Atomistry » Zinc » PDB 5msb-5n2x » 5mxy
Atomistry »
  Zinc »
    PDB 5msb-5n2x »
      5mxy »

Zinc in PDB 5mxy: KUSTC0563 C-Type Cytochrome

Protein crystallography data

The structure of KUSTC0563 C-Type Cytochrome, PDB code: 5mxy was solved by A.Mohd, T.Barends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.14 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 47.820, 47.820, 99.930, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23

Other elements in 5mxy:

The structure of KUSTC0563 C-Type Cytochrome also contains other interesting chemical elements:

Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the KUSTC0563 C-Type Cytochrome (pdb code 5mxy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the KUSTC0563 C-Type Cytochrome, PDB code: 5mxy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 1 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:43.5
occ:1.00
 O A:HOH326 2.1 44.6 1.0
O1D A:HEC200 2.1 39.9 1.0
O A:HOH302 2.2 41.2 1.0
CGD A:HEC200 3.2 38.0 1.0
O2D A:HEC200 3.5 37.4 1.0
OG1 A:THR87 3.8 38.8 1.0
O A:HOH367 4.0 77.8 1.0
OE1 A:GLN82 4.0 39.6 1.0
O A:HOH368 4.3 66.8 1.0
O A:HOH317 4.4 59.8 1.0
CG2 A:THR87 4.5 41.4 1.0
CBD A:HEC200 4.5 36.1 1.0
NH1 A:ARG78 4.6 40.7 1.0
CB A:THR87 4.8 40.6 1.0
CD A:GLN82 4.9 36.6 1.0

Zinc binding site 2 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 2 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:93.0
occ:1.00
 OD1 A:ASP67 2.7 58.0 1.0
OD2 A:ASP67 3.0 65.7 1.0
CG A:ASP67 3.1 61.8 1.0
O A:HOH331 3.2 64.6 1.0
CB A:GLU69 4.1 62.8 1.0
O A:HOH338 4.3 57.0 1.0
CB A:ASP67 4.5 59.5 1.0
N A:GLU69 4.6 57.4 1.0
NZ A:LYS64 4.8 66.1 1.0
CA A:ASP67 4.8 57.4 1.0
CA A:GLU69 5.0 57.6 1.0
N A:ALA68 5.0 56.4 1.0

Zinc binding site 3 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 3 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:66.8
occ:0.75
 OE2 A:GLU89 2.2 66.0 1.0
ZN A:ZN210 2.9 0.1 0.5
CD A:GLU89 3.3 61.6 1.0
OE1 A:GLU89 3.8 65.2 1.0
O A:HOH366 4.3 72.0 1.0
O A:HOH343 4.4 58.5 1.0
O A:HOH344 4.6 80.7 1.0
CG A:GLU89 4.6 58.0 1.0
CA A:GLU89 4.7 47.9 1.0
CB A:GLU89 4.8 51.3 1.0

Zinc binding site 4 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 4 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:43.0
occ:0.50
 OD2 A:ASP76 2.1 45.8 1.0
O A:ACT212 2.3 54.6 1.0
CG A:ASP76 2.8 43.9 1.0
OD1 A:ASP76 3.0 41.9 1.0
C A:ACT212 3.2 54.1 1.0
OXT A:ACT212 3.3 54.6 1.0
CB A:ASP76 4.2 42.9 1.0
CH3 A:ACT212 4.5 55.7 1.0
NE A:ARG111 4.6 45.2 1.0
O A:HOH325 4.6 53.0 1.0
NH2 A:ARG111 4.9 43.6 1.0

Zinc binding site 5 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 5 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:56.7
occ:0.75
 OE1 A:GLU85 2.1 54.7 1.0
OE1 A:GLU81 2.2 48.8 1.0
CD A:GLU85 2.9 51.9 1.0
OE2 A:GLU85 3.0 53.6 1.0
CD A:GLU81 3.1 43.9 1.0
O A:HOH324 3.3 86.5 1.0
CG A:GLU81 3.3 41.3 1.0
O A:HOH339 3.9 69.4 1.0
OE2 A:GLU81 4.3 48.3 1.0
CG A:GLU85 4.4 48.3 1.0
CB A:GLU81 4.6 38.4 1.0
O A:HOH342 4.7 70.2 1.0
O A:HOH352 4.8 47.1 1.0

Zinc binding site 6 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 6 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:75.2
occ:0.50
 O A:HOH346 2.1 81.6 1.0
O A:HOH342 2.1 70.2 1.0
OE2 A:GLU81 2.3 48.3 1.0
O A:HOH339 2.8 69.4 1.0
OE1 A:GLU81 3.0 48.8 1.0
O A:HOH347 3.0 58.0 1.0
CD A:GLU81 3.0 43.9 1.0
O A:HOH324 3.4 86.5 1.0
O A:HOH345 3.4 69.0 1.0
CG A:GLU81 4.5 41.3 1.0
NE A:ARG78 4.6 38.5 1.0
O A:HOH367 4.7 77.8 1.0
NH2 A:ARG78 4.8 40.3 1.0

Zinc binding site 7 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 7 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:63.8
occ:0.50
 ND1 A:HIS42 2.3 57.6 1.0
O A:HOH351 2.4 70.9 1.0
CE1 A:HIS42 3.1 59.5 1.0
O A:HOH304 3.2 51.9 1.0
CG A:HIS42 3.5 54.9 1.0
CB A:HIS42 3.9 51.1 1.0
CE A:LYS97 4.0 65.8 1.0
CA A:HIS42 4.0 49.3 1.0
CE2 A:PHE94 4.3 42.2 1.0
O A:GLN41 4.3 50.5 1.0
NZ A:LYS97 4.3 69.2 1.0
NE2 A:HIS42 4.3 58.4 1.0
CD2 A:HIS42 4.5 55.6 1.0
CD A:LYS97 4.6 63.3 1.0
O A:HIS42 4.7 44.5 1.0
CG A:LYS97 4.9 59.4 1.0
C A:HIS42 4.9 45.7 1.0
C A:GLN41 5.0 52.9 1.0
N A:HIS42 5.0 50.3 1.0

Zinc binding site 8 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 8 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:72.3
occ:0.50
 O A:HOH348 2.3 68.5 1.0
NE2 A:HIS42 2.4 58.4 1.0
NE2 A:GLN41 2.7 67.1 1.0
OE1 A:GLN41 2.9 71.5 1.0
CD A:GLN41 3.1 67.9 1.0
CE1 A:HIS42 3.3 59.5 1.0
CD2 A:HIS42 3.4 55.6 1.0
O A:HOH307 3.5 61.3 1.0
CD2 A:LEU38 4.1 50.6 1.0
ND1 A:HIS42 4.4 57.6 1.0
CG A:GLN41 4.5 63.6 1.0
CG A:HIS42 4.5 54.9 1.0
CD2 A:LEU98 4.7 46.7 1.0
CB A:GLN41 4.9 59.2 1.0

Zinc binding site 9 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 9 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:68.5
occ:0.50
 O A:GLY86 2.8 40.5 1.0
NH2 A:ARG78 2.9 40.3 1.0
OE1 A:GLN82 3.2 39.6 1.0
O A:HOH302 3.3 41.2 1.0
O A:HOH345 3.6 69.0 1.0
CA A:GLN82 3.7 36.7 1.0
CD A:GLN82 3.8 36.6 1.0
C A:GLY86 3.9 40.5 1.0
O A:GLU81 3.9 33.9 1.0
CZ A:ARG78 4.0 40.5 1.0
N A:GLN82 4.1 36.0 1.0
CB A:GLU85 4.2 45.3 1.0
C A:GLU81 4.2 35.7 1.0
OE2 A:GLU85 4.2 53.6 1.0
N A:GLY86 4.3 43.0 1.0
NE2 A:GLN82 4.3 36.3 1.0
NH1 A:ARG78 4.3 40.7 1.0
CB A:GLN82 4.4 37.1 1.0
CG A:GLU81 4.4 41.3 1.0
OG1 A:THR87 4.4 38.8 1.0
OE2 A:GLU81 4.5 48.3 1.0
CA A:GLY86 4.6 42.0 1.0
C A:GLU85 4.6 42.4 1.0
O A:GLN82 4.6 38.6 1.0
CG A:GLN82 4.7 36.2 1.0
C A:GLN82 4.7 36.5 1.0
CD A:GLU81 4.7 43.9 1.0
O A:HOH367 4.9 77.8 1.0
CA A:GLU85 4.9 43.7 1.0
N A:THR87 5.0 40.9 1.0

Zinc binding site 10 out of 10 in 5mxy

Go back to Zinc Binding Sites List in 5mxy
Zinc binding site 10 out of 10 in the KUSTC0563 C-Type Cytochrome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of KUSTC0563 C-Type Cytochrome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:0.1
occ:0.50
 O A:HOH344 2.2 80.7 1.0
O A:HOH343 2.9 58.5 1.0
ZN A:ZN203 2.9 66.8 0.8
OE1 A:GLU89 3.5 65.2 1.0
OE2 A:GLU89 3.6 66.0 1.0
CD A:GLU89 3.9 61.6 1.0

Reference:

A.Mohd, T.Barends. Structure and Function of the C-Type Cytochrome KUSTC0563 From the Anammox Organism Kuenenia Stuttgartiensis To Be Published.
Page generated: Sun Oct 27 22:24:34 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