Atomistry » Zinc » PDB 5f8h-5fi3 » 5fd6
Atomistry »
  Zinc »
    PDB 5f8h-5fi3 »
      5fd6 »

Zinc in PDB 5fd6: Zinc-Bound Manganese Uptake Regulator

Protein crystallography data

The structure of Zinc-Bound Manganese Uptake Regulator, PDB code: 5fd6 was solved by D.Bellini, A.M.Hemmings, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.46 / 2.48
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 94.950, 94.950, 63.020, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Zinc-Bound Manganese Uptake Regulator (pdb code 5fd6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Zinc-Bound Manganese Uptake Regulator, PDB code: 5fd6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 1 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:53.2
occ:1.00
OE2 A:GLU84 2.0 52.2 1.0
NE2 A:HIS93 2.1 46.7 1.0
NE2 A:HIS91 2.2 56.0 1.0
CD A:GLU84 2.7 57.2 1.0
CE1 A:HIS36 2.8 83.9 1.0
OE1 A:GLU84 2.9 63.2 1.0
NE2 A:HIS36 2.9 87.1 1.0
CE1 A:HIS93 3.0 43.4 1.0
CE1 A:HIS91 3.0 57.1 1.0
CD2 A:HIS93 3.1 49.7 1.0
CD2 A:HIS91 3.3 53.6 1.0
ND1 A:HIS36 3.6 86.8 1.0
CD2 A:HIS36 3.9 90.4 1.0
CG A:GLU84 4.0 57.7 1.0
ND1 A:HIS93 4.1 47.0 1.0
ND1 A:HIS91 4.2 55.9 1.0
CG A:HIS93 4.2 44.7 1.0
CG A:HIS36 4.2 78.0 1.0
CG A:HIS91 4.4 57.0 1.0
NE2 A:HIS74 4.5 51.9 1.0
CD2 A:HIS74 4.7 54.6 1.0
CB A:GLU84 4.8 55.9 1.0
CB A:GLU104 4.9 62.8 1.0

Zinc binding site 2 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 2 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:58.5
occ:1.00
OD2 A:ASP92 2.0 49.6 1.0
OE2 A:GLU111 2.3 70.2 1.0
NE2 A:HIS90 2.3 66.2 1.0
NE2 A:HIS128 2.3 57.5 1.0
CG A:ASP92 2.6 49.5 1.0
OD1 A:ASP92 2.6 51.8 1.0
CE1 A:HIS90 2.7 67.7 1.0
CD A:GLU111 3.0 72.4 1.0
OE1 A:GLU111 3.1 74.1 1.0
CE1 A:HIS128 3.1 58.1 1.0
CD2 A:HIS128 3.4 55.4 1.0
CD2 A:HIS90 3.6 62.8 1.0
ND1 A:HIS90 4.0 60.6 1.0
CB A:ASP92 4.0 52.6 1.0
ND1 A:HIS128 4.3 54.4 1.0
CG A:HIS90 4.4 62.1 1.0
CG A:HIS128 4.5 55.3 1.0
CG A:GLU111 4.5 69.9 1.0
N A:ASP92 4.5 51.6 1.0
OE1 A:GLN114 4.6 62.1 1.0
C A:HIS91 4.7 53.6 1.0
CA A:ASP92 4.7 52.6 1.0
CD2 A:LEU130 4.9 55.9 1.0

Zinc binding site 3 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 3 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:57.6
occ:1.00
OE1 B:GLU84 2.2 55.2 1.0
NE2 B:HIS36 2.2 60.5 1.0
NE2 B:HIS91 2.3 80.4 1.0
NE2 B:HIS93 2.3 53.3 1.0
OE2 B:GLU84 2.6 57.7 1.0
CD B:GLU84 2.6 60.8 1.0
CE1 B:HIS91 3.1 82.3 1.0
CE1 B:HIS93 3.1 48.5 1.0
CE1 B:HIS36 3.1 60.7 1.0
CD2 B:HIS91 3.2 79.9 1.0
CD2 B:HIS36 3.3 61.1 1.0
CD2 B:HIS93 3.4 51.9 1.0
CG B:GLU84 4.1 61.1 1.0
ND1 B:HIS91 4.2 84.2 1.0
ND1 B:HIS36 4.2 62.9 1.0
ND1 B:HIS93 4.3 53.4 1.0
CG B:HIS91 4.3 80.3 1.0
CG B:HIS36 4.3 61.2 1.0
CG B:HIS93 4.4 49.6 1.0
CD2 B:HIS74 4.6 61.8 1.0
NE2 B:HIS74 4.6 66.8 1.0
CB B:GLU84 4.7 57.6 1.0

Zinc binding site 4 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 4 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:60.0
occ:1.00
OD2 B:ASP92 2.1 55.1 1.0
NE2 B:HIS128 2.3 54.9 1.0
NE2 B:HIS90 2.4 69.1 1.0
OE2 B:GLU111 2.5 66.3 1.0
OD1 B:ASP92 2.5 52.4 1.0
OE1 B:GLU111 2.6 55.9 1.0
CG B:ASP92 2.6 54.9 1.0
CD B:GLU111 2.9 67.0 1.0
CE1 B:HIS90 3.1 78.4 1.0
CD2 B:HIS128 3.3 54.0 1.0
CE1 B:HIS128 3.3 56.3 1.0
CD2 B:HIS90 3.5 73.2 1.0
CB B:ASP92 4.1 55.2 1.0
ND1 B:HIS90 4.3 78.1 1.0
CG B:GLU111 4.4 67.4 1.0
ND1 B:HIS128 4.4 54.7 1.0
CG B:HIS128 4.4 56.5 1.0
OE1 B:GLN114 4.5 64.7 1.0
CG B:HIS90 4.6 83.3 1.0
N B:ASP92 4.6 55.8 1.0
CA B:ASP92 4.9 55.5 1.0
NE2 B:GLN114 4.9 57.5 1.0
C B:HIS91 5.0 62.9 1.0

Zinc binding site 5 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 5 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:58.8
occ:1.00
NE2 C:HIS93 2.1 54.7 1.0
OE1 C:GLU84 2.2 65.2 1.0
NE2 C:HIS36 2.3 63.5 1.0
NE2 C:HIS91 2.3 58.0 1.0
CD C:GLU84 2.8 64.6 1.0
OE2 C:GLU84 2.9 66.5 1.0
CE1 C:HIS93 3.0 52.7 1.0
CD2 C:HIS36 3.0 66.8 1.0
CD2 C:HIS93 3.1 56.1 1.0
CD2 C:HIS91 3.2 54.3 1.0
CE1 C:HIS36 3.3 61.9 1.0
CE1 C:HIS91 3.3 60.8 1.0
NE2 C:HIS74 4.0 77.0 1.0
CG C:GLU84 4.1 63.2 1.0
ND1 C:HIS93 4.2 50.3 1.0
CG C:HIS36 4.2 67.2 1.0
CD2 C:HIS74 4.2 77.5 1.0
CG C:HIS93 4.2 53.0 1.0
ND1 C:HIS36 4.3 62.9 1.0
CG C:HIS91 4.4 57.0 1.0
ND1 C:HIS91 4.4 57.6 1.0
CB C:GLU84 4.9 59.2 1.0
CE1 C:HIS74 5.0 74.1 1.0

Zinc binding site 6 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 6 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:46.6
occ:1.00
OD2 C:ASP92 2.0 47.4 1.0
NE2 C:HIS90 2.0 45.2 1.0
NE2 C:HIS128 2.1 50.5 1.0
OE2 C:GLU111 2.1 47.4 1.0
CG C:ASP92 2.7 47.7 1.0
CE1 C:HIS90 2.8 46.3 1.0
CE1 C:HIS128 2.8 44.4 1.0
OD1 C:ASP92 2.8 52.5 1.0
CD C:GLU111 2.9 50.4 1.0
OE1 C:GLU111 2.9 52.5 1.0
CD2 C:HIS90 3.2 48.4 1.0
CD2 C:HIS128 3.4 48.0 1.0
ND1 C:HIS90 4.0 46.5 1.0
ND1 C:HIS128 4.0 45.5 1.0
CB C:ASP92 4.1 48.1 1.0
CG C:HIS90 4.2 48.3 1.0
CG C:HIS128 4.3 47.5 1.0
CG C:GLU111 4.3 50.3 1.0
OE1 C:GLN114 4.3 48.4 1.0
N C:ASP92 4.6 44.4 1.0
CD2 C:LEU130 4.8 44.2 1.0
C C:HIS91 4.8 45.0 1.0
CA C:ASP92 4.9 45.7 1.0

Zinc binding site 7 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 7 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:65.2
occ:1.00
OE2 D:GLU84 1.9 53.5 1.0
NE2 D:HIS91 2.2 76.0 1.0
NE2 D:HIS93 2.3 56.2 1.0
NE2 D:HIS36 2.4 65.6 1.0
CD D:GLU84 2.9 57.5 1.0
CE1 D:HIS91 3.0 76.0 1.0
CD2 D:HIS36 3.1 62.6 1.0
OE1 D:GLU84 3.2 66.1 1.0
CE1 D:HIS93 3.3 55.8 1.0
CD2 D:HIS93 3.3 53.0 1.0
CD2 D:HIS91 3.3 77.2 1.0
CE1 D:HIS36 3.5 64.2 1.0
NE2 D:HIS74 4.0 71.3 1.0
ND1 D:HIS91 4.2 74.1 1.0
CG D:GLU84 4.2 59.2 1.0
CD2 D:HIS74 4.3 69.0 1.0
CG D:HIS36 4.3 66.8 1.0
ND1 D:HIS93 4.4 56.6 1.0
CG D:HIS91 4.4 72.5 1.0
CG D:HIS93 4.4 55.1 1.0
ND1 D:HIS36 4.4 68.1 1.0
CB D:GLU84 4.6 59.3 1.0
CG D:GLU104 4.8 67.6 1.0
OE2 D:GLU104 4.8 73.2 1.0
CD D:GLU104 5.0 74.4 1.0

Zinc binding site 8 out of 8 in 5fd6

Go back to Zinc Binding Sites List in 5fd6
Zinc binding site 8 out of 8 in the Zinc-Bound Manganese Uptake Regulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zinc-Bound Manganese Uptake Regulator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:54.7
occ:1.00
OD2 D:ASP92 2.0 57.3 1.0
NE2 D:HIS90 2.1 57.8 1.0
NE2 D:HIS128 2.3 55.4 1.0
OE2 D:GLU111 2.4 65.6 1.0
CG D:ASP92 2.7 59.4 1.0
OE1 D:GLU111 2.8 68.0 1.0
OD1 D:ASP92 2.9 61.7 1.0
CD D:GLU111 3.0 61.1 1.0
CD2 D:HIS90 3.0 61.2 1.0
CE1 D:HIS128 3.0 57.9 1.0
CE1 D:HIS90 3.2 65.7 1.0
CD2 D:HIS128 3.5 55.9 1.0
CB D:ASP92 4.2 56.7 1.0
CG D:HIS90 4.2 63.7 1.0
ND1 D:HIS90 4.2 60.5 1.0
ND1 D:HIS128 4.3 59.0 1.0
CG D:GLU111 4.5 55.8 1.0
CG D:HIS128 4.5 55.6 1.0
OE1 D:GLN114 4.6 68.8 1.0
N D:ASP92 4.7 56.9 1.0
C D:HIS91 4.9 58.6 1.0
CA D:ASP92 5.0 57.9 1.0
NE2 D:GLN114 5.0 59.3 1.0

Reference:

D.Bellini, A.Lebedev, R.Keegan, J.Todd, A.M.Hemmings, A.W.Johnston, M.A.Walsh. Structure of A Zinc-Bound Manganese Uptake Regulator, Mur To Be Published.
Page generated: Sun Oct 27 16:03:42 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