HIS400 4.4 36.0 1.0
CB A:ASP162 4.5 33.1 1.0
CE1 A:HIS380 4.5 29.8 1.0
CG A:HIS64 4.5 33.9 1.0
NE2 A:HIS380 4.7 32.7 1.0
CB A:ASP63 4.8 35.2 1.0
ND1 A:HIS64 4.9 35.9 1.0
OG A:SER15 4.9 32.7 1.0
O3' A:U5P465 5.0 53.0 1.0

Zinc binding site 2 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 2 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn469

b:95.2
occ:1.00
O A:HOH472 2.2 44.3 1.0
NE2 A:HIS141 2.5 27.7 1.0
ND1 A:HIS61 2.7 49.6 1.0
OD1 A:ASP162 2.9 39.8 1.0
NE2 A:HIS59 3.1 37.0 1.0
ZN A:ZN468 3.3 74.8 1.0
CE1 A:HIS141 3.3 27.9 1.0
CE1 A:HIS61 3.4 49.0 1.0
CD2 A:HIS141 3.5 25.8 1.0
CG A:HIS61 3.8 46.6 1.0
CE1 A:HIS59 3.8 36.0 1.0
CG A:ASP162 3.8 37.8 1.0
CD2 A:HIS59 4.0 35.9 1.0
CB A:HIS61 4.1 40.0 1.0
OD1 A:ASP63 4.2 43.1 1.0
CB A:ASP162 4.2 33.1 1.0
NE2 A:HIS380 4.3 32.7 1.0
ND1 A:HIS141 4.5 27.7 1.0
O3' A:U5P465 4.5 53.0 1.0
CE1 A:HIS380 4.5 29.8 1.0
O1 A:SO4448 4.6 0.9 1.0
CG A:HIS141 4.6 25.7 1.0
NE2 A:HIS61 4.6 50.6 1.0
OD2 A:ASP162 4.8 41.5 1.0
ND1 A:HIS59 4.8 37.4 1.0
CD2 A:HIS61 4.8 47.8 1.0
OD2 A:ASP63 4.8 45.4 1.0
CG A:HIS59 4.9 33.0 1.0
CG A:ASP63 4.9 41.1 1.0

Zinc binding site 3 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 3 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn458

b:70.8
occ:1.00
OD1 B:ASP162 2.3 40.8 1.0
NE2 B:HIS400 2.3 18.5 1.0
NE2 B:HIS64 2.8 43.6 1.0
OD2 B:ASP63 2.9 51.0 1.0
CD2 B:HIS64 3.0 43.0 1.0
O B:HOH462 3.1 44.8 1.0
CG B:ASP162 3.2 40.2 1.0
CD2 B:HIS400 3.2 17.4 1.0
CE1 B:HIS400 3.3 20.9 1.0
OD2 B:ASP162 3.3 41.8 1.0
CG B:ASP63 3.3 45.1 1.0
OD1 B:ASP63 3.3 50.5 1.0
ZN B:ZN459 3.7 84.8 1.0
CE1 B:HIS64 4.0 45.2 1.0
O B:VAL12 4.2 40.0 1.0
O B:HOH544 4.3 53.2 1.0
NE2 B:HIS59 4.3 46.1 1.0
CG B:HIS64 4.3 41.0 1.0
ND1 B:HIS400 4.4 23.8 1.0
CG B:HIS400 4.4 22.8 1.0
CE1 B:HIS59 4.4 45.4 1.0
CB B:ASP63 4.5 40.4 1.0
CB B:ASP162 4.6 31.5 1.0
OG B:SER15 4.7 33.4 1.0
O2' B:U5P456 4.7 60.0 1.0
ND1 B:HIS64 4.8 42.6 1.0
CE1 B:HIS380 4.9 24.0 1.0
NE2 B:HIS380 4.9 21.5 1.0
O B:ASP63 4.9 36.7 1.0

Zinc binding site 4 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 4 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn459

b:84.8
occ:1.00
NE2 B:HIS141 2.2 24.4 1.0
OD1 B:ASP162 2.7 40.8 1.0
O B:HOH462 2.7 44.8 1.0
ND1 B:HIS61 2.8 48.4 1.0
NE2 B:HIS59 2.8 46.1 1.0
CD2 B:HIS141 2.9 23.2 1.0
CE1 B:HIS141 3.2 25.2 1.0
CE1 B:HIS59 3.6 45.4 1.0
CD2 B:HIS59 3.6 44.6 1.0
CE1 B:HIS61 3.6 51.0 1.0
ZN B:ZN458 3.7 70.8 1.0
CG B:ASP162 3.7 40.2 1.0
CG B:HIS61 3.8 47.1 1.0
CB B:HIS61 4.1 41.0 1.0
CB B:ASP162 4.1 31.5 1.0
CG B:HIS141 4.1 26.2 1.0
ND1 B:HIS141 4.3 25.5 1.0
OD1 B:ASP63 4.4 50.5 1.0
O B:HOH500 4.5 42.1 1.0
NE2 B:HIS380 4.5 21.5 1.0
ND1 B:HIS59 4.6 45.1 1.0
OD2 B:ASP63 4.6 51.0 1.0
CG B:HIS59 4.6 42.8 1.0
OD2 B:ASP162 4.8 41.8 1.0
NE2 B:HIS61 4.8 52.8 1.0
CE1 B:HIS380 4.8 24.0 1.0
CD2 B:HIS61 4.9 49.7 1.0
CG B:ASP63 5.0 45.1 1.0

Zinc binding site 5 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 5 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn458

b:96.4
occ:1.00
OD2 C:ASP63 2.4 56.0 1.0
OD1 C:ASP162 2.4 46.0 1.0
NE2 C:HIS400 2.4 38.4 1.0
CE1 C:HIS400 3.2 38.7 1.0
NE2 C:HIS64 3.2 50.6 1.0
CG C:ASP63 3.3 50.8 1.0
O C:HOH479 3.3 67.5 1.0
CD2 C:HIS64 3.4 49.6 1.0
CG C:ASP162 3.4 46.0 1.0
ZN C:ZN459 3.4 97.5 1.0
OD1 C:ASP63 3.4 53.5 1.0
CD2 C:HIS400 3.5 38.2 1.0
OD2 C:ASP162 3.6 45.0 1.0
O C:HOH504 3.8 38.7 1.0
O2' C:U5P457 4.3 76.5 1.0
CE1 C:HIS380 4.3 48.0 1.0
ND1 C:HIS400 4.3 41.0 1.0
NE2 C:HIS59 4.4 51.7 1.0
CE1 C:HIS59 4.4 51.8 1.0
NE2 C:HIS380 4.4 45.9 1.0
CE1 C:HIS64 4.5 50.7 1.0
O C:VAL12 4.5 50.0 1.0
CG C:HIS400 4.6 40.3 1.0
CG C:HIS64 4.6 49.9 1.0
CB C:ASP63 4.7 47.1 1.0
CB C:ASP162 4.7 43.0 1.0
O C:HOH491 4.9 51.9 1.0
O3' C:U5P457 4.9 74.4 1.0

Zinc binding site 6 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 6 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn459

b:97.5
occ:1.00
NE2 C:HIS141 2.2 45.6 1.0
O C:HOH479 2.5 67.5 1.0
OD1 C:ASP162 2.7 46.0 1.0
ND1 C:HIS61 2.7 56.4 1.0
NE2 C:HIS59 2.9 51.7 1.0
CE1 C:HIS141 3.1 45.4 1.0
CD2 C:HIS141 3.2 46.6 1.0
CE1 C:HIS59 3.3 51.8 1.0
ZN C:ZN458 3.4 96.4 1.0
CE1 C:HIS61 3.5 56.9 1.0
CG C:HIS61 3.7 55.2 1.0
CG C:ASP162 3.7 46.0 1.0
CD2 C:HIS59 3.8 49.9 1.0
CB C:HIS61 4.0 52.1 1.0
CB C:ASP162 4.1 43.0 1.0
ND1 C:HIS141 4.2 46.1 1.0
OD1 C:ASP63 4.3 53.5 1.0
NE2 C:HIS380 4.3 45.9 1.0
CG C:HIS141 4.3 47.9 1.0
ND1 C:HIS59 4.3 52.9 1.0
CG C:HIS59 4.6 50.3 1.0
CE1 C:HIS380 4.6 48.0 1.0
NE2 C:HIS61 4.7 57.4 1.0
CD2 C:HIS61 4.8 57.0 1.0
OD2 C:ASP162 4.8 45.0 1.0
CD2 C:HIS64 4.9 49.6 1.0
OD2 C:ASP63 4.9 56.0 1.0

Zinc binding site 7 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 7 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn449

b:0.6
occ:1.00
OD1 D:ASP162 2.3 53.4 1.0
NE2 D:HIS400 2.6 62.8 1.0
OD2 D:ASP63 2.6 63.8 1.0
O D:HOH452 2.7 50.1 1.0
NE2 D:HIS64 2.8 64.2 1.0
CD2 D:HIS64 3.2 63.6 1.0
CG D:ASP162 3.2 50.2 1.0
ZN D:ZN450 3.3 0.0 1.0
CG D:ASP63 3.4 63.0 1.0
OD1 D:ASP63 3.4 63.8 1.0
OD2 D:ASP162 3.4 53.4 1.0
CD2 D:HIS400 3.5 62.0 1.0
CE1 D:HIS400 3.5 62.2 1.0
NE2 D:HIS380 4.0 59.2 1.0
CE1 D:HIS64 4.1 62.8 1.0
CE1 D:HIS380 4.1 59.3 1.0
O2' D:U5P448 4.2 94.7 1.0
NE2 D:HIS59 4.4 53.2 1.0
CG D:HIS64 4.5 62.7 1.0
CB D:ASP162 4.6 49.2 1.0
ND1 D:HIS400 4.6 61.6 1.0
CG D:HIS400 4.6 61.4 1.0
O D:VAL12 4.8 58.8 1.0
CE1 D:HIS59 4.8 52.5 1.0
CB D:ASP63 4.8 60.9 1.0
ND1 D:HIS64 4.9 63.2 1.0
O3' D:U5P448 4.9 95.1 1.0

Zinc binding site 8 out of 8 in 3iel

Go back to Zinc Binding Sites List in 3iel
Zinc binding site 8 out of 8 in the Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump


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 TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn450

b:0.0
occ:1.00
NE2 D:HIS141 2.2 50.8 1.0
ND1 D:HIS61 2.4 65.2 1.0
OD1 D:ASP162 2.6 53.4 1.0
NE2 D:HIS59 2.7 53.2 1.0
O D:HOH452 2.8 50.1 1.0
CD2 D:HIS141 3.0 49.8 1.0
CE1 D:HIS141 3.2 51.0 1.0
ZN D:ZN449 3.3 0.6 1.0
CE1 D:HIS61 3.4 64.2 1.0
CG D:HIS61 3.4 63.4 1.0
CD2 D:HIS59 3.4 51.7 1.0
CG D:ASP162 3.6 50.2 1.0
CB D:HIS61 3.6 60.0 1.0
CE1 D:HIS59 3.7 52.5 1.0
CB D:ASP162 4.0 49.2 1.0
CG D:HIS141 4.1 50.4 1.0
ND1 D:HIS141 4.2 51.3 1.0
CD2 D:HIS64 4.2 63.6 1.0
OD1 D:ASP63 4.3 63.8 1.0
NE2 D:HIS380 4.4 59.2 1.0
NE2 D:HIS64 4.4 64.2 1.0
NE2 D:HIS61 4.5 63.5 1.0
CD2 D:HIS61 4.5 63.5 1.0
CG D:HIS59 4.6 50.9 1.0
CE1 D:HIS380 4.6 59.3 1.0
ND1 D:HIS59 4.6 52.0 1.0
CD1 D:LEU142 4.7 53.1 1.0
OD2 D:ASP162 4.7 53.4 1.0

Reference:

H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. Crystal Structure of TTHA0252 From Thermus Thermophilus HB8 Complexed with Ump To Be Published.
Page generated: Wed Dec 16 04:26:06 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy