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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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